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Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: _. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: __. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.data/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Join Keys","text":"teal.data package provides way define primary keys dataset establish relationships datasets. dataset can characterized : Columns constituting primary key Merge keys, analogous SQL foreign keys Typically, application developer specifies keys manually. However, datasets following ADaM standard, teal.data can automatically assign keys using default_cdisc_join_keys object. Refer section “Joining Keys ADaM Datasets” details using object select specific datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"uses-of-join_keys-class-in-teal-applications","dir":"Articles","previous_headings":"Overview","what":"Uses of join_keys class in teal applications","title":"Join Keys","text":"primary function join_keys teal applications facilitate seamless merging datasets using teal.transform. Additionally, plays role data filtering using Filter Panel teal application. filters applied (parent) dataset also applied children.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"anatomy-of-join-keys","dir":"Articles","previous_headings":"","what":"Anatomy of Join Keys","title":"Join Keys","text":"join_keys object contains information foreign/primary keys multiple datasets. key represented pair datasets (name reference) named character vector encodes match column name two datasets. addition, foreign key also contains parent-child attribute used “Filter Panel” mentioned . new join_keys can created empty defining initial set primary foreign keys. initial object can extended adding/modifying/removing keys establishing parent-child relationships datasets. join_keys function used constructor getter. getter used retrieve join_keys contained objects, teal_data. constructor used specify keys join_keys(...) collection multiple join_key entries: dataset_1, dataset_2: names datasets (dataset_2 dataset_1, creates primary key) key (optional): named vector column names Note join keys assumed symmetric, .e., join_key(\"ds1\", \"ds2\", c(\"ds1_col\" = \"ds2_col\")) establishes relationship “x” “y” vice versa.","code":"library(teal.data) jk <- join_keys( join_key(\"ds1\", keys = \"col_1\"), # ds1: [col_1] join_key(\"ds2\", keys = c(\"col_1\", \"col_2\")), # ds2: [col_1, col_2] join_key(\"ds3\", keys = c(\"col_1\", \"col_3\")), # ds3: [col_1, col_3] join_key(\"ds1\", \"ds2\", keys = \"col_1\"), # ds1 <--> ds2 join_key(\"ds1\", \"ds3\", keys = \"col_1\"), # ds1 <--> ds3 join_key(\"ds4\", \"ds5\", keys = c(\"col_4\" = \"col_5\")) # ds4 <--> ds5 ) # The parent of ds2 and ds3 is ds1 # converts relationship to child-parent # ds1 <--> ds2 becomes ds1 <-- ds2 # ds1 <--> ds3 becomes ds1 <-- ds3 parents(jk) <- list(ds2 = \"ds1\", ds3 = \"ds1\") jk"},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"accessing-and-modifying-keys","dir":"Articles","previous_headings":"","what":"Accessing and Modifying keys","title":"Join Keys","text":"subset operator 2 indices used retrieve primary/foreign keys join_keys. indices must string. Note symmetry ds4 ds5 relationship: 1 argument used operator return join_keys object filtered accordingly. Modifying adding key uses notation assignment operator <-. symmetric relationship created automatically. Assigning NULL value delete relationship.","code":"# Using the jk object defined on \"Anatomy of Join Keys\" jk ## A join_keys object containing foreign keys between 5 datasets: ## ds1: [col_1] ## <-- ds2: [col_1] ## <-- ds3: [col_1] ## ds2: [col_1, col_2] ## --> ds1: [col_1] ## --* (implicit via parent with): ds3 ## ds3: [col_1, col_3] ## --> ds1: [col_1] ## --* (implicit via parent with): ds2 ## ds4: [no primary keys] ## <-> ds5: [col_5] ## ds5: [no primary keys] ## <-> ds4: [col_4] # Getting primary key of \"ds1\" jk[\"ds1\", \"ds1\"] ## col_1 ## \"col_1\" # Getting foreign keys between \"ds4\" and \"ds5\" jk[\"ds4\", \"ds5\"] ## col_4 ## \"col_5\" jk[\"ds5\", \"ds4\"] ## col_5 ## \"col_4\" jk[\"ds5\", \"ds4\"] ## col_5 ## \"col_4\" # Using the jk object defined on \"Anatomy of Join Keys\" jk ## A join_keys object containing foreign keys between 5 datasets: ## ds1: [col_1] ## <-- ds2: [col_1] ## <-- ds3: [col_1] ## ds2: [col_1, col_2] ## --> ds1: [col_1] ## --* (implicit via parent with): ds3 ## ds3: [col_1, col_3] ## --> ds1: [col_1] ## --* (implicit via parent with): ds2 ## ds4: [no primary keys] ## <-> ds5: [col_5] ## ds5: [no primary keys] ## <-> ds4: [col_4] # Getting primary key of \"ds1\" jk[\"ds1\"] ## A join_keys object containing foreign keys between 1 datasets: ## ds1: [col_1] # Adding a new ds5 <-> ds1 key jk[\"ds5\", \"ds1\"] <- \"a_column\" # Removing an existing key jk[\"ds4\", \"ds5\"] <- NULL"},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"join-keys-relationships","dir":"Articles","previous_headings":"","what":"Join Keys Relationships","title":"Join Keys","text":"2 types relationships encoded join_keys described following sections. primary foreign keys created explicitly using join_key function. Additionally, join_keys object detects implicit relationships two datasets share foreign keys parent dataset, . implicit relationships available just like another foreign key can used merge datasets, despite defined user.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"primary-key-with-teal_data","dir":"Articles","previous_headings":"Join Keys Relationships","what":"Primary Key with teal_data","title":"Join Keys","text":"using teal_data function, simplest method define join keys use join_keys argument. can specify column(s) dataset (together) uniquely identify rows dataset. can extend previous example define primary keys multiple datasets:","code":"library(teal.data) td_pk <- within( teal_data(), ds1 <- dplyr::mutate(iris, id = factor(dplyr::row_number())) ) datanames(td_pk) <- \"ds1\" join_keys(td_pk) <- join_keys(join_key(\"ds1\", keys = \"id\")) join_keys(td_pk) ## A join_keys object containing foreign keys between 1 datasets: ## ds1: [id] library(teal.data) td_pk <- within( td_pk, { ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2)) ds3 <- data.frame(V = 5:14, N = 4) } ) datanames(td_pk) <- c(datanames(td_pk), \"ds2\", \"ds3\") join_keys(td_pk)[\"ds2\", \"ds2\"] <- c(\"V\", \"W\") join_keys(td_pk)[\"ds3\", \"ds3\"] <- c(\"V\", \"W\") join_keys(td_pk) ## A join_keys object containing foreign keys between 3 datasets: ## ds1: [id] ## ds2: [V, W] ## ds3: [V, W]"},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"foreign-keys-with-teal_data","dir":"Articles","previous_headings":"Join Keys Relationships","what":"Foreign Keys with teal_data","title":"Join Keys","text":"passing multiple datasets teal_data function, dataset relationships set using join_keys join_key used merge datasets together within teal apps. users familiar SQL database schema, relationships symmetric strict SQL foreign key relationships teal validate whether values inserted foreign key columns present parent table. example:","code":"library(teal.data) td_fk <- within( teal_data(), { ds1 <- data.frame(X = 1:10, Y = 21:30, Z = 1:10) ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2)) ds3 <- data.frame(V = 5:14, N = 4) } ) datanames(td_fk) <- c(\"ds1\", \"ds2\", \"ds3\") join_keys(td_fk) <- join_keys( # Primary keys join_key(\"ds1\", keys = c(\"X\")), join_key(\"ds2\", keys = c(\"V\", \"W\")), join_key(\"ds3\", keys = c(\"V\")), # Foreign keys join_key(\"ds2\", \"ds1\", c(\"W\" = \"X\")), join_key(\"ds3\", \"ds2\", c(\"V\" = \"V\")) ) # The parent of ds2 and ds3 is ds1 parents(td_fk) <- list(ds2 = \"ds1\", ds3 = \"ds2\") join_keys(td_fk) ## A join_keys object containing foreign keys between 3 datasets: ## ds1: [X] ## <-- ds2: [W] ## ds2: [V, W] ## --> ds1: [X] ## <-- ds3: [V] ## ds3: [V] ## --> ds2: [V]"},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"implicit-relationships","dir":"Articles","previous_headings":"Join Keys Relationships","what":"Implicit Relationships","title":"Join Keys","text":"Two datasets share common foreign keys parent dataset implicit relationship modeled accessible join_keys. special inferred relationship existing join_keys need explicitly defined can seamlessly accessible just foreign key. foreign key can overwritten. implicit relationships can used merge 2 datasets together, just defined manually. Note definition contains join_key \"ds2\" <-> \"ds4\"","code":"library(teal.data) td <- within( teal_data(), { ds1 <- data.frame(X = 1:10, Y = 21:30, Z = 1:10) ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2)) ds3 <- data.frame(V = 5:14, N = 4) ds4 <- data.frame(V = 5:14, R = rnorm(10)) } ) datanames(td) <- c(\"ds1\", \"ds2\", \"ds3\", \"ds4\") join_keys(td) <- join_keys( # Primary keys join_key(\"ds1\", keys = c(\"X\")), join_key(\"ds2\", keys = c(\"V\", \"W\")), join_key(\"ds3\", keys = c(\"V\")), join_key(\"ds4\", keys = c(\"V\")), # Foreign keys join_key(\"ds2\", \"ds1\", c(\"W\" = \"X\")), join_key(\"ds3\", \"ds2\", c(\"V\" = \"V\")), join_key(\"ds4\", \"ds1\", c(\"V\" = \"X\")) ) # The parent of ds2 and ds3 is ds1 parents(td) <- list(ds2 = \"ds1\", ds3 = \"ds2\", ds4 = \"ds1\") join_keys(td) ## A join_keys object containing foreign keys between 4 datasets: ## ds1: [X] ## <-- ds2: [W] ## <-- ds4: [V] ## ds2: [V, W] ## --> ds1: [X] ## <-- ds3: [V] ## --* (implicit via parent with): ds4 ## ds3: [V] ## --> ds2: [V] ## ds4: [V] ## --> ds1: [X] ## --* (implicit via parent with): ds2 join_keys(td)[\"ds2\", \"ds4\"] ## W ## \"V\""},{"path":"https://insightsengineering.github.io/teal.data/articles/join-keys.html","id":"join-keys-in-adam-datasets","dir":"Articles","previous_headings":"","what":"Join Keys in ADaM Datasets","title":"Join Keys","text":"teal.data provides set default join keys (primary foreign) datasets named according ADaM standard. stored default_cdisc_join_keys. default keys required users can select smaller set datasets subsetting (example: default_cdisc_join_keys[c(\"ADSL\", \"ADTTE\")]). Please note, every element selected, parent also returned (one) well pair-wise relationships resulting selection.","code":"names(default_cdisc_join_keys) |> sort() ## [1] \"ADAE\" \"ADAETTE\" \"ADCM\" \"ADCSSRS\" \"ADDV\" \"ADEG\" ## [7] \"ADEQ5D5L\" \"ADEX\" \"ADHY\" \"ADLB\" \"ADMH\" \"ADQLQC\" ## [13] \"ADQS\" \"ADRS\" \"ADSAFTTE\" \"ADSL\" \"ADSUB\" \"ADTTE\" ## [19] \"ADVS\" default_cdisc_join_keys ## A join_keys object containing foreign keys between 19 datasets: ## ADSL: [STUDYID, USUBJID] ## <-- ADAE: [STUDYID, USUBJID] ## <-- ADEG: [STUDYID, USUBJID] ## <-- ADTTE: [STUDYID, USUBJID] ## <-- ADAETTE: [STUDYID, USUBJID] ## <-- ADCM: [STUDYID, USUBJID] ## <-- ADEX: [STUDYID, USUBJID] ## <-- ADLB: [STUDYID, USUBJID] ## <-- ADMH: [STUDYID, USUBJID] ## <-- ADQS: [STUDYID, USUBJID] ## <-- ADRS: [STUDYID, USUBJID] ## <-- ADSAFTTE: [STUDYID, USUBJID] ## <-- ADVS: [STUDYID, USUBJID] ## <-- ADDV: [STUDYID, USUBJID] ## <-- ADSUB: [STUDYID, USUBJID] ## <-- ADHY: [STUDYID, USUBJID] ## <-- ADQLQC: [STUDYID, USUBJID] ## <-- ADCSSRS: [STUDYID, USUBJID] ## <-- ADEQ5D5L: [STUDYID, USUBJID] ## ADAE: [STUDYID, USUBJID, ASTDTM, AETERM, AESEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADEG: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADAETTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADCM: [STUDYID, USUBJID, ASTDTM, CMSEQ, ATC1CD, ATC2CD, ATC3CD, ATC4CD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADEX: [STUDYID, USUBJID, PARCAT1, PARAMCD, AVISITN, ASTDTM, EXSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADLB: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADMH: [STUDYID, USUBJID, ASTDTM, MHSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADQS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADSAFTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADVS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADDV: [STUDYID, USUBJID, ASTDT, DVTERM, DVSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADSUB: [STUDYID, USUBJID, PARAMCD, AVISITN, ADTM, SRCSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADHY: [STUDYID, USUBJID, PARAMCD, AVISITN, ADTM, SRCSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADQLQC, ADCSSRS, ADEQ5D5L ## ADQLQC: [STUDYID, USUBJID, PARCAT1N, PARAMCD, BASETYPE, AVISITN, ATPTN, ADTM, QSSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADCSSRS, ADEQ5D5L ## ADCSSRS: [STUDYID, USUBJID, PARAMCD, BASETYPE, AVISITN, DTYPE, ADTM] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADEQ5D5L ## ADEQ5D5L: [STUDYID, USUBJID, PARCAT1N, PARAMCD, BASETYPE, AVISITN, ATPTN, ADTM, QSSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS default_cdisc_join_keys[\"ADSL\"] ## A join_keys object containing foreign keys between 1 datasets: ## ADSL: [STUDYID, USUBJID] default_cdisc_join_keys[\"ADTTE\"] ## A join_keys object containing foreign keys between 2 datasets: ## ADSL: [STUDYID, USUBJID] ## <-- ADTTE: [STUDYID, USUBJID] ## ADTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] default_cdisc_join_keys[c(\"ADSL\", \"ADTTE\", \"ADRS\")] ## A join_keys object containing foreign keys between 3 datasets: ## ADSL: [STUDYID, USUBJID] ## <-- ADTTE: [STUDYID, USUBJID] ## <-- ADRS: [STUDYID, USUBJID] ## ADTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADRS ## ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADTTE"},{"path":"https://insightsengineering.github.io/teal.data/articles/preprocessing-delayed-data.html","id":"processing-dependencies","dir":"Articles","previous_headings":"","what":"Processing dependencies","title":"Pre-processing Delayed Data","text":"may required generate delayed data object dependent delayed object constant value. , creating delayed data object ’s possible supply additional variables accessed data loading (pull) using additional arguments ...: ’s also possible supply additional variables creating object using mutate_dataset function. also required creating object depends another delayed data object: possible provide code Data level. However, always return code used generate datasets object: better approach supply code Dataset level. ensures code accessed dataset level contains snippets pertains : Related idea, delayed data object needs supplied code needed reproduce data. can provided Dataset level Data level. comparison two approaches:","code":"get_code(adsl) ## [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\\nADSL$SEX <- as.factor(ADSL$SEX)\" pull_fun_adae <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- dataset_connector( dataname = \"ADAE\", pull_callable = pull_fun_adae, keys = get_cdisc_keys(\"ADAE\") ) get_code(adae) ## [1] \"ADAE <- teal.data::example_cdisc_data(dataname = \\\"ADAE\\\")\" last_run <- Sys.Date() # constant value stored as a variable in the current session adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) %>% mutate_dataset(\"ADSL$last_run <- last_run\", vars = list(last_run = last_run)) cat(get_code(adsl)) ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## last_run <- structure(19696, class = \"Date\") ## ADSL$last_run <- last_run # compared to evaluating the variable at the time of loading adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) %>% mutate_dataset(\"last_run <- Sys.Date()\\nADSL$last_run <- last_run\") adsl %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## last_run <- Sys.Date() ## ADSL$last_run <- last_run adsl <- teal.data::example_cdisc_data(\"ADSL\") adae_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = adae_cf, keys = get_cdisc_keys(\"ADAE\") ) %>% mutate_dataset(\"ADAE$n <- nrow(ADSL)\") cat(get_code(adae)) # the code returned by `adae` is not sufficient to reproduce `adae` ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) adae_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = adae_cf, keys = get_cdisc_keys(\"ADAE\") ) %>% mutate_dataset(\"ADAE$n <- nrow(ADSL)\", vars = list(ADSL = adsl)) cat(get_code(adae)) # this code can be run independently ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE$n <- nrow(ADSL) adsl_adae <- cdisc_data( adsl, adae ) %>% mutate_data(\"ADAE$avg_age <- mean(ADAE$AGE)\") # the output for all 3 are the same adsl_adae %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(dataname = \"ADAE\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(dataname = \"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae <- cdisc_data( adsl, adae %>% mutate_dataset(\"ADAE$avg_age <- mean(ADAE$AGE)\") ) adsl_adae %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(\"ADAE\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(\"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") adsl <- teal.data::example_cdisc_data(\"ADSL\") # no reproducible code provided cdisc_dataset(\"ADSL\", adsl) %>% get_code() %>% cat() # provide the code to reproduce the data: cdisc_dataset(\"ADSL\", adsl, code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) %>% get_code() ## [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" # it's possible to supply the code at the `Data` level: adae <- teal.data::example_cdisc_data(\"ADAE\") adsl_adae <- cdisc_data( cdisc_dataset(\"ADSL\", adsl), cdisc_dataset(\"ADAE\", adae), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\\nADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ) adsl_adae %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(\"ADSL\") ## ADAE <- teal.data::example_cdisc_data(\"ADAE\") # but it's not possible then to access the code at a `Dataset` level: adsl_adae %>% get_code(\"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(\"ADSL\") ## ADAE <- teal.data::example_cdisc_data(\"ADAE\") # this can be avoided by storing the code like so: adsl_adae <- cdisc_data( cdisc_dataset(\"ADSL\", adsl, code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\"), cdisc_dataset(\"ADAE\", adae, code = \"ADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\") ) adsl_adae %>% get_code(\"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(\"ADSL\")"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/articles/reproducibility.html","id":"mechanism","dir":"Articles","previous_headings":"Reproducibility check","what":"Mechanism","title":"Reproducibility check","text":"teal.data classes accumulate raw data accept boolean check argument, e.g. teal_data. boolean flag indicates whether teal performs validation data passed TealData object launch teal application. validation compares raw data passed class dataset returned code stored class. E.g.: check() method called launch can invoked directly returns TRUE raw data passed teal_data matches return value code stored class. returns error comparison fails NULL check = FALSE passed teal_data. Find teal_data() documentation.","code":"library(teal.data) iris_ds <- dataset(\"iris\", iris, code = \"iris <- iris\") data <- teal_data(iris_ds, check = TRUE) ## Warning: The `data_objects` argument of `teal_data()` should use data directly. Using ## TealDatasetConnector and TealDataset is deprecated. Find more information on ## https://github.com/insightsengineering/teal/discussions/945 as of teal.data ## 0.3.1. ## This warning is displayed once every 8 hours. ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was ## generated. data$check() ## [1] TRUE # throws an error: data <- teal_data(dataset(\"iris\", iris, code = \"iris <- mtcars\"), check = TRUE) ## Error in x$check_reproducibility(): Reproducibility check failed. data <- teal_data(dataset(\"iris\", iris, code = \"iris <- mtcars\"), check = FALSE) # returns NULL even though the code does not match the raw data data$check() ## NULL"},{"path":"https://insightsengineering.github.io/teal.data/articles/reproducibility.html","id":"final-considerations","dir":"Articles","previous_headings":"Reproducibility check","what":"Final considerations","title":"Reproducibility check","text":"_connector objects accept raw data input therefore checked even check = TRUE used.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Introduction to teal.data","text":"teal.data package enables teal application developers convert data format can used inside teal applications.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data.html","id":"quick-start","dir":"Articles","previous_headings":"Introduction","what":"Quick Start","title":"Introduction to teal.data","text":"creating ADaM clinical trial data please use cdisc_data cdisc_dataset functions: general data use teal_data dataset functions:","code":"library(teal.data) # create some dummy data adsl <- teal.data::example_cdisc_data(\"ADSL\") adtte <- teal.data::example_cdisc_data(\"ADTTE\") my_data <- cdisc_data( ADSL = adsl, ADTTE = adtte ) my_general_data <- teal_data( iris = iris, mtcars = mtcars )"},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data.html","id":"additional-functionality","dir":"Articles","previous_headings":"Introduction","what":"Additional functionality","title":"Introduction to teal.data","text":"teal.data package provides many features help specify data: Specifying ADaM data Specifying MultiAssayExperiment data Specifying general relational data Specifying relationships datasets Dynamically loading data (DDL) Pre-processing data Pre-processing DDL data Checking reproducibility Using python create data","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal.data-with-python.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"teal.data with Python","text":"possible use Python code (via reticulate package) create teal dataset. python_dataset_connector allows seamless integration teal application Python package(s) required access/create data. recommend thorough understanding reticulate package (see ) using Python functionality described .","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal.data-with-python.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"teal.data with Python","text":"section show simple example Python code can used create teal dataset. example require Python environment pandas installed. See details install Python packages. first load packages: Next define Python code want use create dataset. example, demonstration purposes create trivial dataset easily done directly R. Note use variable num_rows needs passed Python code R. Next create python_dataset_connector object. Finally can test code pulling data R:","code":"library(reticulate) # may need to be installed if not available # reticulate function to call to install the pandas package if not installed: py_install(\"pandas\") library(teal.data) python_code <- \"import pandas as pd data = pd.DataFrame({\\\"id\\\" : range(r.num_rows), \\\"val\\\" : range(r.num_rows)})\" x <- python_dataset_connector( dataname = \"DATA\", # the teal dataset name code = python_code, # the code used to generate the dataset object = \"data\", # the object in the Python code to be converted to a data.frame for the teal dataset keys = \"id\", # the key for teal dataset object vars = list(num_rows = 5L) # any variables passed from R into Python (note this could be an R variable) ) x$pull() print(x)"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/articles/teal.data-with-python.html","id":"reproducibility","dir":"Articles","previous_headings":"Further Concerns","what":"Reproducibility","title":"teal.data with Python","text":"order ensure reproducibility generating teal datasets using Python necessary use reproducible Python environment (example using virtualenv conda) see details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal.data-with-python.html","id":"deployment","dir":"Articles","previous_headings":"Further Concerns","what":"Deployment","title":"teal.data with Python","text":"Python interpreter (Python environment described ) need available deploying app. recommend following example see can done.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/testing-delayed-data.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Examining Delayed Data Objects","text":"delayed data object created described Delayed Data Objects, teal.data provides useful set functions examine object outside shiny application, .e. global environment. exhaustive list functions: basic function get_dataname returns name dataset datasets delayed data object: delayed data objects described also contain launch method can used test data loading screen: also pull method test data can loaded without launching shiny app. See Delayed Data Advanced. Alternatively teal.data provides load_dataset function <...>Dataset<...> objects used pull data without launching delayed loading screen, load_datasetsfunction <...>Data<...> objects launches delayed loading screen used pull datasets connection. loading data, can checked data successfully pulled using is_pulled function:","code":"library(teal.data) library(magrittr) adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) get_dataname(adsl) # \"ADSL\" ## [1] \"ADSL\" adae_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = adae_cf, keys = get_cdisc_keys(\"ADAE\") ) delayed_data <- cdisc_data(adsl, adae) ## Warning: The `data_objects` argument of `teal_data()` should use data directly. Using ## TealDatasetConnector and TealDataset is deprecated. Find more information on ## https://github.com/insightsengineering/teal/discussions/945 as of teal.data ## 0.3.1. ## ℹ The deprecated feature was likely used in the teal.data package. ## Please report the issue at ## . ## This warning is displayed once every 8 hours. ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was ## generated. get_dataname(delayed_data) # \"ADSL\" \"ADAE\" ## [1] \"ADSL\" \"ADAE\" if (interactive()) { delayed_data$launch() } if (interactive()) { load_datasets(delayed_data) } is_pulled(delayed_data) ## [1] FALSE"},{"path":"https://insightsengineering.github.io/teal.data/articles/testing-delayed-data.html","id":"aside-loading-page-ui","dir":"Articles","previous_headings":"Overview","what":"Aside: Loading page UI","title":"Examining Delayed Data Objects","text":"possible set default values boxes loading page using set_ui_input method:","code":"adae$set_ui_input(function(ns) { list(numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 5)) })"},{"path":"https://insightsengineering.github.io/teal.data/articles/testing-delayed-data.html","id":"testing-data-loading-continued","dir":"Articles","previous_headings":"Overview","what":"Testing data loading continued","title":"Examining Delayed Data Objects","text":"data loaded, ’s also possible access individual dataset objects using get_dataset function, <...>Data<...> objects, retrieve dataset objects using get_datasets function: Note connector loaded, result dataset object: view raw dataframe object, use get_raw_data function: get_code function called check processing code expected (reproducibility). See section pre-processing Delayed Data specify additional code instructions transform delayed data also added output get_code.","code":"lapply(delayed_data$get_items(), function(item) item$pull()) # return a particular dataset by name get_dataset(delayed_data, dataname = \"ADSL\") # or return all datasets load_datasets(delayed_data) get_datasets(delayed_data) # \"CDISCTealDatasetConnector\" \"TealDatasetConnector\" \"R6\" class(adsl) ## [1] \"CDISCTealDatasetConnector\" \"TealDatasetConnector\" ## [3] \"R6\" # \"CDISCTealDataset\" \"TealDataset\" \"R6\" class(get_dataset(adsl)) ## [1] \"CDISCTealDataset\" \"TealDataset\" \"R6\" # for a single <...>Dataset<..> object head(get_raw_data(adsl), 2) ## # A data frame: 2 × 55 ## STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL ## * ## 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y ## 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N ## # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , ## # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , ## # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , ## # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , ## # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , ## # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , ## # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , … # or for a <...>Data<...> object containing multiple datasets, specify the name of the dataset of interest raw <- get_raw_data(delayed_data, \"ADSL\") head(raw, 2) ## # A data frame: 2 × 55 ## STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL ## * ## 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y ## 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N ## # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , ## # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , ## # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , ## # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , ## # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , ## # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , ## # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , … # note the raw data is now just a regular R table class(raw) ## [1] \"tbl_df\" \"tbl\" \"data.frame\" get_code(delayed_data) ## [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\\nADAE <- teal.data::example_cdisc_data(dataname = \\\"ADAE\\\")\""},{"path":"https://insightsengineering.github.io/teal.data/articles/testing-delayed-data.html","id":"aside-piping-functions","dir":"Articles","previous_headings":"Overview","what":"Aside: Piping functions","title":"Examining Delayed Data Objects","text":"examples covered basic piping, natural sequence loading inspection delayed data object. reason, magrittr pipe %>% works well many pre-processing tasks. Since functions modify (operate ) objects given , need assign result. introduction pipes, refer documentation %>% resources pipes.","code":"library(teal.data) library(magrittr) adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) %>% mutate_dataset(\"ADSL$TRTDUR <- round(as.numeric(ADSL$TRTEDTM - ADSL$TRTSDTM), 1)\") %>% load_dataset() %>% get_raw_data() %>% head(n = 2) ## # A data frame: 2 × 56 ## STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL ## * ## 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y ## 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N ## # ℹ 45 more variables: INVID , INVNAM , ARM , ARMCD , ## # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , ## # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , ## # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , ## # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , ## # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , ## # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , …"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Creating Delayed Data Classes (Advanced)","text":"teal.data provides several ways include datasets shiny applications. Normally, one develops application way data available app starts. always involves passing data.frame objects using cdisc_data teal_data functions shiny application. way building app applicable data physically available app created. Including data shiny app global objects means fixed won’t change throughout life application session. possible scenario data may available creation initialization application. data need loaded shiny application initialized, may also involve entering user name password credentials via shiny UI components. Delayed data loading applications involves specifying metadata stores information needed pull data right source. delayed data loading applications, main app loads user prompted data loading UI. means delayed data applications can two-staged: Data loading app Main app","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-key-definitions","dir":"Articles","previous_headings":"","what":"Key definitions","title":"Creating Delayed Data Classes (Advanced)","text":"following general descriptions main classes teal.data package. TealDataset contains physical data form single data.frame plus reproducible code. TealDatasetConnector contains instructions obtain single TealDataset object. TealDataConnection opens closes connections (remote data sources). TealDataConnector contains arbitrary many TealDatasetConnector objects optionally one TealDataConnection object. TealData contains arbitrary many TealDataset, TealDatasetConnector / TealDataConnector objects. exception TealDataConnection, classes CDISC equivalent, e.g. TealData -> CDISCTealData.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-callablefunction","dir":"Articles","previous_headings":"Creating an app > Callable","what":"CallableFunction","title":"Creating Delayed Data Classes (Advanced)","text":"class won’t used often developers ’s essential connectors store execute R functions feature get code reproduce function calls. example object class CallableFunction created runs example_cdisc_data function arguments specified user. ’s also possible execute fun$run() function arguments added fly named list. Dynamic arguments won’t reflected reproducible code, consequences places - get back later stages documentation. CallableFunction can also depend R objects example function depends ADSL. function can executed specific environment can copy objects needed execute call. include objects function call, one use $assign_to_env() copy object $set_args(list(ADSL = .name(ADSL))) link object function argument.","code":"library(teal.data) #> Loading required package: shiny # initialize object fun <- callable_function(fun = teal.data::example_cdisc_data) # set arguments to function fun$set_args(list(dataname = \"ADSL\")) # execute function with arguments set df <- fun$run() head(df, 2) #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 14.424934 #> 2 C: Combination B: Placebo C: Combination Asia C S1 4.055463 #> BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 MEDIUM Y Y Y Y N 2019-02-22 2019-02-24 11:09:25 #> 2 LOW Y Y N N Y 2019-02-26 2019-02-26 09:05:10 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-12 04:28:08 2019-02-24 11:09:25 2021-02-11 22:28:08 #> 2 2022-02-26 03:05:10 2019-02-26 09:05:10 2021-02-25 21:05:10 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-11 22:28:08 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2021-02-25 21:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 DISCONTINUED #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-12 1084 DEATH 2022-03-06 ADVERSE EVENT ADVERSE EVENT #> 2 COMPLETED 2022-02-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT #> 1 22 <=30 2022-03-06 1105 Yes #> 2 NA 2022-03-17 NA # check reproducible code cat(fun$get_call()) #> teal.data::example_cdisc_data(dataname = \"ADSL\") # initialize object fun <- callable_function(fun = teal.data::example_cdisc_data) # add arguments on the fly df <- fun$run(args = list(dataname = \"ADAE\")) head(df, 2) #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM ARM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe A: Drug X #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe A: Drug X #> ARMCD ACTARM ACTARMCD TRT01P TRT01A TRT02P TRT02A #> 1 ARM A A: Drug X ARM A A: Drug X A: Drug X B: Placebo A: Drug X #> 2 ARM A A: Drug X ARM A A: Drug X A: Drug X B: Placebo A: Drug X #> REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL #> 1 South America B S2 6.462991 LOW Y Y Y N #> 2 South America B S2 6.462991 LOW Y Y Y N #> AEWITHFL RANDDT TRTSDTM TRTEDTM #> 1 N 2020-11-03 2020-11-04 04:08:58 2022-02-20 03:33:55 #> 2 N 2020-11-03 2020-11-04 04:08:58 2022-02-20 03:33:55 #> TRT01SDTM TRT01EDTM TRT02SDTM #> 1 2020-11-04 04:08:58 2021-02-19 21:33:55 2021-02-19 21:33:55 #> 2 2020-11-04 04:08:58 2021-02-19 21:33:55 2021-02-19 21:33:55 #> TRT02EDTM AP01SDTM AP01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> AP02SDTM AP02EDTM EOSSTT EOTSTT EOSDT #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED DISCONTINUED 2022-02-20 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED DISCONTINUED 2022-02-20 #> EOSDY DCSREAS DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 #> 1 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT 24 <=30 #> 2 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT 24 <=30 #> LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM AELLT #> 1 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 llt B.2.1.2.1 #> 2 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 llt D.1.1.4.2 #> AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV AESER #> 1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE N #> 2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE N #> AEACN AEREL AEOUT AESDTH AESCONG AESDISAB AESHOSP #> 1 DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y N #> 2 DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y N #> AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM AENDTM ASTDY #> 1 N N Y Y 2021-04-15 04:08:58 2021-10-04 04:08:58 162 #> 2 N N Y N 2021-05-19 04:08:58 2021-10-31 04:08:58 196 #> AENDY LDOSEDTM LDRELTM AETOXGR SMQ01NAM SMQ02NAM SMQ01SC #> 1 334 2020-11-07 09:05:04 228663.896 3 #> 2 361 2021-05-17 07:21:09 2687.814 3 #> SMQ02SC CQ01NAM ANL01FL AERELNST AEACNOTH #> 1 Y NONE PROCEDURE/SURGERY #> 2 Y CONCURRENT ILLNESS MEDICATION # dynamic arguments not reflected in the call cat(fun$get_call()) #> teal.data::example_cdisc_data() adsl_raw <- teal.data::example_cdisc_data(dataname = \"ADSL\") fun <- callable_function(fun = function(adsl) { adsl_2 <- adsl adsl_2$new_col <- TRUE adsl_2 }) # copy adsl to CallableFunction environment fun$assign_to_env(\"adsl\", adsl_raw) # set arguments fun$set_args(args = list(adsl = as.name(\"adsl\"))) # execute function df <- fun$run() head(df, 2) #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 14.424934 #> 2 C: Combination B: Placebo C: Combination Asia C S1 4.055463 #> BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 MEDIUM Y Y Y Y N 2019-02-22 2019-02-24 11:09:25 #> 2 LOW Y Y N N Y 2019-02-26 2019-02-26 09:05:10 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-12 04:28:08 2019-02-24 11:09:25 2021-02-11 22:28:08 #> 2 2022-02-26 03:05:10 2019-02-26 09:05:10 2021-02-25 21:05:10 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-11 22:28:08 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2021-02-25 21:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 DISCONTINUED #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-12 1084 DEATH 2022-03-06 ADVERSE EVENT ADVERSE EVENT #> 2 COMPLETED 2022-02-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT new_col #> 1 22 <=30 2022-03-06 1105 Yes TRUE #> 2 NA 2022-03-17 NA TRUE # get R code fun$get_call() #> [1] \"(function(adsl) {\\n adsl_2 <- adsl\\n adsl_2$new_col <- TRUE\\n adsl_2\\n})(adsl = adsl)\""},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-callablecode","dir":"Articles","previous_headings":"Creating an app","what":"CallableCode","title":"Creating Delayed Data Classes (Advanced)","text":"simpler version Callable class CallableCode. Similar CallableFunction, CallableCode stores code can evaluated using run() isn’t able use dynamic arguments make code general. CallableCode also allows assignment objects environment. CallableCode can contain multiple lines (commands) code also allows library calls. Please note objects assigned independent environment can’t modified locked immediately. means CallableCode created allowed make changes x1.","code":"code <- callable_code( \"library(teal.data) ADTTE <- teal.data::example_cdisc_data(\\\"ADTTE\\\") ADTTE$x1 <- x1 ADTTE <- dplyr::filter(ADTTE, PARAMCD %in% c('EFS', 'OS'))\" ) # examine call cat(code$get_call()) #> library(teal.data) #> ADTTE <- teal.data::example_cdisc_data(\"ADTTE\") #> ADTTE$x1 <- x1 #> ADTTE <- dplyr::filter(ADTTE, PARAMCD %in% c(\"EFS\", \"OS\")) # assign x1 to environment (otherwise code would run with error as x1 would not be defined) code$assign_to_env(\"x1\", 1) # evaluate call df <- code$run() head(df$x1, 2) #> [1] 1 1"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-tealdataset-base-class-which-cdisctealdataset-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealDataset (base class which CDISCTealDataset inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"TealDataset R6 class keeps data.frame raw_data slot. One can create TealDataset including data.frame setting data attributes. example first create adsl put data.frame cdisc_dataset function. Together data.frame one also provide dataname optional code reproduce data reproducibility required. Note cdisc_dataset returns object CDISCTealDataset, needed CDISC analysis. object created contains previously defined attributes can extracted.","code":"library(magrittr) adsl_raw <- teal.data::example_cdisc_data(\"ADSL\") %>% head(3) adsl_dataset <- cdisc_dataset( dataname = \"ADSL\", x = adsl_raw, code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\") %>% head(3)\" ) # check if code is reproducible get_dataname(adsl_dataset) #> [1] \"ADSL\" # get label get_dataset_label(adsl_dataset) #> [1] \"Subject Level Analysis Dataset\" # get reproducible code get_code(adsl_dataset) #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\") %>% head(3)\" # get data.frame get_raw_data(adsl_dataset) #> # A tibble: 3 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-RU… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , #> # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , … # get keys (i.e. the primary keys of the dataset) adsl_dataset$get_keys() #> [1] \"STUDYID\" \"USUBJID\""},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-tealdatasetconnector-base-class-which-cdisctealdatasetconnector-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealDatasetConnector (base class which CDISCTealDatasetConnector inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"TealDatasetConnector contains Callable object obtain single TealDataset object. code chunk , connector created based example_cdisc_data function. Initially, adsl_conn doesn’t contain data. Attempting fetch unavailable data produce error. Data can loaded using load_dataset() function. data loaded, adsl_conn contains reproducible code also code pull data. TealDatasetConnector also allows variables passed Callable object may depend . code adsl_raw object - created - added CallableFunction. properly link ADSL argument function inside CallableFunction object raw data adsl_raw several parameters match: .name(\"dummy_name\") must value name \"ADSL\" - set_args(list(ADSL = .name(\"dummy_name\"))) dummy_name must linked raw data adsl_raw - vars = list(dummy_name = adsl_raw) name ADSL fixed name argument function inside CallableFunction. name dummy_name free valid R name. TealDatasetConnector like delayed data objects contains launch method can used obtain data using shiny application. function can used check objects specified correctly investigate potential mistakes. default shiny app won’t render inputs datasets specify . set inputs use $set_ui_input(), passing UI module function, ns argument (shiny namespace ID object). example , callable_function object contains two arguments, ADSL n. ADSL given n entered shiny app launch method called.","code":"adsl_conn <- dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"Subject-Level Analysis Dataset\" ) # get raw data try(get_raw_data(adsl_conn)) #> Error : 'ADSL' has not been pulled yet #> - please use `load_dataset()` first. # execution/reproducible code get_code(adsl_conn) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" # pull data load_dataset(adsl_conn) # get raw data get_raw_data(adsl_conn) #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … # here we use the general dataset_connector function which pulls an object of type TealDataset # there is also a cdisc_dataset_connector function which pulls an object of type CDISCTealDataset adsl_2 <- dataset_connector( dataname = \"ADSL_2\", pull_callable = callable_function(fun = function(ADSL) ADSL_2 <- ADSL) %>% # nolint set_args(list(ADSL = as.name(\"dummy_name\"))), keys = get_cdisc_keys(\"ADSL\"), label = \"Example label\", vars = list(dummy_name = adsl_raw) ) load_dataset(adsl_2) adsl_3 <- dataset_connector( dataname = \"ADSL_3\", pull_callable = callable_function(fun = function(ADSL, n) ADSL_3 <- head(ADSL, n)) %>% # nolint set_args(list(ADSL = as.name(\"ADSL\"))), keys = get_cdisc_keys(\"ADSL\"), label = \"Example label\", vars = list(ADSL = adsl_raw) ) adsl_3$set_ui_input(function(ns) { list( numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1) ) }) if (interactive()) { adsl_3$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-tealdataconnection","dir":"Articles","previous_headings":"Creating an app","what":"TealDataConnection","title":"Creating Delayed Data Classes (Advanced)","text":"Objects class responsible set connection remote data sources. TealDataConnection opens closes connections calling CallableFunction appropriate arguments. Note app pulls data remote source, outputs change even code data remote source changes. shiny applications, connection arguments need linked inputs, TealDataConnection contains module. Developers can customize UI inputs open connection using set_open_ui() specify relevant server function using set_open_server(). ’s important keep mind server module needs connection argument open() close() needed.","code":"open_fun <- callable_function(data.frame) # define opening function open_fun$set_args(list(x = 1:5)) # define fixed arguments to opening function close_fun <- callable_function(sum) # define closing function close_fun$set_args(list(x = 1:5)) # define fixed arguments to closing function ping_fun <- callable_function(function() TRUE) x <- data_connection( ping_fun = ping_fun, # define ping function open_fun = open_fun, # define opening function close_fun = close_fun # define closing function )"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-tealdataconnector-base-class-which-cdisctealdataconnector-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealDataConnector (base class which CDISCTealDataConnector inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"class combines multiple TealDatasetConnector (CDISCTealDatasetConnector) single TealDataConnection object. creates module manage connection load data. create two TealDatasetConnector objects TealDataConnection object combine together TealDataConnector object. object created can used pull data obtain code. combines code pull datasets preceded open connection code followed close connection code. Please note TealDataConnector doesn’t limit kind connectors set within, one must aware rather contain similar connectors (.e. calling functions share arguments). example, execute data$set_pull_args(args = list(n = 5)), argument set connectors. case connector contains CallableFunction doesn’t n formals fail. CallableCode can’t hold additional arguments ’s fixed ignore every arguments set set_pull_args. default TealDataConnector creates simple shiny module without inputs arguments callable_function connectors. means , opening, closing, pulling datasets done default arguments. However, users can easily extend module using set_ui() set_server() specify UI server function . general rule creating modules callback server UI possible, server module executed submit button clicked. see set_preopen_server TealDataConnection object slight relaxation rule. extend app interface adding text input passed scda function. UI created conn connectors object server module requires connectors connection objects additional arguments. Executing data$launch() open shiny application prompts user input load data. Remember data can loaded . run code data$pull() please reinitialize connectors, connection data object running code .","code":"# create TealDatasetConnectors slice_example_cdisc_data <- function(dataname, n) { teal.data::example_cdisc_data(dataname) %>% head(n) } adsl <- dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(slice_example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"Subject-Level Analysis Dataset\" ) adsl_3 <- dataset_connector( dataname = \"ADSL_3\", pull_callable = callable_function(fun = function(ADSL, n = 5) { # nolint ADSL_3 <- head(ADSL, n) # nolint }) %>% set_args(list(ADSL = as.name(\"ADSL\"))), keys = get_cdisc_keys(\"ADSL\"), label = \"Example label\", vars = list(ADSL = adsl) ) adsl_3$set_ui_input(function(ns) { list( numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1) ) }) connectors <- list(adsl, adsl_3) # create connection open_fun <- callable_function(fun = library) open_fun$set_args(list(package = \"teal.data\")) conn <- teal.data:::TealDataConnection$new(open_fun = open_fun) # nolint # create TealDataConnector data <- teal.data:::TealDataConnector$new( connection = conn, connectors = connectors ) cat(get_code(data)) #> library(package = \"teal.data\") #> ADSL <- (function(dataname, n) { #> teal.data::example_cdisc_data(dataname) %>% head(n) #> })(dataname = \"ADSL\") #> ADSL_3 <- (function(ADSL, n = 5) { #> ADSL_3 <- head(ADSL, n) #> })(ADSL = ADSL) # pull ADSL and ADSL_3 data$set_pull_args(args = list(n = 5)) data$pull() data$set_ui( function(id, ...) { ns <- NS(id) tagList( conn$get_open_ui(ns(\"open_connection\")), textInput(ns(\"name\"), p(\"Choose\", code(\"name\")), value = \"latest\"), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) data$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection if (!is.null(connection$get_open_server())) { connection$get_open_server()( id = \"open_connection\", connection = connection ) } for (connector in connectors) { # set_args before to return them in the code (fixed args) set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } ) } ) if (interactive()) { data$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-tealdata-base-class-which-cdisctealdata-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealData (base class which CDISCTealData inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"TealData manages TealDataset, TealDatasetConnector / TealDataConnector objects. CDISCTealData equivalent object creating apps analyze CDISC data. objects created using teal_data cdisc_data respectively. using teal package objects passed data argument init. One can combine multiple delayed data objects using [teal|cdisc]_data functions include shiny application. TealData gathers objects sets combined UI shiny inputs objects. code chunk specified four dataset connectors, works arbitrary many objects combination classes TealDataset, TealDatasetConnector / TealDataConnector. TealData also contains launch() method investigate data set correctly. However, TealData lacks pull() method. Reproducible code attached data object combined code components, one can also extract code single dataset specifying dataname argument. Developers can also extract datasets connectors included TealData.","code":"data <- cdisc_data( cdisc_dataset( dataname = \"ADSL\", teal.data::example_cdisc_data(dataname = \"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" ), cdisc_dataset( dataname = \"ADTTE\", teal.data::example_cdisc_data(\"ADTTE\"), code = \"ADTTE <- teal.data::example_cdisc_data(dataname = \\\"ADTTE\\\")\" ) ) #> Warning: The `data_objects` argument of `teal_data()` should use data directly. Using #> TealDatasetConnector and TealDataset is deprecated. Find more information on #> https://github.com/insightsengineering/teal/discussions/945 as of teal.data #> 0.3.1. #> ℹ The deprecated feature was likely used in the teal.data package. #> Please report the issue at #> . #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was #> generated. # nolint start example_cdisc_dataset_connector <- function(dataname) { cdisc_dataset_connector( dataname = dataname, pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = dataname)), keys = get_cdisc_keys(dataname), label = sprintf(\"%s connector\", dataname) ) } adsl <- example_cdisc_dataset_connector(\"ADSL\") adae <- example_cdisc_dataset_connector(\"ADAE\") advs <- example_cdisc_dataset_connector(\"ADVS\") adtte <- example_cdisc_dataset_connector(\"ADTTE\") data <- cdisc_data(adsl, adae, advs, adtte) # nolint end if (interactive()) { data$launch() } get_code(data) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\\nADAE <- teal.data::example_cdisc_data(dataname = \\\"ADAE\\\")\\nADVS <- teal.data::example_cdisc_data(dataname = \\\"ADVS\\\")\\nADTTE <- teal.data::example_cdisc_data(dataname = \\\"ADTTE\\\")\" get_code(data, dataname = \"ADSL\") #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" get_code(data, dataname = \"ADTTE\") #> [1] \"ADTTE <- teal.data::example_cdisc_data(dataname = \\\"ADTTE\\\")\" # if you launched the shiny app and pressed the submit button above to load the data, # then these 4 lines do not need to be run adsl$pull() adae$pull() advs$pull() adtte$pull() # get loaded datasets data$get_datasets() # get single dataset data$get_dataset(dataname = \"ADSL\") # get data and dataset connectors data$get_connectors() # get all datasets/connectors data$get_items()"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-data-modification","dir":"Articles","previous_headings":"Creating an app","what":"Data modification","title":"Creating Delayed Data Classes (Advanced)","text":"modify single dataset one use mutate_dataset specifying code argument code single character script location script file. case delayed data, pre-processing code passed mutate_dataset run data becomes available. get_code() function returns loading code CallableFunction mutation code provided using mutate_dataset. mutate_dataset can also used TealData objects applies code dataset specified dataname. important, TealData can track call affects particular dataset. Check code , create data containing two datasets using cdisc_data function. can still use mutate_dataset object contains multiple datasets, one requirement - one needs specify dataname. Afterwards, one can extract reproducible code data affects particular dataname. One can also pipe multiple mutate_dataset calls applied different datasets. Sometimes code one object can depend another, case can link way link TealDatasetConnector objects. object code dependent another, ADTTE depends ADSL , get_code return everything need executed reproduce dataset. Using mutate_dataset creates tree calls, can subset dataname, developers can also use mutate_data function doesn’t require dataname specified. mutate_data used, code single dataset possible subset, instead code datasets returned.","code":"adsl <- cdisc_dataset( dataname = \"ADSL\", teal.data::example_cdisc_data(dataname = \"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" ) %>% mutate_dataset(code = \"ADSL$x1 <- 1\") cat(get_code(adsl)) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 data <- cdisc_data(adsl, adtte) %>% mutate_dataset(code = \"ADSL$x3 <- 3\", dataname = \"ADSL\") # get reproducible code of all datasets cat(get_code(data)) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 # get ADSL reproducible code cat(get_code(data, dataname = \"ADSL\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADSL$x3 <- 3 data <- mutate_dataset(data, code = \"ADTTE$x4 <- 4\", dataname = \"ADTTE\") %>% mutate_dataset(code = \"ADSL <- dplyr::filter(ADSL, SEX == 'F')\", dataname = \"ADSL\") cat(get_code(data, \"ADSL\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADSL$x3 <- 3 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") # note that the code for ADTTE below does not contain any mention of ADSL cat(get_code(data, \"ADTTE\")) #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADTTE$x4 <- 4 data <- mutate_dataset( data, code = \"ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID)\", dataname = \"ADTTE\", vars = list(ADSL = adsl) # vars = list( = )) ) %>% mutate_dataset(\"ADSL$var_created_after <- NA\", dataname = \"ADSL\") # note that the code that defines ADSL is now part of the code of ADTTE below cat(get_code(data, dataname = \"ADTTE\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 #> ADTTE$x4 <- 4 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") #> ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID) # moreover, note that the code inserted to the mutate_dataset after the pipe was not included. data <- mutate_data(data, code = \" ADSL$x3 <- 3 proxy_var <- 4 ADTTE$x4 <- proxy_var \" ) # single dataset code is not possible to obtain anymore cat(adsl_code <- get_code(data, \"ADSL\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 #> ADTTE$x4 <- 4 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") #> ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID) #> ADSL$var_created_after <- NA #> ADSL$x3 <- 3 #> proxy_var <- 4 #> ADTTE$x4 <- proxy_var cat(adtte_code <- get_code(data, \"ADTTE\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 #> ADTTE$x4 <- 4 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") #> ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID) #> ADSL$var_created_after <- NA #> ADSL$x3 <- 3 #> proxy_var <- 4 #> ADTTE$x4 <- proxy_var # TRUE as.character(adsl_code) == as.character(adtte_code) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-advanced.html","id":"section-teal-data-in-a-shiny-app","dir":"Articles","previous_headings":"Creating an app","what":"teal.data in a shiny app","title":"Creating Delayed Data Classes (Advanced)","text":"","code":"# nolint start library(teal.data) library(magrittr) slice_example_cdisc_data <- function(dataname, n) { teal.data::example_cdisc_data(dataname) %>% head(n) } adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(slice_example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADSL connector\" ) adrs <- cdisc_dataset_connector( dataname = \"ADRS\", pull_callable = callable_function(slice_example_cdisc_data) %>% set_args(list(dataname = \"ADRS\")), keys = get_cdisc_keys(\"ADRS\"), label = \"ADRS connector\" ) x <- dataset(\"x\", data.frame(x = 1, b = 2), code = \"x <- data.frame(x = 1, b = 2)\") data <- teal_data(adsl, adrs, x) shinyApp( ui = fluidPage( shinyjs::useShinyjs(), titlePanel(\"Delayed data loading\"), sidebarLayout( sidebarPanel(data$get_ui(\"data\"), uiOutput(\"dataset\")), mainPanel(tableOutput(\"dist_plot\")) ) ), server = function(input, output, session) { data_reactive <- data$get_server()(\"data\") observeEvent(data_reactive(), ignoreNULL = TRUE, { shinyjs::hide(\"data-delayed_data\") }) output$dataset <- renderUI({ req(data_reactive()) datanames <- names(get_raw_data(data_reactive())) radioButtons(\"dataname\", \"Select dataname\", datanames, datanames[1]) }) output$dist_plot <- renderTable({ req(input$dataname) dataset <- get_raw_data(data_reactive())[[input$dataname]] head(dataset) }) } ) # nolint end"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-basic.html","id":"basic-understanding","dir":"Articles","previous_headings":"","what":"Basic understanding","title":"Using Delayed Data Loading (Basic)","text":"Delayed data objects R objects contain instructions acquire data. practice, pass DDL objects instructions teal application can launch teal app first pull data afterwards. main difference DDL object non-DDL object data available immediately creating non-DDL object. contrast, data DDL object available construction, pulling (executing instructions stored object).","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-basic.html","id":"key-concepts","dir":"Articles","previous_headings":"Basic understanding","what":"Key concepts","title":"Using Delayed Data Loading (Basic)","text":"TealDatasetConnector object used pull single delayed data set teal app. Connectors pull data proprietary data storage included package. TealDataConnector object used pull set delayed data sets teal app share common connection (see Delayed Data Loading definition connection object). cdisc_data function takes set TealDataConnector, TealDatasetConnector / cdisc_datasets (non-delayed datasets) create TealData object used create teal applications.","code":"# nolint start library(teal.data) # generalized function to create delayed data from code - see package help for other connectors x <- code_dataset_connector( dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) # nolint end # nolint start library(teal.data) library(magrittr) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADSL connector\" ) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADAE connector\" ) adsl_adae <- relational_data_connector( connection = data_connection(), connectors = list(adsl, adae) ) # nolint end # nolint start # create a TealDatasetConnector for ADVS library(teal.data) library(magrittr) advs <- cdisc_dataset_connector( dataname = \"ADVS\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADVS\")), keys = get_cdisc_keys(\"ADVS\"), label = \"ADVS connector\" ) # use cdisc_data() to create a `DDL` object delayed_data <- cdisc_data(adsl_adae, advs) ## Warning: The `data_objects` argument of `teal_data()` should use data directly. Using ## TealDatasetConnector and TealDataset is deprecated. Find more information on ## https://github.com/insightsengineering/teal/discussions/945 as of teal.data ## 0.3.1. ## ℹ The deprecated feature was likely used in the teal.data package. ## Please report the issue at ## . ## This warning is displayed once every 8 hours. ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was ## generated. # nolint end"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-basic.html","id":"constructors","dir":"Articles","previous_headings":"Basic understanding","what":"Constructors","title":"Using Delayed Data Loading (Basic)","text":"list constructors available teal.data create TealDataset delayed TealDatasetConnector objects: Notes: xyz_dataset_connector functions equivalent xyz_cdisc_dataset_connector function (example rds_cdisc_dataset_connector) specifies additional dataset metadata. cdisc_data standard function used create data object used within teal apps standard CDISC study data. general teal_data function can used allow arbitrary relational data used within teal apps.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-basic.html","id":"dataset-dependencies","dir":"Articles","previous_headings":"Basic understanding","what":"Dataset dependencies","title":"Using Delayed Data Loading (Basic)","text":"datasets passed teal_data cdisc_data pulled order inputted. datasets depend datasets available placed later argument list:","code":"# nolint start library(teal.data) library(magrittr) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADSL connector\" ) adsl_2 <- code_cdisc_dataset_connector(\"ADSL_2\", code = \"head(ADSL, 5)\", keys = get_cdisc_keys(\"ADSL\"), ADSL = adsl ) # launch method will be able to load the data as adsl will be pulled first cdisc_data(adsl, adsl_2) ## A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): ## --> Element 1: ## A CDISCTealDatasetConnector object, named ADSL, containing a TealDataset object that has not been loaded/pulled ## --> Element 2: ## A CDISCTealDatasetConnector object, named ADSL_2, containing a TealDataset object that has not been loaded/pulled # launch method will not be able to load the data as adae is pulled first but it depends on adsl cdisc_data(adsl_2, adsl) ## A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): ## --> Element 1: ## A CDISCTealDatasetConnector object, named ADSL_2, containing a TealDataset object that has not been loaded/pulled ## --> Element 2: ## A CDISCTealDatasetConnector object, named ADSL, containing a TealDataset object that has not been loaded/pulled # nolint end"},{"path":"https://insightsengineering.github.io/teal.data/articles/using-delayed-data-basic.html","id":"suggested-development-workflow","dir":"Articles","previous_headings":"","what":"Suggested development workflow","title":"Using Delayed Data Loading (Basic)","text":"following workflow facilitates building teal apps DDL minimizing debugging overhead. Run teal app configured without delayed data verify app starts expected. Replace cdisc_dataset functions appropriate TealDatasetConnector objects. Add preprocessing code (see Delayed Data Advanced preprocessing documentation) verify running newly created object’s $launch method. First, include just single module verify teal app starts loads expected data. , add rest modules one one, replacing dataset calls strings iteratively verify app functions expected.","code":""},{"path":"https://insightsengineering.github.io/teal.data/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dawid Kaledkowski. Author, maintainer. Pawel Rucki. Author. Mahmoud Hallal. Author. Nikolas Burkoff. Author. Maciej Nasinski. Author. Konrad Pagacz. Author. Junlue Zhao. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.data/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kaledkowski D, Rucki P, Hallal M, Burkoff N, Nasinski M, Pagacz K, Zhao J (2023). teal.data: Data Model 'teal' Applications. R package version 0.3.0.9016, https://github.com/insightsengineering/teal.data/, https://insightsengineering.github.io/teal.data/.","code":"@Manual{, title = {teal.data: Data Model for 'teal' Applications}, author = {Dawid Kaledkowski and Pawel Rucki and Mahmoud Hallal and Nikolas Burkoff and Maciej Nasinski and Konrad Pagacz and Junlue Zhao}, year = {2023}, note = {R package version 0.3.0.9016, https://github.com/insightsengineering/teal.data/}, url = {https://insightsengineering.github.io/teal.data/}, }"},{"path":"https://insightsengineering.github.io/teal.data/index.html","id":"tealdata","dir":"","previous_headings":"","what":"Data Model for teal Applications","title":"Data Model for teal Applications","text":"package used create data needed teal applications. data can : Independent data frames CDISC data (clinical trial reporting) Relational data MultiAssayExperiment objects package provides: mechanism pulling data existing systems ability mutate (.e. pre-process) data record operations used create data enable reproducibility","code":""},{"path":"https://insightsengineering.github.io/teal.data/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Data Model for teal Applications","text":"Alternatively, might want use development version available r-universe.","code":"# stable versions install.packages('teal.data', repos = c('https://insightsengineering.r-universe.dev', getOption('repos'))) # install.packages(\"pak\") pak::pak(\"insightsengineering/teal.data@*release\") # beta versions install.packages('teal.data', repos = c('https://pharmaverse.r-universe.dev', getOption('repos'))) # install.packages(\"pak\") pak::pak(\"insightsengineering/teal.data\")"},{"path":"https://insightsengineering.github.io/teal.data/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Data Model for teal Applications","text":"understand use package, please refer Introduction teal.data article, provides multiple examples code implementation. showcase example usage","code":"library(teal.data) # quick start for clinical trial data adsl <- teal.data::example_cdisc_data(\"ADSL\") adtte <- teal.data::example_cdisc_data(\"ADTTE\") my_data <- cdisc_data( cdisc_dataset(\"ADSL\", adsl), cdisc_dataset(\"ADTTE\", adtte) ) # quick start for general data my_general_data <- teal_data( dataset(\"iris\", iris), dataset(\"mtcars\", mtcars) ) # reproducibility check data <- teal_data(dataset(\"iris\", iris, code = \"iris <- mtcars\"), check = TRUE) #> Error in x$check_reproducibility() : Reproducibility check failed. # code extraction iris2 <- iris[1:6, ] iris2_data <- teal_data(dataset(\"iris2\", iris2, code = \"iris2 <- iris[1:6, ]\")) iris2_data$get_code() #> \"iris2 <- iris[1:6, ]\""},{"path":"https://insightsengineering.github.io/teal.data/index.html","id":"getting-help","dir":"","previous_headings":"","what":"Getting help","title":"Data Model for teal Applications","text":"encounter bug feature request - please file issue. questions, discussions staying date, please use “teal” channel pharmaverse slack workspace.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/pull_request_template.html","id":null,"dir":"","previous_headings":"","what":"Pull Request","title":"Pull Request","text":"Fixes #nnn","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"Class manages TealDatasetConnector specify additional dynamic arguments open/close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"teal.data::TealDataAbstract -> teal.data::TealDataConnector -> CDISCTealDataConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"teal.data::TealDataAbstract$check() teal.data::TealDataAbstract$check_reproducibility() teal.data::TealDataAbstract$execute_mutate() teal.data::TealDataAbstract$get_check() teal.data::TealDataAbstract$get_check_result() teal.data::TealDataAbstract$get_code() teal.data::TealDataAbstract$get_datanames() teal.data::TealDataAbstract$get_dataset() teal.data::TealDataAbstract$get_datasets() teal.data::TealDataAbstract$get_items() teal.data::TealDataAbstract$is_pulled() teal.data::TealDataAbstract$mutate_dataset() teal.data::TealDataAbstract$reassign_datasets_vars() teal.data::TealDataAbstract$set_check() teal.data::TealDataAbstract$set_pull_code() teal.data::TealDataConnector$get_code_class() teal.data::TealDataConnector$get_connection() teal.data::TealDataConnector$get_preopen_server() teal.data::TealDataConnector$get_server() teal.data::TealDataConnector$get_ui() teal.data::TealDataConnector$is_failed() teal.data::TealDataConnector$launch() teal.data::TealDataConnector$mutate() teal.data::TealDataConnector$print() teal.data::TealDataConnector$pull() teal.data::TealDataConnector$set_preopen_server() teal.data::TealDataConnector$set_pull_args() teal.data::TealDataConnector$set_server() teal.data::TealDataConnector$set_ui()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"CDISCTealDataConnector$new() CDISCTealDataConnector$get_parent() CDISCTealDataConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"Create new CDISCTealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"","code":"CDISCTealDataConnector$new(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"method-get-parent-","dir":"Reference","previous_headings":"","what":"Method get_parent()","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"Get datasets parent names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"","code":"CDISCTealDataConnector$get_parent()"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"(named list) dataset name corresponding parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"","code":"CDISCTealDataConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"data.frame object can stored inside object. difference compared TealDataset class parent field indicates name parent dataset. Note parent field might empty (.e. character(0)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"teal.data::TealDataset -> CDISCTealDataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"teal.data::TealDataset$check() teal.data::TealDataset$check_keys() teal.data::TealDataset$get_character_colnames() teal.data::TealDataset$get_code() teal.data::TealDataset$get_code_class() teal.data::TealDataset$get_colnames() teal.data::TealDataset$get_column_labels() teal.data::TealDataset$get_dataname() teal.data::TealDataset$get_datanames() teal.data::TealDataset$get_dataset() teal.data::TealDataset$get_dataset_label() teal.data::TealDataset$get_factor_colnames() teal.data::TealDataset$get_keys() teal.data::TealDataset$get_metadata() teal.data::TealDataset$get_mutate_code_class() teal.data::TealDataset$get_mutate_vars() teal.data::TealDataset$get_ncol() teal.data::TealDataset$get_nrow() teal.data::TealDataset$get_numeric_colnames() teal.data::TealDataset$get_raw_data() teal.data::TealDataset$get_row_labels() teal.data::TealDataset$get_rownames() teal.data::TealDataset$get_var_r6() teal.data::TealDataset$get_vars() teal.data::TealDataset$is_mutate_delayed() teal.data::TealDataset$is_pulled() teal.data::TealDataset$mutate() teal.data::TealDataset$print() teal.data::TealDataset$reassign_datasets_vars() teal.data::TealDataset$set_code() teal.data::TealDataset$set_dataset_label() teal.data::TealDataset$set_keys() teal.data::TealDataset$set_vars()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"CDISCTealDataset$new() CDISCTealDataset$recreate() CDISCTealDataset$get_attrs() CDISCTealDataset$get_parent() CDISCTealDataset$set_parent() CDISCTealDataset$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Create new object CDISCTealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$new( dataname, x, keys, parent, code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys (character) vector primary keys parent optional, (character) parent dataset name code (character) character string defining code needed produce data set x label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"method-recreate-","dir":"Reference","previous_headings":"","what":"Method recreate()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Recreate dataset current attributes useful way access class initialize method basing class object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$recreate( dataname = self$get_dataname(), x = self$get_raw_data(), keys = self$get_keys(), parent = self$get_parent(), code = private$code, label = self$get_dataset_label(), vars = list(), metadata = self$get_metadata() )"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys (character) vector primary keys parent optional, (character) parent dataset name code (character) character string defining code needed produce data set x label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"new object CDISCTealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"method-get-attrs-","dir":"Reference","previous_headings":"","what":"Method get_attrs()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Get dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$get_attrs()"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"(named list) dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"method-get-parent-","dir":"Reference","previous_headings":"","what":"Method get_parent()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Get parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$get_parent()"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"(character) indicating parent dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"method-set-parent-","dir":"Reference","previous_headings":"","what":"Method set_parent()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Set parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$set_parent(parent)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"parent (character) indicating parent dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"x <- cdisc_dataset( dataname = \"XYZ\", x = data.frame(x = c(1, 2), y = c(\"a\", \"b\"), stringsAsFactors = FALSE), keys = \"y\", parent = \"ABC\", code = \"XYZ <- data.frame(x = c(1, 2), y = c('aa', 'bb'), stringsAsFactors = FALSE)\", metadata = list(type = \"example\") ) x$ncol #> NULL x$get_code() #> [1] \"XYZ <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\" x$get_dataname() #> [1] \"XYZ\" x$get_keys() #> [1] \"y\" x$get_parent() #> [1] \"ABC\""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Objects class store connection function fetch single dataset. difference compared TealDatasetConnector parent field indicates name parent dataset. Note parent field might empty (.e. character(0)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"teal.data::TealDatasetConnector -> CDISCTealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"teal.data::TealDatasetConnector$check() teal.data::TealDatasetConnector$get_code() teal.data::TealDatasetConnector$get_code_class() teal.data::TealDatasetConnector$get_dataname() teal.data::TealDatasetConnector$get_datanames() teal.data::TealDatasetConnector$get_dataset() teal.data::TealDatasetConnector$get_dataset_label() teal.data::TealDatasetConnector$get_error_message() teal.data::TealDatasetConnector$get_keys() teal.data::TealDatasetConnector$get_pull_args() teal.data::TealDatasetConnector$get_pull_callable() teal.data::TealDatasetConnector$get_raw_data() teal.data::TealDatasetConnector$get_server() teal.data::TealDatasetConnector$get_ui() teal.data::TealDatasetConnector$get_var_r6() teal.data::TealDatasetConnector$is_failed() teal.data::TealDatasetConnector$is_mutate_delayed() teal.data::TealDatasetConnector$is_pulled() teal.data::TealDatasetConnector$launch() teal.data::TealDatasetConnector$mutate() teal.data::TealDatasetConnector$print() teal.data::TealDatasetConnector$reassign_datasets_vars() teal.data::TealDatasetConnector$set_args() teal.data::TealDatasetConnector$set_dataset_label() teal.data::TealDatasetConnector$set_keys() teal.data::TealDatasetConnector$set_ui_input()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"CDISCTealDatasetConnector$new() CDISCTealDatasetConnector$get_parent() CDISCTealDatasetConnector$pull() CDISCTealDatasetConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Create new TealDatasetConnector object. Set pulling function CallableFunction returns data.frame, e.g. reading function creating fly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$new( dataname, pull_callable, keys, parent, code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys (character) vector dataset primary keys column names parent optional, (character) parent dataset name code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script label (character) Label describe dataset. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"method-get-parent-","dir":"Reference","previous_headings":"","what":"Method get_parent()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Get parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$get_parent()"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"(character) indicating parent dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"method-pull-","dir":"Reference","previous_headings":"","what":"Method pull()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Pull data Read create data using pull_callable specified constructor.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$pull(args = NULL, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"args (NULL named list) additional dynamic arguments pull function. args can omitted pull_callable constructor already contains necessary arguments pull data. One can try execute pull_callable directly x$pull_callable$run() get code using x$pull_callable$get_code(). args specified pull used temporary get data saved code. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"self invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CDISCTealDatasetConnector.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":null,"dir":"Reference","previous_headings":"","what":"A Callable class of objects — Callable","title":"A Callable class of objects — Callable","text":"Object stores function name arguments. Methods get call run .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A Callable class of objects — Callable","text":"Callable$new() Callable$assign_to_env() Callable$run() Callable$is_failed() Callable$get_error_message() Callable$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A Callable class of objects — Callable","text":"Create new CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A Callable class of objects — Callable","text":"","code":"Callable$new(env)"},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A Callable class of objects — Callable","text":"env (environment) environment call evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A Callable class of objects — Callable","text":"new CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"method-assign-to-env-","dir":"Reference","previous_headings":"","what":"Method assign_to_env()","title":"A Callable class of objects — Callable","text":"Assigns x <- value object env. Assigned object modified within local environment locked using lockBinding. also means object reassigned throw error.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A Callable class of objects — Callable","text":"","code":"Callable$assign_to_env(x, value)"},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A Callable class of objects — Callable","text":"x (character value) name variable class environment value (data.frame) object assigned x","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A Callable class of objects — Callable","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"method-run-","dir":"Reference","previous_headings":"","what":"Method run()","title":"A Callable class of objects — Callable","text":"Execute Callable function code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A Callable class of objects — Callable","text":"","code":"Callable$run(return = TRUE, args = NULL, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A Callable class of objects — Callable","text":"return (logical value) whether return object args (NULL named list) supplied callable functions , dynamic arguments passed function. Dynamic arguments executed call saved means self$get_call() include later. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"A Callable class of objects — Callable","text":"nothing output function depending return argument. run fails return object class simple-error error try = TRUE stop try = FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"method-is-failed-","dir":"Reference","previous_headings":"","what":"Method is_failed()","title":"A Callable class of objects — Callable","text":"Check evaluation function failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A Callable class of objects — Callable","text":"","code":"Callable$is_failed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"A Callable class of objects — Callable","text":"(logical) TRUE evaluation function failed FALSE evaluation failed function yet called.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"method-get-error-message-","dir":"Reference","previous_headings":"","what":"Method get_error_message()","title":"A Callable class of objects — Callable","text":"Get error message last function execution","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"A Callable class of objects — Callable","text":"","code":"Callable$get_error_message()"},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"A Callable class of objects — Callable","text":"(character) object error message character(0) last function evaluation successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A Callable class of objects — Callable","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"A Callable class of objects — Callable","text":"","code":"Callable$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/Callable.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"A Callable class of objects — Callable","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":null,"dir":"Reference","previous_headings":"","what":"A CallableCode class of objects — CallableCode","title":"A CallableCode class of objects — CallableCode","text":"Object stores code reproduce object. includes methods get run code return object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"A CallableCode class of objects — CallableCode","text":"teal.data::Callable -> CallableCode","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"A CallableCode class of objects — CallableCode","text":"teal.data::Callable$assign_to_env() teal.data::Callable$get_error_message() teal.data::Callable$is_failed() teal.data::Callable$run()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A CallableCode class of objects — CallableCode","text":"CallableCode$new() CallableCode$get_call() CallableCode$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A CallableCode class of objects — CallableCode","text":"Create new CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableCode class of objects — CallableCode","text":"","code":"CallableCode$new(code, env = new.env(parent = parent.env(globalenv())))"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableCode class of objects — CallableCode","text":"code (character) string containing R code reproduce desired object. env (environment) environment function evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallableCode class of objects — CallableCode","text":"new CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"method-get-call-","dir":"Reference","previous_headings":"","what":"Method get_call()","title":"A CallableCode class of objects — CallableCode","text":"Get sequence calls code supplied produce object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableCode class of objects — CallableCode","text":"","code":"CallableCode$get_call(deparse = TRUE, args = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableCode class of objects — CallableCode","text":"deparse (logical value) whether return deparsed version call args (NULL) available consistent CallableFunction used retrieve call.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallableCode class of objects — CallableCode","text":"list calls character depending deparse argument","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A CallableCode class of objects — CallableCode","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableCode class of objects — CallableCode","text":"","code":"CallableCode$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableCode.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableCode class of objects — CallableCode","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":null,"dir":"Reference","previous_headings":"","what":"A CallableFunction class of objects — CallableFunction","title":"A CallableFunction class of objects — CallableFunction","text":"Object stores function name together arguments. Methods available get function call evaluate .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"A CallableFunction class of objects — CallableFunction","text":"teal.data::Callable -> CallableFunction","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"A CallableFunction class of objects — CallableFunction","text":"teal.data::Callable$assign_to_env() teal.data::Callable$get_error_message() teal.data::Callable$is_failed() teal.data::Callable$run()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A CallableFunction class of objects — CallableFunction","text":"CallableFunction$new() CallableFunction$get_args() CallableFunction$get_call() CallableFunction$set_args() CallableFunction$set_arg_value() CallableFunction$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A CallableFunction class of objects — CallableFunction","text":"Create new CallableFunction object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableFunction class of objects — CallableFunction","text":"","code":"CallableFunction$new(fun, env = new.env(parent = parent.env(globalenv())))"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableFunction class of objects — CallableFunction","text":"fun (function) function evaluated class. either function object name string. env (environment) environment function evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallableFunction class of objects — CallableFunction","text":"new CallableFunction object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"method-get-args-","dir":"Reference","previous_headings":"","what":"Method get_args()","title":"A CallableFunction class of objects — CallableFunction","text":"get arguments function gets called ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableFunction class of objects — CallableFunction","text":"","code":"CallableFunction$get_args()"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallableFunction class of objects — CallableFunction","text":"arguments function gets called ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"method-get-call-","dir":"Reference","previous_headings":"","what":"Method get_call()","title":"A CallableFunction class of objects — CallableFunction","text":"Get function call substituted arguments args. arguments stored object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableFunction class of objects — CallableFunction","text":"","code":"CallableFunction$get_call(deparse = TRUE, args = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableFunction class of objects — CallableFunction","text":"deparse (logical value) whether return deparsed version call args (NULL named list) dynamic arguments function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallableFunction class of objects — CallableFunction","text":"call character depending deparse argument","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"method-set-args-","dir":"Reference","previous_headings":"","what":"Method set_args()","title":"A CallableFunction class of objects — CallableFunction","text":"Set function arguments","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableFunction class of objects — CallableFunction","text":"","code":"CallableFunction$set_args(args)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableFunction class of objects — CallableFunction","text":"args (NULL named list) function arguments stored persistently object. Setting args remove args, create new modify previous name. clean arguments specify args = NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallableFunction class of objects — CallableFunction","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"method-set-arg-value-","dir":"Reference","previous_headings":"","what":"Method set_arg_value()","title":"A CallableFunction class of objects — CallableFunction","text":"Set single function argument value","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableFunction class of objects — CallableFunction","text":"","code":"CallableFunction$set_arg_value(name, value)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableFunction class of objects — CallableFunction","text":"name (character) argument name value argument value","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallableFunction class of objects — CallableFunction","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A CallableFunction class of objects — CallableFunction","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallableFunction class of objects — CallableFunction","text":"","code":"CallableFunction$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallableFunction.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallableFunction class of objects — CallableFunction","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":null,"dir":"Reference","previous_headings":"","what":"A CallablePythonCode class of objects — CallablePythonCode","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"CallablePythonCode class objects CallablePythonCode class objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"teal.data::Callable -> teal.data::CallableFunction -> CallablePythonCode","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"teal.data::Callable$assign_to_env() teal.data::Callable$get_error_message() teal.data::Callable$is_failed() teal.data::CallableFunction$get_args() teal.data::CallableFunction$get_call() teal.data::CallableFunction$set_arg_value() teal.data::CallableFunction$set_args()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"CallablePythonCode$new() CallablePythonCode$set_object() CallablePythonCode$run() CallablePythonCode$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"Create new CallablePythonCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"","code":"CallablePythonCode$new(fun, env = new.env(parent = parent.env(globalenv())))"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"fun (function) function evaluated class. Function named env (environment) environment result python code evaluation stored","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"new CallablePythonCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"method-set-object-","dir":"Reference","previous_headings":"","what":"Method set_object()","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"scripts code contain multiple objects, save name object corresponds final dataset interest. required running python scripts reticulate.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"","code":"CallablePythonCode$set_object(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"x (character) name object produced code script.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"method-run-","dir":"Reference","previous_headings":"","what":"Method run()","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"Execute Callable python code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"","code":"CallablePythonCode$run(args = NULL, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"args (NULL named list) supplied callable functions , dynamic arguments passed reticulate::py_run_string reticulate::py_run_file. Dynamic arguments executed call saved means self$get_call() include later. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"nothing output function depending return argument. run fails return object class simple-error error try = TRUE stop try = FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"","code":"CallablePythonCode$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CallablePythonCode.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — CallablePythonCode","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":null,"dir":"Reference","previous_headings":"","what":"Code Class — CodeClass","title":"Code Class — CodeClass","text":"Code Class Code Class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"Code Class — CodeClass","text":"code (list) Derive code dataset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Code Class — CodeClass","text":"CodeClass$new() CodeClass$append() CodeClass$set_code() CodeClass$get_code() CodeClass$eval() CodeClass$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Code Class — CodeClass","text":"CodeClass constructor","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$new( code = character(0), dataname = character(0), deps = character(0) )"},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"code (character) vector code text set dataname optional, (character) vector datanames assign code . empty code considered \"global\" deps optional, (character) vector datanames given code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"object class CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"method-append-","dir":"Reference","previous_headings":"","what":"Method append()","title":"Code Class — CodeClass","text":"Append CodeClass object given CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$append(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"x (CodeClass) object appended","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"changed CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"method-set-code-","dir":"Reference","previous_headings":"","what":"Method set_code()","title":"Code Class — CodeClass","text":"Set code form character","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$set_code(code, dataname = character(0), deps = character(0))"},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"code (character) vector code text set dataname optional, (character) vector datanames assign code . empty code considered \"global\" deps optional, (character) vector datanames given code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"changed CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"Code Class — CodeClass","text":"Get code given data names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$get_code(dataname = NULL, deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"dataname optional, (character) vector datanames code extracted. NULL get code data names deparse optional, (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"character list calls","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"method-eval-","dir":"Reference","previous_headings":"","what":"Method eval()","title":"Code Class — CodeClass","text":"Evaluates internal code within given environment","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$eval(envir = new.env(parent = parent.env(.GlobalEnv)))"},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"envir (environment) environment code evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"invisibly NULL","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Code Class — CodeClass","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/CodeClass.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Code Class — CodeClass","text":"","code":"cc <- teal.data:::CodeClass$new() cc$set_code(c(\"foo <- function() {1}\", \"foo2 <- function() {2}\")) cc$get_code() #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\" cc$get_code(deparse = FALSE) #> [[1]] #> foo <- function() { #> 1 #> } #> #> [[2]] #> foo2 <- function() { #> 2 #> } #> cc$set_code(c(\"DF <- data.frame(x = 1:10)\", \"DF$y <- 1\"), \"DF\") cc$set_code(\"DF$a <- foo()\", \"DF\") # dependent dataset cc$set_code(c(\"DF2 <- data.frame(x2 = 1:10)\", \"DF2$y2 <- DF$y\"), \"DF2\", deps = \"DF\") cc$set_code(\"baz <- function() {2}\") cc$set_code(\"DF2$a <- baz()\", \"DF2\") cc$get_code() #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\\nDF <- data.frame(x = 1:10)\\nDF$y <- 1\\nDF$a <- foo()\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$y2 <- DF$y\\nbaz <- function() {\\n 2\\n}\\nDF2$a <- baz()\" cc$get_code(\"DF\") #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\\nDF <- data.frame(x = 1:10)\\nDF$y <- 1\\nDF$a <- foo()\" cc$get_code(\"DF2\") #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\\nDF <- data.frame(x = 1:10)\\nDF$y <- 1\\nDF$a <- foo()\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$y2 <- DF$y\\nbaz <- function() {\\n 2\\n}\\nDF2$a <- baz()\" x1 <- teal.data:::CodeClass$new() x1$set_code(\"DF <- data.frame(x = 1:10)\", \"DF\") x1$get_code() #> [1] \"DF <- data.frame(x = 1:10)\" x2 <- teal.data:::CodeClass$new() x2$set_code(c(\"DF2 <- data.frame(x2 = 1:10)\", \"DF2$x2 <- DF$x\"), \"DF2\", deps = \"DF\") x2$get_code() #> [1] \"DF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x <- teal.data:::CodeClass$new() x$append(x1) x$append(x2) x$get_code() #> [1] \"DF <- data.frame(x = 1:10)\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x$get_code(\"DF\") #> [1] \"DF <- data.frame(x = 1:10)\" x$get_code(\"DF2\") #> [1] \"DF <- data.frame(x = 1:10)\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x$get_code(c(\"DF\", \"DF2\")) #> [1] \"DF <- data.frame(x = 1:10)\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x3 <- teal.data:::CodeClass$new() x3$set_code(\"DF3 <- data.frame(x3 = 1:10) \", \"DF3\") x3$get_code() #> [1] \"DF3 <- data.frame(x3 = 1:10)\" x$append(x3) x$get_code(\"DF3\") #> [1] \"DF3 <- data.frame(x3 = 1:10)\" # mutation simulation x$set_code(\"DF3$x <- foo(DF$x)\", \"DF3\", deps = \"DF\") x$get_code(\"DF3\") #> [1] \"DF <- data.frame(x = 1:10)\\nDF3 <- data.frame(x3 = 1:10)\\nDF3$x <- foo(DF$x)\""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"MultiAssayExperiment object can stored inside MAETealDataset. attributes like colnames, dimension column names specific type automatically derived.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"teal.data::TealDataset -> MAETealDataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"teal.data::TealDataset$get_attrs() teal.data::TealDataset$get_character_colnames() teal.data::TealDataset$get_code() teal.data::TealDataset$get_code_class() teal.data::TealDataset$get_dataname() teal.data::TealDataset$get_datanames() teal.data::TealDataset$get_dataset() teal.data::TealDataset$get_dataset_label() teal.data::TealDataset$get_factor_colnames() teal.data::TealDataset$get_keys() teal.data::TealDataset$get_metadata() teal.data::TealDataset$get_mutate_code_class() teal.data::TealDataset$get_mutate_vars() teal.data::TealDataset$get_numeric_colnames() teal.data::TealDataset$get_raw_data() teal.data::TealDataset$get_row_labels() teal.data::TealDataset$get_var_r6() teal.data::TealDataset$get_vars() teal.data::TealDataset$is_mutate_delayed() teal.data::TealDataset$is_pulled() teal.data::TealDataset$mutate() teal.data::TealDataset$reassign_datasets_vars() teal.data::TealDataset$recreate() teal.data::TealDataset$set_code() teal.data::TealDataset$set_dataset_label() teal.data::TealDataset$set_keys() teal.data::TealDataset$set_vars()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"MAETealDataset$new() MAETealDataset$check() MAETealDataset$check_keys() MAETealDataset$get_colnames() MAETealDataset$get_column_labels() MAETealDataset$get_ncol() MAETealDataset$get_nrow() MAETealDataset$get_rownames() MAETealDataset$print() MAETealDataset$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Create new object MAETealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$new( dataname, x, keys = character(0), code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"dataname (character) given name dataset may contain spaces x (MultiAssayExperiment) keys optional, (character) vector primary keys code (character CodeClass) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order. label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Check determine raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$check()"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"TRUE dataset generated evaluating get_code() code identical raw data, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-check-keys-","dir":"Reference","previous_headings":"","what":"Method check_keys()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Check keys specified correctly dataset. Set keys distinguish unique rows character(0).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$check_keys(keys = private$.keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"keys optional, (character) vector primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-get-colnames-","dir":"Reference","previous_headings":"","what":"Method get_colnames()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Derive column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-get-column-labels-","dir":"Reference","previous_headings":"","what":"Method get_column_labels()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Derive column labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_column_labels()"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-get-ncol-","dir":"Reference","previous_headings":"","what":"Method get_ncol()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Get number columns data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_ncol()"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-get-nrow-","dir":"Reference","previous_headings":"","what":"Method get_nrow()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Get number rows data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_nrow()"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-get-rownames-","dir":"Reference","previous_headings":"","what":"Method get_rownames()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Derive row names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_rownames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Prints MAETealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/MAETealDataset.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"deep Whether make deep clone.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"teal.data::CodeClass -> PythonCodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"teal.data::CodeClass$append() teal.data::CodeClass$get_code() teal.data::CodeClass$initialize() teal.data::CodeClass$set_code()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"PythonCodeClass$eval() PythonCodeClass$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"method-eval-","dir":"Reference","previous_headings":"","what":"Method eval()","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"Evaluates internal code within environment","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"","code":"PythonCodeClass$eval( vars = list(), dataname = NULL, envir = new.env(parent = parent.env(.GlobalEnv)) )"},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"vars (named list) additional pre-requisite vars execute code dataname (character) name data frame object returned envir (environment) environment code evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"data.frame containing mutated dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"","code":"PythonCodeClass$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/PythonCodeClass.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Class manages TealDataConnector, TealDatasetConnector TealDataset objects aggregate one collection. Class also decides whether launch app initialize teal application.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"teal.data::TealDataAbstract -> TealData","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"teal.data::TealDataAbstract$check() teal.data::TealDataAbstract$check_reproducibility() teal.data::TealDataAbstract$execute_mutate() teal.data::TealDataAbstract$get_check() teal.data::TealDataAbstract$get_check_result() teal.data::TealDataAbstract$get_code() teal.data::TealDataAbstract$get_code_class() teal.data::TealDataAbstract$get_datanames() teal.data::TealDataAbstract$get_dataset() teal.data::TealDataAbstract$get_datasets() teal.data::TealDataAbstract$is_pulled() teal.data::TealDataAbstract$mutate() teal.data::TealDataAbstract$mutate_dataset() teal.data::TealDataAbstract$reassign_datasets_vars() teal.data::TealDataAbstract$set_check() teal.data::TealDataAbstract$set_pull_code()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"TealData$new() TealData$copy() TealData$print() TealData$get_connectors() TealData$get_items() TealData$get_join_keys() TealData$get_parents() TealData$get_ui() TealData$get_server() TealData$launch() TealData$mutate_join_keys() TealData$check_metadata() TealData$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Create new object TealData class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$new(..., check = FALSE, join_keys = teal.data::join_keys())"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"... (TealDataConnector, TealDataset, TealDatasetConnector) objects check (logical) reproducibility check - whether evaluated preprocessing code gives objects provided arguments. Check run flag true preprocessing code empty. join_keys (join_keys) single (join_key_set) (optional) object dataset column relationships used joining. empty empty join_keys object passed default.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-copy-","dir":"Reference","previous_headings":"","what":"Method copy()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Creates copy object keeping valid references TealDataset TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$copy(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"deep (logical(1)) argument passed clone method. TRUE deep copy made","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"self invisible","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Prints TealData.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-get-connectors-","dir":"Reference","previous_headings":"","what":"Method get_connectors()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get data connectors.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_connectors()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"(list) TealDatasetConnector TealDataConnector objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-get-items-","dir":"Reference","previous_headings":"","what":"Method get_items()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get datasets dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_items(dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"dataname (character value) name dataset connector returned. NULL, connectors returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"list datasets connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-get-join-keys-","dir":"Reference","previous_headings":"","what":"Method get_join_keys()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get join keys two datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_join_keys(dataset_1 = NULL, dataset_2 = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"dataset_1 (character) name first dataset. dataset_2 (character) name second dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"(character) named character vector x names(x) columns dataset_1 values (x) corresponding join keys dataset_2 character(0) relationship","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-get-parents-","dir":"Reference","previous_headings":"","what":"Method get_parents()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"returns parents list datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_parents()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"named (list) parents datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-get-ui-","dir":"Reference","previous_headings":"","what":"Method get_ui()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get shiny-module UI render necessary app derive TealDataConnector object's data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"id (character) item ID shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"shiny ui function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-get-server-","dir":"Reference","previous_headings":"","what":"Method get_server()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get shiny-module server render necessary app derive TealDataConnector object's data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_server()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"shiny server module.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Launch app allows run user-interfaces TealDataConnector TealDatasetConnector modules piece mainly used debugging.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$launch()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-mutate-join-keys-","dir":"Reference","previous_headings":"","what":"Method mutate_join_keys()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Change join_keys given pair dataset names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$mutate_join_keys(dataset_1, dataset_2, val)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"dataset_1, dataset_2 (character) datasets join_keys returned val (named character) column names used join","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-check-metadata-","dir":"Reference","previous_headings":"","what":"Method check_metadata()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Check consistency datasets join_keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$check_metadata()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"raise error invisible TRUE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"adsl_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADSL\")) adlb_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADLB\")) adrs_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADRS\")) adtte_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADTTE\")) x1 <- cdisc_dataset_connector(\"ADSL\", adsl_cf, keys = get_cdisc_keys(\"ADSL\")) x2 <- cdisc_dataset_connector(\"ADRS\", adrs_cf, keys = get_cdisc_keys(\"ADRS\")) x3 <- cdisc_dataset( dataname = \"ADAE\", x = teal.data::example_cdisc_data(\"ADAE\"), code = \"library(teal.data)\\nADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ) x4 <- cdisc_dataset_connector(\"ADTTE\", adtte_cf, keys = get_cdisc_keys(\"ADTTE\")) tc <- teal.data:::TealData$new(x1, x2, x3, x4) tc$get_datanames() #> [1] \"ADSL\" \"ADRS\" \"ADAE\" \"ADTTE\" if (FALSE) { tc$launch() get_datasets(tc) # equivalent to tc$get_datasets() tc$get_dataset(\"ADAE\") tc$check() } x <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) x2 <- cdisc_dataset_connector(\"ADTTE\", adtte_cf, keys = get_cdisc_keys(\"ADTTE\")) tc <- teal.data:::TealData$new(x, x2) if (FALSE) { # This errors as we have not pulled the data # tc$get_datasets() # pull the data and then we can get the datasets tc$launch() tc$get_datasets() get_raw_data(tc) }"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":null,"dir":"Reference","previous_headings":"","what":"TealDataAbstract class — TealDataAbstract","title":"TealDataAbstract class — TealDataAbstract","text":"Abstract class containing code handling set datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"TealDataAbstract class — TealDataAbstract","text":"id String used create unique GUI elements","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TealDataAbstract class — TealDataAbstract","text":"TealDataAbstract$new() TealDataAbstract$check() TealDataAbstract$check_reproducibility() TealDataAbstract$execute_mutate() TealDataAbstract$get_check_result() TealDataAbstract$get_code() TealDataAbstract$get_code_class() TealDataAbstract$get_datanames() TealDataAbstract$get_dataset() TealDataAbstract$get_datasets() TealDataAbstract$get_items() TealDataAbstract$get_check() TealDataAbstract$is_pulled() TealDataAbstract$mutate() TealDataAbstract$mutate_dataset() TealDataAbstract$set_check() TealDataAbstract$set_pull_code() TealDataAbstract$reassign_datasets_vars() TealDataAbstract$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"TealDataAbstract class — TealDataAbstract","text":"create TealDataAbstract object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$new()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"throws error","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"TealDataAbstract class — TealDataAbstract","text":"Check object raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$check()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"NULL check step disabled TRUE datasets generated evaluating get_code() code identical raw data, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-check-reproducibility-","dir":"Reference","previous_headings":"","what":"Method check_reproducibility()","title":"TealDataAbstract class — TealDataAbstract","text":"Execute check() raise error reproducible.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$check_reproducibility()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"error code reproducible else invisibly nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-execute-mutate-","dir":"Reference","previous_headings":"","what":"Method execute_mutate()","title":"TealDataAbstract class — TealDataAbstract","text":"Execute mutate code. Using mutate_data(set).TealDataAbstract cause instant execution, mutate_code delayed can evaluated using method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$execute_mutate()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-check-result-","dir":"Reference","previous_headings":"","what":"Method get_check_result()","title":"TealDataAbstract class — TealDataAbstract","text":"Get result reproducibility check","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_check_result()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"NULL check called yet, TRUE / FALSE otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"TealDataAbstract class — TealDataAbstract","text":"Get code datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_code(dataname = NULL, deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character) dataname NULL datasets deparse (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"(character) vector code generate datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"TealDataAbstract class — TealDataAbstract","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_code_class(only_pull = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"only_pull (logical value) TRUE code pull datasets returned without mutate code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-datanames-","dir":"Reference","previous_headings":"","what":"Method get_datanames()","title":"TealDataAbstract class — TealDataAbstract","text":"Get names datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_datanames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"character vector names datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-dataset-","dir":"Reference","previous_headings":"","what":"Method get_dataset()","title":"TealDataAbstract class — TealDataAbstract","text":"Get TealDataset object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_dataset(dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character value) name dataset returned. NULL, datasets returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"TealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-datasets-","dir":"Reference","previous_headings":"","what":"Method get_datasets()","title":"TealDataAbstract class — TealDataAbstract","text":"Get list TealDataset objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_datasets()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"list TealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-items-","dir":"Reference","previous_headings":"","what":"Method get_items()","title":"TealDataAbstract class — TealDataAbstract","text":"Get datasets dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_items(dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character value) name dataset connector returned. NULL, connectors returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"list datasets connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-get-check-","dir":"Reference","previous_headings":"","what":"Method get_check()","title":"TealDataAbstract class — TealDataAbstract","text":"data data subjected reproducibility check","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_check()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"logical","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-is-pulled-","dir":"Reference","previous_headings":"","what":"Method is_pulled()","title":"TealDataAbstract class — TealDataAbstract","text":"Check dataset already pulled.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$is_pulled()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"TealDataAbstract class — TealDataAbstract","text":"Mutate data code. Code used mutation linked particular refers datasets. Consequence using get_code() part code returned specified dataset. method used particular call involve changing multiple datasets. Otherwise please use mutate_dataset. Execution mutate_code delayed datasets pulled (isTRUE(is_pulled)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$mutate(code, vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"code (character) Code mutate dataset. Must contain dataset$dataname vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"self invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-mutate-dataset-","dir":"Reference","previous_headings":"","what":"Method mutate_dataset()","title":"TealDataAbstract class — TealDataAbstract","text":"Mutate dataset code. Execution mutate_code delayed datasets pulled (isTRUE(is_pulled)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$mutate_dataset(dataname, code, vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character) Dataname mutated code (character) Code mutate dataset. Must contain dataset$dataname vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"self invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-set-check-","dir":"Reference","previous_headings":"","what":"Method set_check()","title":"TealDataAbstract class — TealDataAbstract","text":"Set reproducibility check","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$set_check(check = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"check (logical) whether perform reproducibility check.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-set-pull-code-","dir":"Reference","previous_headings":"","what":"Method set_pull_code()","title":"TealDataAbstract class — TealDataAbstract","text":"Set pull code","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$set_pull_code(code)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"code (character value) code reproduce data TealDataset objects. set dataset code set already.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-reassign-datasets-vars-","dir":"Reference","previous_headings":"","what":"Method reassign_datasets_vars()","title":"TealDataAbstract class — TealDataAbstract","text":"Reassign vars TealDataset TealDatasetConnector objects keep valid reference deep cloning example TealDatasetConnector dependency TealDataset, TealDataset reassigned inside TealDatasetConnector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$reassign_datasets_vars()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TealDataAbstract class — TealDataAbstract","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataAbstract.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":null,"dir":"Reference","previous_headings":"","what":"A TealDataConnection class of objects — TealDataConnection","title":"A TealDataConnection class of objects — TealDataConnection","text":"Objects class store connection data source. can database server connection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A TealDataConnection class of objects — TealDataConnection","text":"TealDataConnection$new() TealDataConnection$finalize() TealDataConnection$is_opened() TealDataConnection$is_failed() TealDataConnection$launch() TealDataConnection$open() TealDataConnection$get_conn() TealDataConnection$get_open_call() TealDataConnection$get_open_error_message() TealDataConnection$get_preopen_server() TealDataConnection$get_open_server() TealDataConnection$get_open_ui() TealDataConnection$is_open_failed() TealDataConnection$set_open_args() TealDataConnection$set_preopen_server() TealDataConnection$set_open_server() TealDataConnection$set_open_ui() TealDataConnection$close() TealDataConnection$get_close_call() TealDataConnection$get_close_error_message() TealDataConnection$get_close_server() TealDataConnection$is_close_failed() TealDataConnection$set_close_args() TealDataConnection$set_close_ui() TealDataConnection$set_close_server() TealDataConnection$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Create new TealDataConnection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$new( open_fun = NULL, close_fun = NULL, ping_fun = NULL, if_conn_obj = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"open_fun (CallableFunction) function open connection close_fun (CallableFunction) function close connection ping_fun (CallableFunction) function ping connection if_conn_obj optional, (logical) whether store conn object returned opening connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"new TealDataConnection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-finalize-","dir":"Reference","previous_headings":"","what":"Method finalize()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Finalize method closing connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$finalize()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"NULL","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-is-opened-","dir":"Reference","previous_headings":"","what":"Method is_opened()","title":"A TealDataConnection class of objects — TealDataConnection","text":"connection opened open connection successfully evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_opened()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) connection open","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-is-failed-","dir":"Reference","previous_headings":"","what":"Method is_failed()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Check connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_failed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) TRUE connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Run simple application uses ui server fields open connection. Useful debugging","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$launch()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"object represents app","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-open-","dir":"Reference","previous_headings":"","what":"Method open()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Open connection. Note connection already opened nothing.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$open(args = NULL, silent = FALSE, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"args (NULL named list) additional arguments set previously silent (logical) whether convert \"missing function\" errors messages try (logical) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"returns self successful connection already opened. open_fun fails, app returns error form shinyjs::alert (try = TRUE) breaks app (try = FALSE)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-conn-","dir":"Reference","previous_headings":"","what":"Method get_conn()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get internal connection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_conn()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"connection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-open-call-","dir":"Reference","previous_headings":"","what":"Method get_open_call()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get executed open connection call","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_call(deparse = TRUE, args = NULL, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"deparse (logical) whether return deparsed form call args (NULL named list) additional arguments set previously silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-open-error-message-","dir":"Reference","previous_headings":"","what":"Method get_open_error_message()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get error message last connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_error_message()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(character) text error message character(0) last connection successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-preopen-server-","dir":"Reference","previous_headings":"","what":"Method get_preopen_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get shiny server module prior opening connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_preopen_server()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(function) shiny server prior opening connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-open-server-","dir":"Reference","previous_headings":"","what":"Method get_open_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get shiny server module open connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_server()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(function) shiny server open connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-open-ui-","dir":"Reference","previous_headings":"","what":"Method get_open_ui()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get Shiny module inputs open connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"id character shiny element id","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(function) shiny UI set arguments open connection function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-is-open-failed-","dir":"Reference","previous_headings":"","what":"Method is_open_failed()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Check open connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_open_failed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) TRUE open connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-set-open-args-","dir":"Reference","previous_headings":"","what":"Method set_open_args()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set open connection function argument","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_open_args(args, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"args (NULL named list) values list names argument names silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-set-preopen-server-","dir":"Reference","previous_headings":"","what":"Method set_preopen_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set pre-open connection server function function called submit button hit.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_preopen_server(preopen_module)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"preopen_module (function) shiny module server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-set-open-server-","dir":"Reference","previous_headings":"","what":"Method set_open_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set open connection server function function called submit button hit. possibility specify dynamic ui server function executed hitting submit button.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_open_server(open_module)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"open_module (function) shiny module server function load data connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-set-open-ui-","dir":"Reference","previous_headings":"","what":"Method set_open_ui()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set open connection UI function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_open_ui(open_module)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"open_module (function) shiny module function. Inputs specified ui passed server module defined set_open_server method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-16","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-close-","dir":"Reference","previous_headings":"","what":"Method close()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$close(silent = FALSE, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"silent (logical) whether convert \"missing function\" errors messages try (logical) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-17","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"returns (self) successful. unsuccessful evaluation depends try argument: try = TRUE returns error, try = FALSE otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-close-call-","dir":"Reference","previous_headings":"","what":"Method get_close_call()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get executed close connection call","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_close_call(deparse = TRUE, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"deparse (logical) whether return deparsed form call silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-18","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-close-error-message-","dir":"Reference","previous_headings":"","what":"Method get_close_error_message()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get error message last connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_close_error_message()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-19","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(character) text error message character(0) last connection successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-get-close-server-","dir":"Reference","previous_headings":"","what":"Method get_close_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get shiny server module close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_close_server()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-20","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"server function close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-is-close-failed-","dir":"Reference","previous_headings":"","what":"Method is_close_failed()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Check close connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_close_failed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-21","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) TRUE close connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-set-close-args-","dir":"Reference","previous_headings":"","what":"Method set_close_args()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set close connection function argument","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_close_args(args, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"args (named list) values list names argument names silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-22","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-set-close-ui-","dir":"Reference","previous_headings":"","what":"Method set_close_ui()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set close connection UI function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_close_ui(close_module)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"close_module (function) shiny module function. Inputs specified ui passed server module defined set_close_server method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-23","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-set-close-server-","dir":"Reference","previous_headings":"","what":"Method set_close_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set close-connection server function function called submit button hit. possibility specify dynamic ui server function executed hitting submit button.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_close_server(close_module)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"close_module (function) shiny module server function load data connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"returns-24","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A TealDataConnection class of objects — TealDataConnection","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnection.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"open_fun <- callable_function(data.frame) # define opening function open_fun$set_args(list(x = 1:5)) # define fixed arguments to opening function close_fun <- callable_function(sum) # define closing function close_fun$set_args(list(x = 1:5)) # define fixed arguments to closing function ping_fun <- callable_function(function() TRUE) x <- data_connection( # define connection ping_fun = ping_fun, # define ping function open_fun = open_fun, # define opening function close_fun = close_fun # define closing function ) x$set_open_args(args = list(y = letters[1:5])) # define additional arguments if necessary x$open() # call opening function x$get_open_call() # check reproducible R code #> [1] \"data.frame(x = 1:5, y = c(\\\"a\\\", \\\"b\\\", \\\"c\\\", \\\"d\\\", \\\"e\\\"))\" # get data from connection via TealDataConnector$get_dataset() if (FALSE) { x$open(args = list(x = 1:5, y = letters[1:5])) # able to call opening function with arguments x$close() # call closing function }"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Class manages TealDatasetConnector specify additional dynamic arguments open/close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"teal.data::TealDataAbstract -> TealDataConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"teal.data::TealDataAbstract$check() teal.data::TealDataAbstract$check_reproducibility() teal.data::TealDataAbstract$execute_mutate() teal.data::TealDataAbstract$get_check() teal.data::TealDataAbstract$get_check_result() teal.data::TealDataAbstract$get_code() teal.data::TealDataAbstract$get_datanames() teal.data::TealDataAbstract$get_dataset() teal.data::TealDataAbstract$get_datasets() teal.data::TealDataAbstract$get_items() teal.data::TealDataAbstract$is_pulled() teal.data::TealDataAbstract$mutate_dataset() teal.data::TealDataAbstract$reassign_datasets_vars() teal.data::TealDataAbstract$set_check() teal.data::TealDataAbstract$set_pull_code()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"TealDataConnector$new() TealDataConnector$print() TealDataConnector$get_connection() TealDataConnector$get_code_class() TealDataConnector$get_server() TealDataConnector$get_preopen_server() TealDataConnector$get_ui() TealDataConnector$set_pull_args() TealDataConnector$set_ui() TealDataConnector$set_server() TealDataConnector$set_preopen_server() TealDataConnector$pull() TealDataConnector$launch() TealDataConnector$mutate() TealDataConnector$is_failed() TealDataConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Create new TealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$new(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Prints TealDataConnector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-get-connection-","dir":"Reference","previous_headings":"","what":"Method get_connection()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Get connection data source","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_connection()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"connector's connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_code_class()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-get-server-","dir":"Reference","previous_headings":"","what":"Method get_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"get server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_server()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-get-preopen-server-","dir":"Reference","previous_headings":"","what":"Method get_preopen_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"get preopen server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_preopen_server()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-get-ui-","dir":"Reference","previous_headings":"","what":"Method get_ui()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Get Shiny module inputs TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"id character shiny element id","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"ui function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-set-pull-args-","dir":"Reference","previous_headings":"","what":"Method set_pull_args()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set argument pull_fun","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_pull_args(args)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"args (named list) arguments values separate list elements named argument name. arguments passed dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-set-ui-","dir":"Reference","previous_headings":"","what":"Method set_ui()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set connector UI function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_ui(f)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"f (function) shiny module function. Inputs specified ui passed server module defined set_server method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-set-server-","dir":"Reference","previous_headings":"","what":"Method set_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set connector server function function called submit button hit. possibility specify dynamic ui server function executed hitting submit button.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_server(f)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"f (function) shiny module server function load data connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-set-preopen-server-","dir":"Reference","previous_headings":"","what":"Method set_preopen_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set connector pre-open server function function called submit button hit.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_preopen_server(f)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"f (function) shiny module server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-pull-","dir":"Reference","previous_headings":"","what":"Method pull()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Load data TealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$pull(con_args = NULL, args = NULL, try = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"con_args (NULL named list) additional dynamic arguments connection function. args passed TealDatasetConnector object evaluate CallableFunction assigned dataset. args null default set arguments used, otherwise call executed arguments (arguments set ignored). pull function update reproducible call, just evaluate function. args (NULL named list) additional dynamic arguments pull dataset. args passed TealDatasetConnector object evaluate CallableFunction assigned dataset. args null default set arguments used, otherwise call executed arguments (arguments set ignored). pull function update reproducible call, just evaluate function. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"(self) invisibly chaining. order get data please use get_datasets method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Run simple application uses ui server fields pull data connection. Useful debugging","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$launch()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"object represents app","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Mutate data code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$mutate(...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"... parameters inherited TealDataAbstract.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Informational message use mutate_data() TealDataConnectors.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-is-failed-","dir":"Reference","previous_headings":"","what":"Method is_failed()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Check pull connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$is_failed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"TRUE pull connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataConnector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"library(magrittr) #> #> Attaching package: ‘magrittr’ #> The following objects are masked from ‘package:testthat’: #> #> equals, is_less_than, not random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } open_fun <- callable_function(library) open_fun$set_args(list(package = \"teal.data\")) con <- data_connection(open_fun = open_fun) con$set_open_server( function(id, connection) { moduleServer( id = id, module = function(input, output, session) { connection$open(try = TRUE) return(invisible(connection)) } ) } ) x <- teal.data:::TealDataConnector$new( connection = con, connectors = list( random_data_connector(dataname = \"ADSL\"), random_data_connector(dataname = \"ADLB\") ) ) x$set_ui( function(id, connection, connectors) { ns <- NS(id) tagList( connection$get_open_ui(ns(\"open_connection\")), numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) x$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection connection$get_open_server()(id = \"open_connection\", connection = connection) if (connection$is_opened()) { for (connector in connectors) { set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } } ) } ) if (FALSE) { x$launch() x$get_datasets() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class representing a dataset with its attributes — TealDataset","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"data.frame object can stored inside object. attributes like colnames, dimension column names specific type automatically derived.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"raw_data data.frame behind R6 class data data.frame behind R6 class var_names column names data","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TealDataset$new() TealDataset$recreate() TealDataset$print() TealDataset$get_dataset() TealDataset$get_attrs() TealDataset$get_raw_data() TealDataset$get_numeric_colnames() TealDataset$get_character_colnames() TealDataset$get_factor_colnames() TealDataset$get_colnames() TealDataset$get_column_labels() TealDataset$get_ncol() TealDataset$get_nrow() TealDataset$get_rownames() TealDataset$get_row_labels() TealDataset$get_dataname() TealDataset$get_datanames() TealDataset$get_dataset_label() TealDataset$get_keys() TealDataset$get_metadata() TealDataset$get_var_r6() TealDataset$reassign_datasets_vars() TealDataset$set_dataset_label() TealDataset$set_keys() TealDataset$set_vars() TealDataset$set_code() TealDataset$get_code() TealDataset$get_code_class() TealDataset$get_mutate_code_class() TealDataset$get_vars() TealDataset$get_mutate_vars() TealDataset$is_mutate_delayed() TealDataset$mutate() TealDataset$check() TealDataset$check_keys() TealDataset$is_pulled() TealDataset$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Create new object TealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$new( dataname, x, keys = character(0), code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys optional, (character) Vector primary keys code (character) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order. label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-recreate-","dir":"Reference","previous_headings":"","what":"Method recreate()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Recreate TealDataset current attributes.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$recreate( dataname = self$get_dataname(), x = self$get_raw_data(), keys = self$get_keys(), code = private$code, label = self$get_dataset_label(), vars = list(), metadata = self$get_metadata() )"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys optional, (character) Vector primary keys code (character) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order. label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"new object TealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Prints TealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-dataset-","dir":"Reference","previous_headings":"","what":"Method get_dataset()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Performs delayed mutate calls returning self.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_dataset()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"dataset (TealDataset)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-attrs-","dir":"Reference","previous_headings":"","what":"Method get_attrs()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_attrs()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(named list) dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-raw-data-","dir":"Reference","previous_headings":"","what":"Method get_raw_data()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive raw data frame inside object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_raw_data()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"data.frame","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-numeric-colnames-","dir":"Reference","previous_headings":"","what":"Method get_numeric_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive names numeric columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_numeric_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-character-colnames-","dir":"Reference","previous_headings":"","what":"Method get_character_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive names character columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_character_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-factor-colnames-","dir":"Reference","previous_headings":"","what":"Method get_factor_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive names factor columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_factor_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-colnames-","dir":"Reference","previous_headings":"","what":"Method get_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-column-labels-","dir":"Reference","previous_headings":"","what":"Method get_column_labels()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive column labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_column_labels()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-ncol-","dir":"Reference","previous_headings":"","what":"Method get_ncol()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get number columns data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_ncol()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-nrow-","dir":"Reference","previous_headings":"","what":"Method get_nrow()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get number rows data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_nrow()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-rownames-","dir":"Reference","previous_headings":"","what":"Method get_rownames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive row names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_rownames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-row-labels-","dir":"Reference","previous_headings":"","what":"Method get_row_labels()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive row labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_row_labels()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-dataname-","dir":"Reference","previous_headings":"","what":"Method get_dataname()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive name formerly called dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_dataname()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character name dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-datanames-","dir":"Reference","previous_headings":"","what":"Method get_datanames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_datanames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character name dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-dataset-label-","dir":"Reference","previous_headings":"","what":"Method get_dataset_label()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive label former called datalabel","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_dataset_label()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-16","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character label dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-keys-","dir":"Reference","previous_headings":"","what":"Method get_keys()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get primary keys dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_keys()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-17","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(character vector) dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-metadata-","dir":"Reference","previous_headings":"","what":"Method get_metadata()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get metadata dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_metadata()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-18","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(named list)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-var-r-","dir":"Reference","previous_headings":"","what":"Method get_var_r6()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get list dependencies TealDataset TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_var_r6()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-19","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-reassign-datasets-vars-","dir":"Reference","previous_headings":"","what":"Method reassign_datasets_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Overwrites TealDataset TealDatasetConnector dependencies TealDataset found datasets. Reassignment refers provided datasets, vars remains .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$reassign_datasets_vars(datasets)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"datasets (named list TealDataset(s) TealDatasetConnector(s)) objects valid pointers.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Reassign vars object keep references date deep clone. Update done based objects passed datasets argument. Overwrites dependencies names matching names objects passed datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-20","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"NULL invisible","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"test_dataset <- teal.data:::TealDataset$new( dataname = \"iris\", x = iris, vars = list(dep = teal.data:::TealDataset$new(\"iris2\", iris)) ) test_dataset$reassign_datasets_vars( list(iris2 = teal.data:::TealDataset$new(\"iris2\", head(iris))) )"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-set-dataset-label-","dir":"Reference","previous_headings":"","what":"Method set_dataset_label()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Set label dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_dataset_label(label)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"label (character) Label describe dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-21","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-set-keys-","dir":"Reference","previous_headings":"","what":"Method set_keys()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Set new keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_keys(keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"keys optional, (character) Vector primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-22","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-set-vars-","dir":"Reference","previous_headings":"","what":"Method set_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Adds variables code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_vars(vars)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"vars (named list) contains R object code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-23","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-set-code-","dir":"Reference","previous_headings":"","what":"Method set_code()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Sets reproducible code","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_code(code)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"code (character) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-24","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get code get data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-26","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_code(deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"deparse (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-25","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-27","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_code_class(nodeps = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"nodeps (logical(1)) whether CodeClass contain code dependent vars mutate","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-26","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-mutate-code-class-","dir":"Reference","previous_headings":"","what":"Method get_mutate_code_class()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-28","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_mutate_code_class()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-27","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-vars-","dir":"Reference","previous_headings":"","what":"Method get_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal vars object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-29","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_vars()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-28","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-get-mutate-vars-","dir":"Reference","previous_headings":"","what":"Method get_mutate_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal mutate_vars object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-30","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_mutate_vars()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-29","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-is-mutate-delayed-","dir":"Reference","previous_headings":"","what":"Method is_mutate_delayed()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Whether mutate code delayed evaluation.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-31","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$is_mutate_delayed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-30","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"logical","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Mutate dataset code","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-32","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$mutate(code, vars = list(), force_delay = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"code (CodeClass) (character) R expressions executed vars named list R objects code depends execute force_delay (logical) used containing TealDatasetConnector object Either code script must provided, .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-31","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Check determine raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-33","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$check()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-32","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TRUE dataset generated evaluating get_code() code identical raw data, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-check-keys-","dir":"Reference","previous_headings":"","what":"Method check_keys()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Check keys specified correctly dataset. Set keys distinguish unique rows character(0).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-34","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$check_keys(keys = private$.keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"keys optional, (character) Vector primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-33","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-is-pulled-","dir":"Reference","previous_headings":"","what":"Method is_pulled()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Check dataset already pulled.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-35","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$is_pulled()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"returns-34","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"usage-36","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"## ------------------------------------------------ ## Method `TealDataset$reassign_datasets_vars` ## ------------------------------------------------ test_dataset <- teal.data:::TealDataset$new( dataname = \"iris\", x = iris, vars = list(dep = teal.data:::TealDataset$new(\"iris2\", iris)) ) test_dataset$reassign_datasets_vars( list(iris2 = teal.data:::TealDataset$new(\"iris2\", head(iris))) )"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"A TealDatasetConnector class of objects — TealDatasetConnector","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Objects class store connection function fetch single dataset. Note specific connection types, object class TealDataConnection must provided. Data can pulled via pull method accessed directly dataset active binding. Pulled data inherits class TealDataset","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TealDatasetConnector$new() TealDatasetConnector$print() TealDatasetConnector$get_dataname() TealDatasetConnector$get_datanames() TealDatasetConnector$get_dataset_label() TealDatasetConnector$get_keys() TealDatasetConnector$get_code() TealDatasetConnector$get_code_class() TealDatasetConnector$get_pull_args() TealDatasetConnector$get_dataset() TealDatasetConnector$get_error_message() TealDatasetConnector$get_pull_callable() TealDatasetConnector$get_raw_data() TealDatasetConnector$get_var_r6() TealDatasetConnector$reassign_datasets_vars() TealDatasetConnector$set_dataset_label() TealDatasetConnector$set_keys() TealDatasetConnector$pull() TealDatasetConnector$set_args() TealDatasetConnector$mutate() TealDatasetConnector$is_failed() TealDatasetConnector$is_pulled() TealDatasetConnector$is_mutate_delayed() TealDatasetConnector$check() TealDatasetConnector$set_ui_input() TealDatasetConnector$get_ui() TealDatasetConnector$get_server() TealDatasetConnector$launch() TealDatasetConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Create new TealDatasetConnector object. Set pulling function CallableFunction returns data.frame MultiAssayExperiment, e.g. reading function creating fly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$new( dataname, pull_callable, keys = character(0), label = character(0), code = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Prints TealDatasetConnector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-dataname-","dir":"Reference","previous_headings":"","what":"Method get_dataname()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_dataname()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-datanames-","dir":"Reference","previous_headings":"","what":"Method get_datanames()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_datanames()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-dataset-label-","dir":"Reference","previous_headings":"","what":"Method get_dataset_label()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get label dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_dataset_label()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character dataset label","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-keys-","dir":"Reference","previous_headings":"","what":"Method get_keys()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get primary keys dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_keys()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character vector dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get code get data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_code(deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"deparse (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_code_class()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-pull-args-","dir":"Reference","previous_headings":"","what":"Method get_pull_args()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Derive arguments connector pull ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_pull_args()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"list pull function fixed arguments","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-dataset-","dir":"Reference","previous_headings":"","what":"Method get_dataset()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_dataset()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"dataset (TealDataset)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-error-message-","dir":"Reference","previous_headings":"","what":"Method get_error_message()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get error message last pull","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_error_message()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character object error message character(0) last pull successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-pull-callable-","dir":"Reference","previous_headings":"","what":"Method get_pull_callable()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get pull function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_pull_callable()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"CallableFunction","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-raw-data-","dir":"Reference","previous_headings":"","what":"Method get_raw_data()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get raw data dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_raw_data()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"data.frame MultiAssayExperiment data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-var-r-","dir":"Reference","previous_headings":"","what":"Method get_var_r6()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get list dependencies TealDataset TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_var_r6()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-reassign-datasets-vars-","dir":"Reference","previous_headings":"","what":"Method reassign_datasets_vars()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Reassign vars object keep references date deep clone. Update done based objects passed datasets argument. Reassignment refers provided datasets, vars remains .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$reassign_datasets_vars(datasets)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"datasets (named list TealDataset(s) TealDatasetConnector(s)) objects valid pointers.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"NULL invisible","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-set-dataset-label-","dir":"Reference","previous_headings":"","what":"Method set_dataset_label()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Set label dataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_dataset_label(label)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"label (character) Label describe dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-set-keys-","dir":"Reference","previous_headings":"","what":"Method set_keys()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Set new keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_keys(keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"keys optional, (character) vector dataset primary keys column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-pull-","dir":"Reference","previous_headings":"","what":"Method pull()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Pull data (metadata Callable) Read create data using pull_callable specified constructor.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$pull(args = NULL, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"args (NULL named list) additional dynamic arguments pull function. args can omitted pull_callable constructor already contains necessary arguments pull data. One can try execute pull_callable directly x$pull_callable$run() get code using x$pull_callable$get_code(). args specified pull used temporary get data saved code. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-16","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-set-args-","dir":"Reference","previous_headings":"","what":"Method set_args()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Set arguments pulling function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_args(args)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"args (NULL named list) dynamic arguments function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-17","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Dispatcher either eager delayed mutate methods Either code script must provided, .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$mutate(code, vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-18","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-is-failed-","dir":"Reference","previous_headings":"","what":"Method is_failed()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check pull failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$is_failed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-19","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TRUE pull failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-is-pulled-","dir":"Reference","previous_headings":"","what":"Method is_pulled()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check dataset already pulled.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$is_pulled()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-20","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TRUE connector already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-is-mutate-delayed-","dir":"Reference","previous_headings":"","what":"Method is_mutate_delayed()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check dataset mutations delayed","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$is_mutate_delayed()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-21","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"logical","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check determine raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$check()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-22","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TRUE always connectors avoid evaluating code multiple times.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-set-ui-input-","dir":"Reference","previous_headings":"","what":"Method set_ui_input()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Sets shiny UI according given inputs. Inputs must provide scalar (length 1) variables.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_ui_input(inputs = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"inputs (function) shiny module UI function single argument ns. function needs return list shiny inputs inputId wrapped function ns. inputId must match exactly argument name set. See example. Nested lists allowed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-23","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) \\dontrun{ ds$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-ui-","dir":"Reference","previous_headings":"","what":"Method get_ui()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get shiny ui function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"id (character) namespace id","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-24","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"shiny UI given namespace id","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-get-server-","dir":"Reference","previous_headings":"","what":"Method get_server()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get shiny server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-26","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_server()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-25","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"shiny server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Launches shiny app.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-27","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$launch()"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"returns-26","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Shiny app","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) \\dontrun{ ds$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"usage-28","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealDatasetConnector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"## ------------------------------------------------ ## Method `TealDatasetConnector$set_ui_input` ## ------------------------------------------------ ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) if (FALSE) { ds$launch() } ## ------------------------------------------------ ## Method `TealDatasetConnector$launch` ## ------------------------------------------------ ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) if (FALSE) { ds$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/all.equal.join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":".equal(target, current) utility compare join_keys objects target current testing near equality.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/all.equal.join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":"","code":"# S3 method for equal.join_keys all(target, current, ...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/all.equal.join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":"target R object. current R object, compared target. ... arguments different methods. used join_keys.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/all.equal.join_keys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":"different, comparison still made extent, report differences returned. use .equal directly expressions—either use isTRUE(.equal(....)) identical appropriate. parents attribute comparison tolerates NULL empty lists find difference. list containing relationships treated like map ignores entries NULL exist.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/as_cdisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"","code":"as_cdisc( x, parent = if (identical(get_dataname(x), \"ADSL\")) character(0) else \"ADSL\" ) # S3 method for TealDataset as_cdisc( x, parent = if (identical(get_dataname(x), \"ADSL\")) character(0) else \"ADSL\" ) # S3 method for TealDatasetConnector as_cdisc( x, parent = if (identical(get_dataname(x), \"ADSL\")) character(0) else \"ADSL\" )"},{"path":"https://insightsengineering.github.io/teal.data/reference/as_cdisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"x object TealDataset TealDatasetConnector class parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/as_cdisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"(CDISCTealDataset CDISCTealDatasetConnector) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/as_cdisc.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"Convert TealDataset(Connector) object CDISCTealDataset(Connector) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/as_cdisc.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"passed CDISC-flavored object returns unmodified object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/as_cdisc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"","code":"# TealDataset -------- as_cdisc( dataset( \"ADSL\", teal.data::example_cdisc_data(\"ADSL\"), keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ) #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... as_cdisc( dataset( \"ADAE\", teal.data::example_cdisc_data(\"ADAE\"), keys = get_cdisc_keys(\"ADAE\"), code = \"ADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ), parent = \"ADSL\" ) #> A CDISCTealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ... # TealDatasetConnector -------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) as_cdisc( dataset_connector( \"ADSL\", pull_fun_adsl, keys = get_cdisc_keys(\"ADSL\") ) ) #> A CDISCTealDatasetConnector object, named ADSL, containing a TealDataset object that has not been loaded/pulled pull_fun_adae <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) as_cdisc( dataset_connector( \"ADAE\", pull_fun_adae, keys = get_cdisc_keys(\"ADAE\") ), parent = \"ADSL\" ) #> A CDISCTealDatasetConnector object, named ADAE, containing a TealDataset object that has not been loaded/pulled"},{"path":"https://insightsengineering.github.io/teal.data/reference/assert_compatible_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to assert if two key sets contain incompatible keys — assert_compatible_keys","title":"Helper function to assert if two key sets contain incompatible keys — assert_compatible_keys","text":"return TRUE compatible, throw error otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/assert_compatible_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to assert if two key sets contain incompatible keys — assert_compatible_keys","text":"","code":"assert_compatible_keys(join_key_1, join_key_2)"},{"path":"https://insightsengineering.github.io/teal.data/reference/assert_parent_child.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function checks the parent-child relations are valid — assert_parent_child","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"Helper function checks parent-child relations valid","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/assert_parent_child.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"","code":"assert_parent_child(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/assert_parent_child.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"x (join_keys) object assert validity relations","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/assert_parent_child.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"join_keys invisibly","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/build_cdisc_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","title":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","text":"Helper method build default_cdisc_join_keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/build_cdisc_join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","text":"","code":"build_cdisc_join_keys(default_cdisc_keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/build_cdisc_join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","text":"default_cdisc_keys (list) default definition primary foreign keys CDISC datasets","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Create CallableCode object — callable_code","title":"Create CallableCode object — callable_code","text":"Create CallableCode object execute specific code get reproducible call.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create CallableCode object — callable_code","text":"","code":"callable_code(code)"},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create CallableCode object — callable_code","text":"code (character) string containing R code reproduce desired object. Please aware objects assigned temporary environment locked means modified.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create CallableCode object — callable_code","text":"CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create CallableCode object — callable_code","text":"","code":"cf <- callable_code(code = \"mtcars\") cf$run() #> mpg cyl disp hp drat wt qsec vs am gear carb #> Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 #> Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 #> Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 #> Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 #> Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 #> Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 #> Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 #> Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 #> Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 #> Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 #> Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 #> Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 #> Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 #> Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 #> Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 #> Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 #> Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 #> Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 #> Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 #> Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 #> Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 #> Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 #> AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 #> Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 #> Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 #> Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 #> Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 #> Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 #> Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 #> Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 #> Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 #> Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 cf$get_call() #> [1] \"mtcars\""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Create CallableFunction object — callable_function","title":"Create CallableFunction object — callable_function","text":"Create CallableFunction object execute specific function get reproducible call.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_function.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create CallableFunction object — callable_function","text":"","code":"callable_function(fun)"},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_function.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create CallableFunction object — callable_function","text":"fun (function) R function, directly name character string.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_function.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create CallableFunction object — callable_function","text":"CallableFunction object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/callable_function.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create CallableFunction object — callable_function","text":"","code":"cf <- callable_function(fun = stats::median) cf$set_args(list(x = 1:10, na.rm = FALSE)) cf$run() #> [1] 5.5 cf$get_call() #> [1] \"stats::median(x = 1:10, na.rm = FALSE)\""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Data input for teal app — cdisc_data","title":"Data input for teal app — cdisc_data","text":"Function wrapper around teal_data() guesses join_keys given datasets whose names match ADAM datasets names.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data input for teal app — cdisc_data","text":"","code":"cdisc_data( ..., join_keys = teal.data::default_cdisc_join_keys[names(rlang::list2(...))], code = character(0), check = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data input for teal app — cdisc_data","text":"... (TealDataConnector, TealDataset, TealDatasetConnector, ) Either 1) object Teal* class, deprecated removed next release, 2) number objects provided name = value pairs, available version 0.4.0. join_keys (join_keys) single (join_key_set) (optional) object datasets column names used joining. empty automatically derived basing intersection datasets primary keys. ADAM datasets automatically derived. code (character, language) code reproduce datasets. check (logical) reproducibility check - whether perform check pre-processing code included object definitions actually produces objects. check true preprocessing code empty error thrown.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data input for teal app — cdisc_data","text":"TealData object TealDataset TealDatasetConnector, TealDataConnector provided, teal_data object otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data input for teal app — cdisc_data","text":"function checks keys added data sets","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data input for teal app — cdisc_data","text":"","code":"data <- cdisc_data( join_keys = join_keys( join_key(\"ADSL\", \"ADTTE\", c(\"STUDYID\" = \"STUDYID\", \"USUBJID\" = \"USUBJID\")) ) ) data <- within(data, { ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADTTE <- teal.data::example_cdisc_data(\"ADTTE\") })"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"","code":"cdisc_data_connector(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"CDISCTealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"","code":"adsl_cf <- callable_function( function() as.data.frame(as.list(setNames(nm = get_cdisc_keys(\"ADSL\")))) ) adae_cf <- callable_function( function() as.data.frame(as.list(setNames(nm = get_cdisc_keys(\"ADAE\")))) ) adsl <- cdisc_dataset_connector( \"ADSL\", adsl_cf, keys = get_cdisc_keys(\"ADSL\"), parent = character(0) ) adae <- cdisc_dataset_connector( \"ADAE\", adae_cf, keys = get_cdisc_keys(\"ADAE\"), parent = \"ADSL\" ) data <- cdisc_data_connector( connection = data_connection(open_fun = callable_function(function() \"open function\")), connectors = list(adsl, adae) )"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealData object from a file — cdisc_data_file","text":"","code":"cdisc_data_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealData object from a file — cdisc_data_file","text":"path (connection) (character) string giving pathname file URL read . \"\" indicates connection stdin. code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealData object from a file — cdisc_data_file","text":"TealData object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_data_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealData object from a file — cdisc_data_file","text":"","code":"file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"# code> ADSL <- teal.data::example_cdisc_data('ADSL') ADTTE <- teal.data::example_cdisc_data('ADTTE') cdisc_data( cdisc_dataset(\\\"ADSL\\\", ADSL), cdisc_dataset(\\\"ADTTE\\\", ADTTE), code = \\\"ADSL <- teal.data::example_cdisc_data('ADSL') ADTTE <- teal.data::example_cdisc_data('ADTTE')\\\", check = FALSE ) # Warning: `cdisc_data_file()` was deprecated in teal.data 0.1.3. #> ℹ Please use `teal_data_file()` instead. #> Warning: The `data_objects` argument of `teal_data()` should use data directly. Using #> TealDatasetConnector and TealDataset is deprecated. Find more information on #> https://github.com/insightsengineering/teal/discussions/945 as of teal.data #> 0.3.1. #> ℹ The deprecated feature was likely used in the teal.data package. #> Please report the issue at #> . #> A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... #> --> Element 2: #> A CDISCTealDataset object containing the following data.frame (2000 rows and 67 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 2 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 3 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 4 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 5 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 6 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 2 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 3 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 4 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 5 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 6 WHITE NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 6 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 ITTFL #> 1 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 2 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 3 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 4 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 5 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 6 B: Placebo A: Drug X South America B S2 6.462991 LOW Y #> SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 2 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 3 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 4 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 5 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 6 Y Y N N 2020-11-03 2020-11-04 04:08:58 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 2 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 3 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 4 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 5 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 6 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 2 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 3 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 4 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 5 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 6 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 2 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 3 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 4 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 5 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 6 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS #> 1 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 2 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 3 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 4 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 5 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 6 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT #> DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ TTESEQ #> 1 NA 2022-03-09 NA 4 4 #> 2 NA 2022-03-09 NA 2 2 #> 3 NA 2022-03-09 NA 3 3 #> 4 NA 2022-03-09 NA 1 1 #> 5 NA 2022-03-09 NA NA NA #> 6 ADVERSE EVENT 24 <=30 2022-03-16 496 Yes 2 2 #> PARAM PARAMCD AVAL AVALU ADTM #> 1 Duration of Confirmed Response CRSD 1273.8498 DAYS 2021-05-27 05:39:28 #> 2 Event Free Survival EFS 135.9787 DAYS 2020-09-25 05:39:28 #> 3 Overall Survival OS 1759.8678 DAYS 2020-11-25 05:39:28 #> 4 Progression Free Survival PFS 241.1912 DAYS 2020-03-30 05:39:28 #> 5 Total Number of Exacerbations TNE 1.0000 COUNT #> 6 Duration of Confirmed Response CRSD 544.5728 DAYS 2021-10-05 04:08:58 #> ADY CNSR EVNTDESC CNSDTDSC lgTMATRSK #> 1 445 1 Last Date Known To Be Alive End of AE Reporting Period NA #> 2 201 0 Death NA #> 3 262 0 Death NA #> 4 22 0 Disease Progression NA #> 5 NA 1 End of AE Reporting Period -2.802988 #> 6 335 0 Death NA #> ..."},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a new object of CDISCTealDataset class — cdisc_dataset","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"Function creates CDISCTealDataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"","code":"cdisc_dataset( dataname, x, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0) else \"ADSL\", label = data_label(x), code = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"dataname (character) given name dataset, contain spaces x (data.frame MultiAssayExperiment) object dataset created keys optional, (character) vector primary keys parent (character, optional) parent dataset name label (character) label describe dataset code (character) character string defining code needed produce data set x vars (named list) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"(CDISCTealDataset) dataset connected metadata","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"","code":"ADSL <- example_cdisc_data(\"ADSL\") cdisc_dataset(\"ADSL\", ADSL, metadata = list(type = \"teal.data\")) #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ..."},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"","code":"cdisc_dataset_connector( dataname, pull_callable, keys, parent = if (identical(dataname, \"ADSL\")) character(0) else \"ADSL\", label = character(0), code = character(0), script = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys optional, (character) vector dataset primary keys column names parent (character, optional) parent dataset name label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"new CDISCTealDatasetConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"Create CDISCTealDatasetConnector callable_function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Load CDISCTealDataset object from a file — cdisc_dataset_file","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"","code":"cdisc_dataset_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"path (character) string giving pathname file read . code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"(CDISCTealDataset) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/cdisc_dataset_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"","code":"# simple example file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) cdisc_dataset(dataname = \\\"ADSL\\\", x = teal.data::example_cdisc_data(\\\"ADSL\\\"), code = \\\"ADSL <- teal.data::example_cdisc_data('ADSL')\\\")\" ), con = file_example ) x <- cdisc_dataset_file(file_example, code = character(0)) get_code(x) #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_ellipsis.html","id":null,"dir":"Reference","previous_headings":"","what":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"Ellipsis, ..., needed part method arguments allow arguments different generic's arguments pass check(). Hence, ..., always empty. function check condition.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_ellipsis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"","code":"check_ellipsis(..., stop = FALSE, allowed_args = character(0))"},{"path":"https://insightsengineering.github.io/teal.data/reference/check_ellipsis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"... literally just ... stop TRUE raise error; FALSE output warning message allowed_args character vector naming arguments allowed .... allow unnamed arguments, let \"\" one elements character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_ellipsis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"NULL ... empty","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_ellipsis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"","code":"method.class <- function(a, b, c, ...) { check_ellipsis(...) } method.class <- function(a, b, c, ...) { check_ellipsis(..., allowed_args = c(\"y\", \"z\")) }"},{"path":"https://insightsengineering.github.io/teal.data/reference/check_pkg_quietly.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if package can be loaded — check_pkg_quietly","title":"Check if package can be loaded — check_pkg_quietly","text":"Check package can loaded","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_pkg_quietly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if package can be loaded — check_pkg_quietly","text":"","code":"check_pkg_quietly(pckg, msg)"},{"path":"https://insightsengineering.github.io/teal.data/reference/check_pkg_quietly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if package can be loaded — check_pkg_quietly","text":"pckg character package name. msg character error message display package available.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_pkg_quietly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if package can be loaded — check_pkg_quietly","text":"Error invisible NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_simple_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Whether the variable name is good to use within Show R Code — check_simple_name","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"Spaces problematic variables must escaped backticks. Also, start number R may silently make valid changing . Therefore, allow alphanumeric characters underscores. first character name must alphabetic character can followed alphanumeric characters.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_simple_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"","code":"check_simple_name(name)"},{"path":"https://insightsengineering.github.io/teal.data/reference/check_simple_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"name character, single vector name check","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/check_simple_name.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"","code":"teal.data:::check_simple_name(\"aas2df\") teal.data:::check_simple_name(\"ADSL\") teal.data:::check_simple_name(\"ADSLmodified\") teal.data:::check_simple_name(\"ADSL_2\") teal.data:::check_simple_name(\"a1\") # the following fail if (FALSE) { teal.data:::check_simple_name(\"1a\") teal.data:::check_simple_name(\"ADSL.modified\") teal.data:::check_simple_name(\"ADSL_modified\") teal.data:::check_simple_name(\"a1...\") }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Code TealDatasetConnector — code_dataset_connector","text":"","code":"code_dataset_connector( dataname, code, keys = character(0), label = character(0), mutate_code = character(0), mutate_script = character(0), metadata = NULL, ... ) code_cdisc_dataset_connector( dataname, code, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), mutate_code = character(0), metadata = NULL, ... )"},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code TealDatasetConnector — code_dataset_connector","text":"dataname (character) given name dataset may contain spaces code (character) String containing code produce object. code must end call object. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. mutate_code (character) String containing code used mutate object produced. mutate_script (character) Alternatively mutate_code - location file containing modification code. used simultaneously mutate_script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... Additional arguments applied pull function. case object code depends raw_data TealDataset, TealDatasetConnector object(s) constant value, /object(s) included. Please note vars included object local vars modified within another dataset. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Code TealDatasetConnector — code_dataset_connector","text":"Create TealDatasetConnector string code. Create CDISCTealDatasetConnector string code keys assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Code TealDatasetConnector — code_dataset_connector","text":"","code":"x <- code_dataset_connector( dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\"); ADSL\" ) x$get_code() #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\\nADSL <- ADSL\" mutate_dataset(x, code = \"ADSL$new_variable <- 1\") x$get_code() #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\\nADSL <- ADSL\\nADSL$new_variable <- 1\" file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"seed <- 1; ADSL <- radsl(cached = TRUE, seed = seed)\\nADSL\" ), con = file_example ) y <- code_dataset_connector( dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = paste0(readLines(file_example), collapse = \"\\n\") )"},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dependency.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Object Dependencies Structure Within Parsed Code — code_dependency","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"function constructs dependency structure identifies relationships objects parsed code. helps understand objects needed recreate specific object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dependency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"","code":"code_dependency(code, object_names)"},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dependency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"code expression srcref attribute character code. object_names (character(n)) vector containing names existing objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dependency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"list three components: occurrence: named list object names names existing objects, element numeric vector indicating calls object appears. cooccurrence: list length number calls parsed_code (parsed_code = parse(text = code) code input character parsed_code = code expression input. contains NULL values co-occurrence objects character vector indicating co-occurrence objects specific parsed_code call element. character vector, first element name dependent object, rest influencing objects. effects: named list object names names existing objects, element numeric vector indicating calls effect object. side-effects pointing object, element NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/code_dependency.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"function assumes object relationships established using <-, =, -> assignment operators. support object creation methods like assign <<-, non-standard-evaluation methods. specify relationships side-effects objects, can use comment tag # @linksto object_name end line side-effect occurs.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/code_exclude.html","id":null,"dir":"Reference","previous_headings":"","what":"Exclude from code — code_exclude","title":"Exclude from code — code_exclude","text":"Excludes lines code. possible exclude one line ended # nocode","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/code_exclude.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Exclude from code — code_exclude","text":"","code":"code_exclude(lines, exclude_comments, file_path)"},{"path":"https://insightsengineering.github.io/teal.data/reference/code_exclude.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Exclude from code — code_exclude","text":"lines (character) preprocessing code. exclude_comments (logical) whether exclude commented-lines code. Lines excluded ended # nocode. multiple line exclusions one enclose ignored block code # nocode> # Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> NA NA NA NA NA col_labels(x) <- paste(\"label for\", names(iris)) col_labels(x) #> Sepal.Length Sepal.Width Petal.Length #> \"label for Sepal.Length\" \"label for Sepal.Width\" \"label for Petal.Length\" #> Petal.Width Species #> \"label for Petal.Width\" \"label for Species\" if (interactive()) { View(x) # in RStudio data viewer labels are displayed }"},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Label Attributes of Variables in a data.frame — col_labels","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"Variable labels can stored label attribute variable. functions returns named character vector variable labels (empty sting specified)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"","code":"col_labels(x, fill = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"function taken 1-1 formatters package, reduce complexity dependency tree.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"x data.frame object fill boolean case label attribute exist TRUE variable names returned, otherwise NA","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"named character vector variable labels, names correspond variable names","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"","code":"x <- iris col_labels(x) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> NA NA NA NA NA col_labels(x) <- paste(\"label for\", names(iris)) col_labels(x) #> Sepal.Length Sepal.Width Petal.Length #> \"label for Sepal.Length\" \"label for Sepal.Width\" \"label for Petal.Length\" #> Petal.Width Species #> \"label for Petal.Width\" \"label for Species\""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_relabel.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy and Change Variable Labels of a data.frame — col_relabel","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"Relabel subset variables","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_relabel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"","code":"col_relabel(x, ...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/col_relabel.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"function taken 1-1 formatters package, reduce complexity dependency tree.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_relabel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"x data.frame object ... name-value pairs, name corresponds variable name x value new variable label","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_relabel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"copy x changed labels according ...","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/col_relabel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"","code":"x <- col_relabel(iris, Sepal.Length = \"Sepal Length of iris flower\") col_labels(x) #> Sepal.Length Sepal.Width #> \"Sepal Length of iris flower\" NA #> Petal.Length Petal.Width #> NA NA #> Species #> NA"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/csv_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"csv TealDatasetConnector — csv_dataset_connector","text":"","code":"csv_dataset_connector( dataname, file, keys = character(0), label = character(0), code = character(0), script = character(0), metadata = list(type = \"csv\", file = file), ... ) csv_cdisc_dataset_connector( dataname, file, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), metadata = list(type = \"csv\", file = file), ... )"},{"path":"https://insightsengineering.github.io/teal.data/reference/csv_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"csv TealDatasetConnector — csv_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) path (.csv) (general delimited) file contains data.frame object keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... (optional) additional arguments applied pull function (readr::read_delim) default delim = \",\". parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/csv_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"csv TealDatasetConnector — csv_dataset_connector","text":"Create TealDatasetConnector csv (general delimited file). Create CDISCTealDatasetConnector csv (general delimited) file keys parent name assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/csv_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"csv TealDatasetConnector — csv_dataset_connector","text":"","code":"if (FALSE) { x <- csv_dataset_connector( dataname = \"ADSL\", file = \"path/to/file.csv\", delim = \",\", col_types = quote(readr::cols(AGE = \"i\")) ) x$get_code() }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/data_connection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor for TealDataConnection class. — data_connection","text":"","code":"data_connection( open_fun = NULL, close_fun = NULL, ping_fun = NULL, if_conn_obj = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/reference/data_connection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor for TealDataConnection class. — data_connection","text":"open_fun (CallableFunction) function open connection close_fun (CallableFunction) function close connection ping_fun (CallableFunction) function ping connection if_conn_obj optional, (logical) whether store conn object returned opening","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/data_connection.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The constructor for TealDataConnection class. — data_connection","text":"TealDataConnection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/data_connection.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor for TealDataConnection class. — data_connection","text":"","code":"open_fun <- callable_function(data.frame) # define opening function open_fun$set_args(list(x = 1:5)) # define fixed arguments to opening function close_fun <- callable_function(sum) # define closing function close_fun$set_args(list(x = 1:5)) # define fixed arguments to closing function ping_fun <- callable_function(function() TRUE) x <- data_connection( # define connection ping_fun = ping_fun, # define ping function open_fun = open_fun, # define opening function close_fun = close_fun # define closing function ) x$set_open_args(args = list(y = letters[1:5])) # define additional arguments if necessary x$open() # call opening function x$get_open_call() # check reproducible R code #> [1] \"data.frame(x = 1:5, y = c(\\\"a\\\", \\\"b\\\", \\\"c\\\", \\\"d\\\", \\\"e\\\"))\" # get data from connection via TealDataConnector$get_dataset() if (FALSE) { x$open(args = list(x = 1:5, y = letters[1:5])) # able to call opening function with arguments x$close() # call closing function }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label-set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dataset label attribute — data_label<-","text":"","code":"data_label(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label-set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dataset label attribute — data_label<-","text":"x data.frame attribute set value (character) label","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label-set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dataset label attribute — data_label<-","text":"modified x object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label-set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set dataset label attribute — data_label<-","text":"","code":"x <- teal.data::example_cdisc_data(\"ADSL\") data_label(x) <- \"My custom label\" data_label(x) #> [1] \"My custom label\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset label attribute — data_label","text":"","code":"data_label(data)"},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset label attribute — data_label","text":"data data.frame attribute extracted","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset label attribute — data_label","text":"(character) label NULL missing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/data_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset label attribute — data_label","text":"","code":"data_label(example_cdisc_data(\"ADSL\")) #> [1] \"Subject Level Analysis Dataset\""},{"path":"https://insightsengineering.github.io/teal.data/reference/datanames.html","id":null,"dir":"Reference","previous_headings":"","what":"Names of Data Sets in teal_data Object — datanames","title":"Names of Data Sets in teal_data Object — datanames","text":"Get set value datanames slot.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/datanames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Names of Data Sets in teal_data Object — datanames","text":"","code":"datanames(x) datanames(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/reference/datanames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Names of Data Sets in teal_data Object — datanames","text":"x (teal_data) object access modify value (character) new value @datanames; elements must names variables existing @env","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/datanames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Names of Data Sets in teal_data Object — datanames","text":"contents @datanames teal_data updated @datanames.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/datanames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Names of Data Sets in teal_data Object — datanames","text":"@datanames slot teal_data object specifies variables stored environment (@env slot) data sets taken consideration. contents @datanames can specified upon creation default variables @env. Variables created later, may well data sets, automatically considered . Use function update slot.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/datanames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Names of Data Sets in teal_data Object — datanames","text":"","code":"td <- teal_data(iris = iris) td <- within(td, mtcars <- mtcars) datanames(td) #> [1] \"iris\" datanames(td) <- c(\"iris\", \"mtcars\")"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"","code":"# S3 method for MultiAssayExperiment dataset( dataname, x, keys = character(0), label = data_label(x), code = character(0), vars = list(), metadata = NULL ) dataset( dataname, x, keys = character(0), label = data_label(x), code = character(0), vars = list(), metadata = NULL ) # S3 method for data.frame dataset( dataname, x, keys = character(0), label = data_label(x), code = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"dataname (character) given name dataset, contain spaces x (data.frame MultiAssayExperiment) object dataset created keys optional, (character) vector primary keys label (character) label describe dataset code (character) character string defining code needed produce data set x vars (named list) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"TealDataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"","code":"# Simple example utils::data(miniACC, package = \"MultiAssayExperiment\") mae_d <- dataset( \"MAE\", miniACC, keys = c(\"STUDYID\", \"USUBJID\"), metadata = list(type = \"example\") ) #> Loading required package: MultiAssayExperiment #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #> #> Attaching package: ‘MatrixGenerics’ #> The following objects are masked from ‘package:matrixStats’: #> #> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #> colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #> colWeightedMeans, colWeightedMedians, colWeightedSds, #> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #> rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #> rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #> #> Attaching package: ‘BiocGenerics’ #> The following objects are masked from ‘package:stats’: #> #> IQR, mad, sd, var, xtabs #> The following objects are masked from ‘package:base’: #> #> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, #> as.data.frame, basename, cbind, colnames, dirname, do.call, #> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, #> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, #> tapply, union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #> #> Attaching package: ‘S4Vectors’ #> The following object is masked from ‘package:utils’: #> #> findMatches #> The following objects are masked from ‘package:base’: #> #> I, expand.grid, unname #> Loading required package: IRanges #> Loading required package: GenomeInfoDb #> #> Attaching package: ‘GenomicRanges’ #> The following object is masked from ‘package:magrittr’: #> #> subtract #> Loading required package: Biobase #> Welcome to Bioconductor #> #> Vignettes contain introductory material; view with #> 'browseVignettes()'. To cite Bioconductor, see #> 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'. #> #> Attaching package: ‘Biobase’ #> The following object is masked from ‘package:MatrixGenerics’: #> #> rowMedians #> The following objects are masked from ‘package:matrixStats’: #> #> anyMissing, rowMedians mae_d$get_dataname() #> [1] \"MAE\" mae_d$get_dataset_label() #> character(0) mae_d$get_metadata() #> $type #> [1] \"example\" #> mae_d$get_code() #> [1] \"\" mae_d$get_raw_data() #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns #> [2] gistict: SummarizedExperiment with 198 rows and 90 columns #> [3] RPPAArray: SummarizedExperiment with 33 rows and 46 columns #> [4] Mutations: matrix with 97 rows and 90 columns #> [5] miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files # Simple example dataset(\"iris\", iris) #> A TealDataset object containing the following data.frame (150 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa #> ... # Example with more arguments if (FALSE) { ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset(dataname = \"ADSL\", x = ADSL) ADSL_dataset$get_dataname() ADSL_dataset <- dataset( dataname = \"ADSL\", x = ADSL, label = \"AdAM subject-level dataset\", code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ADSL_dataset$get_metadata() ADSL_dataset$get_dataset_label() ADSL_dataset$get_code() }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new TealDatasetConnector object — dataset_connector","text":"","code":"dataset_connector( dataname, pull_callable, keys = character(0), label = character(0), code = character(0), script = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new TealDatasetConnector object — dataset_connector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new TealDatasetConnector object — dataset_connector","text":"new TealDatasetConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a new TealDatasetConnector object — dataset_connector","text":"Create TealDatasetConnector callable_function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a new TealDatasetConnector object — dataset_connector","text":"","code":"library(MultiAssayExperiment) # data.frame example pull_fun2 <- callable_function(data.frame) pull_fun2$set_args(args = list(a = c(1, 2, 3))) dataset_connector(\"test\", pull_fun2) #> A TealDatasetConnector object, named test, containing a TealDataset object that has not been loaded/pulled # MultiAssayExperiment example pull_fun <- callable_function( function() { library(\"MultiAssayExperiment\") data(\"miniACC\") return(miniACC) } ) dataset_connector( \"miniacc\", pull_fun, code = 'library(\"MultiAssayExperiment\"); data(\"miniACC\"); return(miniACC)' ) #> A TealDatasetConnector object, named miniacc, containing a TealDataset object that has not been loaded/pulled"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"","code":"dataset_connector_file(path) cdisc_dataset_connector_file(path)"},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"path (character) string giving pathname file read .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"TealDatasetConnector object CDISCTealDatasetConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector_file.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"Please note script end call creating desired object. error raised otherwise. Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_connector_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"","code":"# simple example library(magrittr) file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) pull_callable <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \\\"ADSL\\\")) dataset_connector(\\\"ADSL\\\", pull_callable, get_cdisc_keys(\\\"ADSL\\\"))\" ), con = file_example ) x <- dataset_connector_file(file_example) get_code(x) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" # simple example library(magrittr) file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) pull_callable <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \\\"ADSL\\\")) cdisc_dataset_connector(\\\"ADSL\\\", pull_callable, get_cdisc_keys(\\\"ADSL\\\"))\" ), con = file_example ) x <- cdisc_dataset_connector_file(file_example) get_code(x) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Load TealDataset object from a file — dataset_file","title":"Load TealDataset object from a file — dataset_file","text":"Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealDataset object from a file — dataset_file","text":"","code":"dataset_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealDataset object from a file — dataset_file","text":"path (character) string giving pathname file read . code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealDataset object from a file — dataset_file","text":"TealDataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dataset_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealDataset object from a file — dataset_file","text":"","code":"# simple example file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) dataset(dataname = \\\"iris\\\", x = iris, code = \\\"iris\\\")\" ), con = file_example ) x <- dataset_file(file_example, code = character(0)) get_code(x) #> [1] \"iris\" # custom code file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) # code> x <- iris x$a1 <- 1 x$a2 <- 2 # [1] \"x <- iris\\nx$a1 <- 1\\nx$a2 <- 2\""},{"path":"https://insightsengineering.github.io/teal.data/reference/deep_clone_r6.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to deep copy R6 object — deep_clone_r6","title":"Helper function to deep copy R6 object — deep_clone_r6","text":"cloning R6 object private function deep_clone automatically used. ensure complete clone private function call function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/deep_clone_r6.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to deep copy R6 object — deep_clone_r6","text":"","code":"deep_clone_r6(name, value)"},{"path":"https://insightsengineering.github.io/teal.data/reference/deep_clone_r6.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to deep copy R6 object — deep_clone_r6","text":"name (character) argument passed deep_clone function. value (R object) argument passed deep_clone function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/default_cdisc_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"List containing the default CDISC join keys — default_cdisc_join_keys","title":"List containing the default CDISC join keys — default_cdisc_join_keys","text":"List containing default CDISC join keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/default_cdisc_join_keys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List containing the default CDISC join keys — default_cdisc_join_keys","text":"data object created loading time cdisc_datasets/cdisc_datasets.yaml.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/deprecated_join_keys_extract.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extrapolate parents from TealData classes — deprecated_join_keys_extract","text":"","code":"deprecated_join_keys_extract(data_objects, join_keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/deprecated_join_keys_extract.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extrapolate parents from TealData classes — deprecated_join_keys_extract","text":"note: function removed following classes defunct: TealDataConnector, TealDataset, TealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/detect_symbol.html","id":null,"dir":"Reference","previous_headings":"","what":"Detects ","title":"Detects ","text":"Detects \"SYMBOL\" tokens row bounded getParseData() structure","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/detect_symbol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detects ","text":"","code":"detect_symbol(object, calls_pd)"},{"path":"https://insightsengineering.github.io/teal.data/reference/detect_symbol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detects ","text":"object character containing name object calls_pd list data.frames, result get_children(utils::getParseData(), parent = 0) applied parse(text = code, keep.source = TRUE) code_dependency(code).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/detect_symbol.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detects ","text":"logical vector pointing elements pd SYMBOL token row object text column","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dot-merge_parents.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge parents for 2 join_keys object — .merge_parents","title":"Merge parents for 2 join_keys object — .merge_parents","text":"Merge parents 2 join_keys object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dot-merge_parents.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge parents for 2 join_keys object — .merge_parents","text":"","code":".merge_parents(x, y)"},{"path":"https://insightsengineering.github.io/teal.data/reference/dot-merge_parents.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge parents for 2 join_keys object — .merge_parents","text":"x, y (join_keys) objects merge parents","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/dot-merge_parents.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge parents for 2 join_keys object — .merge_parents","text":"list parents merged 2 join_keys. object .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code enclosed within — enclosed_with","title":"Get code enclosed within — enclosed_with","text":"Extracts lines code enclosed within regexp starts_at stops_at","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get code enclosed within — enclosed_with","text":"","code":"enclosed_with(lines)"},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get code enclosed within — enclosed_with","text":"lines (character) preprocessing code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get code enclosed within — enclosed_with","text":"(character) subset lines start end preprocessing start stop tags.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with_dataname.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code enclosed within — enclosed_with_dataname","title":"Get code enclosed within — enclosed_with_dataname","text":"Extracts lines code enclosed within regexp starts_at stops_at","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with_dataname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get code enclosed within — enclosed_with_dataname","text":"","code":"enclosed_with_dataname(lines, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with_dataname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get code enclosed within — enclosed_with_dataname","text":"lines (character) preprocessing code. dataname (character) metadata returned lines","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/enclosed_with_dataname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get code enclosed within — enclosed_with_dataname","text":"(list) list lines numbers certain chunks code specific file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/example_cdisc_data.html","id":null,"dir":"Reference","previous_headings":"","what":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"meant retrieve SCDA dataset, dataset maintained .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/example_cdisc_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"","code":"example_cdisc_data(dataname)"},{"path":"https://insightsengineering.github.io/teal.data/reference/example_cdisc_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"dataname name CDISC dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/example_cdisc_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"cdisc_data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/example_cdisc_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"function creates copy SCDA data testing purposes. CDISC data includes ADSL, ADAE, ADLB, ADCM, ADEX, ADRS, ADTR ADTTE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/find_source_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Finds lines of code with source call — find_source_code","title":"Finds lines of code with source call — find_source_code","text":"Finds lines preprocessing code source() call located","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/find_source_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finds lines of code with source call — find_source_code","text":"","code":"find_source_code(lines)"},{"path":"https://insightsengineering.github.io/teal.data/reference/find_source_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finds lines of code with source call — find_source_code","text":"lines (character) preprocessing code.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/fun_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function Dataset Connector — fun_dataset_connector","text":"","code":"fun_dataset_connector( dataname, fun, fun_args = NULL, keys = character(0), label = character(0), code = character(0), script = character(0), func_name = substitute(fun), metadata = NULL, ... ) fun_cdisc_dataset_connector( dataname, fun, fun_args = NULL, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), func_name = substitute(fun), metadata = NULL, ... )"},{"path":"https://insightsengineering.github.io/teal.data/reference/fun_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function Dataset Connector — fun_dataset_connector","text":"dataname (character) given name dataset may contain spaces fun (function) custom function obtain dataset. fun_args (list) additional arguments (func). keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. func_name (name) internal purposes, please keep default metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... Additional arguments applied pull function. case object code depends raw_data TealDataset, TealDatasetConnector object(s) constant value, /object(s) included. Please note vars included object local vars modified within another dataset. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/fun_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function Dataset Connector — fun_dataset_connector","text":"Create TealDatasetConnector function arguments. Create CDISCTealDatasetConnector function arguments keys parent name assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/fun_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function Dataset Connector — fun_dataset_connector","text":"","code":"my_data <- function(...) { data.frame( ID = paste0(\"ABC_\", seq_len(10)), var1 = rnorm(n = 10), var2 = rnorm(n = 10), var3 = rnorm(n = 10) ) } y <- fun_dataset_connector( dataname = \"XYZ\", fun = my_data ) y$get_code() #> [1] \"my_data <- function(...) {\\n data.frame(ID = paste0(\\\"ABC_\\\", seq_len(10)), var1 = rnorm(n = 10), var2 = rnorm(n = 10), var3 = rnorm(n = 10))\\n}\\nXYZ <- (function(...) {\\n data.frame(ID = paste0(\\\"ABC_\\\", seq_len(10)), var1 = rnorm(n = 10), var2 = rnorm(n = 10), var3 = rnorm(n = 10))\\n})()\" y$pull() get_raw_data(y) #> ID var1 var2 var3 #> 1 ABC_1 -1.67537372 1.0195769 0.73268871 #> 2 ABC_2 -0.70114973 0.4532490 0.20832726 #> 3 ABC_3 0.42969125 0.8243697 -0.61936527 #> 4 ABC_4 -1.25086426 0.6144842 0.09432247 #> 5 ABC_5 -0.33998223 -0.3325400 0.65914064 #> 6 ABC_6 1.65082381 -0.4185447 -0.04291810 #> 7 ABC_7 0.94785568 0.3379617 1.40202883 #> 8 ABC_8 1.33692879 -0.8392215 0.59208309 #> 9 ABC_9 0.92528696 0.4659020 -1.90823250 #> 10 ABC_10 -0.06008311 -1.1272970 -0.69203847"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_attrs.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dataset attributes — get_attrs","title":"Get dataset attributes — get_attrs","text":"Get dataset attributes form named list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_attrs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset attributes — get_attrs","text":"","code":"get_attrs(x) # S3 method for TealDataset get_attrs(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_attrs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset attributes — get_attrs","text":"x object (TealDataset) class","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_attrs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset attributes — get_attrs","text":"named list object attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_attrs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset attributes — get_attrs","text":"","code":"# TealDataset -------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") x1 <- dataset(\"ADSL\", x = ADSL, label = \"custom label\") get_attrs(x1) #> $names #> [1] \"STUDYID\" \"USUBJID\" \"SUBJID\" \"SITEID\" \"AGE\" \"AGEU\" #> [7] \"SEX\" \"RACE\" \"ETHNIC\" \"COUNTRY\" \"DTHFL\" \"INVID\" #> [13] \"INVNAM\" \"ARM\" \"ARMCD\" \"ACTARM\" \"ACTARMCD\" \"TRT01P\" #> [19] \"TRT01A\" \"TRT02P\" \"TRT02A\" \"REGION1\" \"STRATA1\" \"STRATA2\" #> [25] \"BMRKR1\" \"BMRKR2\" \"ITTFL\" \"SAFFL\" \"BMEASIFL\" \"BEP01FL\" #> [31] \"AEWITHFL\" \"RANDDT\" \"TRTSDTM\" \"TRTEDTM\" \"TRT01SDTM\" \"TRT01EDTM\" #> [37] \"TRT02SDTM\" \"TRT02EDTM\" \"AP01SDTM\" \"AP01EDTM\" \"AP02SDTM\" \"AP02EDTM\" #> [43] \"EOSSTT\" \"EOTSTT\" \"EOSDT\" \"EOSDY\" \"DCSREAS\" \"DTHDT\" #> [49] \"DTHCAUS\" \"DTHCAT\" \"LDDTHELD\" \"LDDTHGR1\" \"LSTALVDT\" \"DTHADY\" #> [55] \"ADTHAUT\" #> #> $row.names #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 #> [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 #> [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 #> [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 #> [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 #> [91] 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 #> [109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 #> [127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 #> [145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 #> [163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 #> [181] 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 #> [199] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 #> [217] 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 #> [235] 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 #> [253] 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 #> [271] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 #> [289] 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 #> [307] 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 #> [325] 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 #> [343] 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 #> [361] 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 #> [379] 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 #> [397] 397 398 399 400 #> #> $class #> [1] \"tbl_df\" \"tbl\" \"data.frame\" #> #> $label #> [1] \"Subject Level Analysis Dataset\" #> #> $study_duration_secs #> [1] 63115200 #> #> $`creation date` #> [1] \"2023-03-22\" #> #> $column_labels #> STUDYID #> \"Study Identifier\" #> USUBJID #> \"Unique Subject Identifier\" #> SUBJID #> \"Subject Identifier for the Study\" #> SITEID #> \"Study Site Identifier\" #> AGE #> \"Age\" #> AGEU #> \"Age Units\" #> SEX #> \"Sex\" #> RACE #> \"Race\" #> ETHNIC #> \"Ethnicity\" #> COUNTRY #> \"Country\" #> DTHFL #> \"Subject Death Flag\" #> INVID #> \"Investigator Identifier\" #> INVNAM #> \"Investigator Name\" #> ARM #> \"Description of Planned Arm\" #> ARMCD #> \"Planned Arm Code\" #> ACTARM #> \"Description of Actual Arm\" #> ACTARMCD #> \"Actual Arm Code\" #> TRT01P #> \"Planned Treatment for Period 01\" #> TRT01A #> \"Actual Treatment for Period 01\" #> TRT02P #> \"Planned Treatment for Period 02\" #> TRT02A #> \"Actual Treatment for Period 02\" #> REGION1 #> \"Geographic Region 1\" #> STRATA1 #> \"Stratification Factor 1\" #> STRATA2 #> \"Stratification Factor 2\" #> BMRKR1 #> \"Continuous Level Biomarker 1\" #> BMRKR2 #> \"Categorical Level Biomarker 2\" #> ITTFL #> \"Intent-To-Treat Population Flag\" #> SAFFL #> \"Safety Population Flag\" #> BMEASIFL #> \"Response Evaluable Population Flag\" #> BEP01FL #> \"Biomarker Evaluable Population Flag\" #> AEWITHFL #> \"AE Leading to Drug Withdrawal Flag\" #> RANDDT #> \"Date of Randomization\" #> TRTSDTM #> \"Datetime of First Exposure to Treatment\" #> TRTEDTM #> \"Datetime of Last Exposure to Treatment\" #> TRT01SDTM #> \"Datetime of First Exposure to Treatment in Period 01\" #> TRT01EDTM #> \"Datetime of Last Exposure in Period 01\" #> TRT02SDTM #> \"Datetime of First Exposure to Treatment in Period 02\" #> TRT02EDTM #> \"Datetime of Last Exposure to Treatment in Period 02\" #> AP01SDTM #> \"Period 01 Start Datetime\" #> AP01EDTM #> \"Period 01 End Datetime\" #> AP02SDTM #> \"Period 02 Start Datetime\" #> AP02EDTM #> \"Period 02 End Datetime\" #> EOSSTT #> \"End of Study Status\" #> EOTSTT #> \"End of Treatment Status\" #> EOSDT #> \"End of Study Date\" #> EOSDY #> \"End of Study Relative Day\" #> DCSREAS #> \"Reason for Discontinuation from Study\" #> DTHDT #> \"Date of Death\" #> DTHCAUS #> \"Cause of Death\" #> DTHCAT #> \"Cause of Death Category\" #> LDDTHELD #> \"Elapsed Days from Last Dose to Death\" #> LDDTHGR1 #> \"Last Dose to Death - Days Elapsed Grp 1\" #> LSTALVDT #> \"Date Last Known Alive\" #> DTHADY #> \"Relative Day of Death\" #> ADTHAUT #> \"Autopsy Performed\" #> #> $row_labels #> NULL #> #> $dataname #> [1] \"ADSL\" #> #> $dataset_label #> [1] \"custom label\" #> #> $keys #> character(0) #> x2 <- dataset( \"ADSL\", x = ADSL, keys = get_cdisc_keys(\"ADSL\"), label = \"custom label\" ) get_attrs(x2) #> $names #> [1] \"STUDYID\" \"USUBJID\" \"SUBJID\" \"SITEID\" \"AGE\" \"AGEU\" #> [7] \"SEX\" \"RACE\" \"ETHNIC\" \"COUNTRY\" \"DTHFL\" \"INVID\" #> [13] \"INVNAM\" \"ARM\" \"ARMCD\" \"ACTARM\" \"ACTARMCD\" \"TRT01P\" #> [19] \"TRT01A\" \"TRT02P\" \"TRT02A\" \"REGION1\" \"STRATA1\" \"STRATA2\" #> [25] \"BMRKR1\" \"BMRKR2\" \"ITTFL\" \"SAFFL\" \"BMEASIFL\" \"BEP01FL\" #> [31] \"AEWITHFL\" \"RANDDT\" \"TRTSDTM\" \"TRTEDTM\" \"TRT01SDTM\" \"TRT01EDTM\" #> [37] \"TRT02SDTM\" \"TRT02EDTM\" \"AP01SDTM\" \"AP01EDTM\" \"AP02SDTM\" \"AP02EDTM\" #> [43] \"EOSSTT\" \"EOTSTT\" \"EOSDT\" \"EOSDY\" \"DCSREAS\" \"DTHDT\" #> [49] \"DTHCAUS\" \"DTHCAT\" \"LDDTHELD\" \"LDDTHGR1\" \"LSTALVDT\" \"DTHADY\" #> [55] \"ADTHAUT\" #> #> $row.names #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 #> [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 #> [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 #> [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 #> [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 #> [91] 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 #> [109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 #> [127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 #> [145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 #> [163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 #> [181] 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 #> [199] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 #> [217] 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 #> [235] 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 #> [253] 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 #> [271] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 #> [289] 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 #> [307] 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 #> [325] 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 #> [343] 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 #> [361] 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 #> [379] 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 #> [397] 397 398 399 400 #> #> $class #> [1] \"tbl_df\" \"tbl\" \"data.frame\" #> #> $label #> [1] \"Subject Level Analysis Dataset\" #> #> $study_duration_secs #> [1] 63115200 #> #> $`creation date` #> [1] \"2023-03-22\" #> #> $column_labels #> STUDYID #> \"Study Identifier\" #> USUBJID #> \"Unique Subject Identifier\" #> SUBJID #> \"Subject Identifier for the Study\" #> SITEID #> \"Study Site Identifier\" #> AGE #> \"Age\" #> AGEU #> \"Age Units\" #> SEX #> \"Sex\" #> RACE #> \"Race\" #> ETHNIC #> \"Ethnicity\" #> COUNTRY #> \"Country\" #> DTHFL #> \"Subject Death Flag\" #> INVID #> \"Investigator Identifier\" #> INVNAM #> \"Investigator Name\" #> ARM #> \"Description of Planned Arm\" #> ARMCD #> \"Planned Arm Code\" #> ACTARM #> \"Description of Actual Arm\" #> ACTARMCD #> \"Actual Arm Code\" #> TRT01P #> \"Planned Treatment for Period 01\" #> TRT01A #> \"Actual Treatment for Period 01\" #> TRT02P #> \"Planned Treatment for Period 02\" #> TRT02A #> \"Actual Treatment for Period 02\" #> REGION1 #> \"Geographic Region 1\" #> STRATA1 #> \"Stratification Factor 1\" #> STRATA2 #> \"Stratification Factor 2\" #> BMRKR1 #> \"Continuous Level Biomarker 1\" #> BMRKR2 #> \"Categorical Level Biomarker 2\" #> ITTFL #> \"Intent-To-Treat Population Flag\" #> SAFFL #> \"Safety Population Flag\" #> BMEASIFL #> \"Response Evaluable Population Flag\" #> BEP01FL #> \"Biomarker Evaluable Population Flag\" #> AEWITHFL #> \"AE Leading to Drug Withdrawal Flag\" #> RANDDT #> \"Date of Randomization\" #> TRTSDTM #> \"Datetime of First Exposure to Treatment\" #> TRTEDTM #> \"Datetime of Last Exposure to Treatment\" #> TRT01SDTM #> \"Datetime of First Exposure to Treatment in Period 01\" #> TRT01EDTM #> \"Datetime of Last Exposure in Period 01\" #> TRT02SDTM #> \"Datetime of First Exposure to Treatment in Period 02\" #> TRT02EDTM #> \"Datetime of Last Exposure to Treatment in Period 02\" #> AP01SDTM #> \"Period 01 Start Datetime\" #> AP01EDTM #> \"Period 01 End Datetime\" #> AP02SDTM #> \"Period 02 Start Datetime\" #> AP02EDTM #> \"Period 02 End Datetime\" #> EOSSTT #> \"End of Study Status\" #> EOTSTT #> \"End of Treatment Status\" #> EOSDT #> \"End of Study Date\" #> EOSDY #> \"End of Study Relative Day\" #> DCSREAS #> \"Reason for Discontinuation from Study\" #> DTHDT #> \"Date of Death\" #> DTHCAUS #> \"Cause of Death\" #> DTHCAT #> \"Cause of Death Category\" #> LDDTHELD #> \"Elapsed Days from Last Dose to Death\" #> LDDTHGR1 #> \"Last Dose to Death - Days Elapsed Grp 1\" #> LSTALVDT #> \"Date Last Known Alive\" #> DTHADY #> \"Relative Day of Death\" #> ADTHAUT #> \"Autopsy Performed\" #> #> $row_labels #> NULL #> #> $dataname #> [1] \"ADSL\" #> #> $dataset_label #> [1] \"custom label\" #> #> $keys #> [1] \"STUDYID\" \"USUBJID\" #> # CDISCTealDataset -------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") x3 <- cdisc_dataset( \"ADSL\", x = ADSL, keys = get_cdisc_keys(\"ADSL\"), label = \"custom label\" ) get_attrs(x3) #> $names #> [1] \"STUDYID\" \"USUBJID\" \"SUBJID\" \"SITEID\" \"AGE\" \"AGEU\" #> [7] \"SEX\" \"RACE\" \"ETHNIC\" \"COUNTRY\" \"DTHFL\" \"INVID\" #> [13] \"INVNAM\" \"ARM\" \"ARMCD\" \"ACTARM\" \"ACTARMCD\" \"TRT01P\" #> [19] \"TRT01A\" \"TRT02P\" \"TRT02A\" \"REGION1\" \"STRATA1\" \"STRATA2\" #> [25] \"BMRKR1\" \"BMRKR2\" \"ITTFL\" \"SAFFL\" \"BMEASIFL\" \"BEP01FL\" #> [31] \"AEWITHFL\" \"RANDDT\" \"TRTSDTM\" \"TRTEDTM\" \"TRT01SDTM\" \"TRT01EDTM\" #> [37] \"TRT02SDTM\" \"TRT02EDTM\" \"AP01SDTM\" \"AP01EDTM\" \"AP02SDTM\" \"AP02EDTM\" #> [43] \"EOSSTT\" \"EOTSTT\" \"EOSDT\" \"EOSDY\" \"DCSREAS\" \"DTHDT\" #> [49] \"DTHCAUS\" \"DTHCAT\" \"LDDTHELD\" \"LDDTHGR1\" \"LSTALVDT\" \"DTHADY\" #> [55] \"ADTHAUT\" #> #> $row.names #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 #> [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 #> [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 #> [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 #> [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 #> [91] 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 #> [109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 #> [127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 #> [145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 #> [163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 #> [181] 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 #> [199] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 #> [217] 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 #> [235] 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 #> [253] 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 #> [271] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 #> [289] 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 #> [307] 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 #> [325] 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 #> [343] 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 #> [361] 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 #> [379] 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 #> [397] 397 398 399 400 #> #> $class #> [1] \"tbl_df\" \"tbl\" \"data.frame\" #> #> $label #> [1] \"Subject Level Analysis Dataset\" #> #> $study_duration_secs #> [1] 63115200 #> #> $`creation date` #> [1] \"2023-03-22\" #> #> $column_labels #> STUDYID #> \"Study Identifier\" #> USUBJID #> \"Unique Subject Identifier\" #> SUBJID #> \"Subject Identifier for the Study\" #> SITEID #> \"Study Site Identifier\" #> AGE #> \"Age\" #> AGEU #> \"Age Units\" #> SEX #> \"Sex\" #> RACE #> \"Race\" #> ETHNIC #> \"Ethnicity\" #> COUNTRY #> \"Country\" #> DTHFL #> \"Subject Death Flag\" #> INVID #> \"Investigator Identifier\" #> INVNAM #> \"Investigator Name\" #> ARM #> \"Description of Planned Arm\" #> ARMCD #> \"Planned Arm Code\" #> ACTARM #> \"Description of Actual Arm\" #> ACTARMCD #> \"Actual Arm Code\" #> TRT01P #> \"Planned Treatment for Period 01\" #> TRT01A #> \"Actual Treatment for Period 01\" #> TRT02P #> \"Planned Treatment for Period 02\" #> TRT02A #> \"Actual Treatment for Period 02\" #> REGION1 #> \"Geographic Region 1\" #> STRATA1 #> \"Stratification Factor 1\" #> STRATA2 #> \"Stratification Factor 2\" #> BMRKR1 #> \"Continuous Level Biomarker 1\" #> BMRKR2 #> \"Categorical Level Biomarker 2\" #> ITTFL #> \"Intent-To-Treat Population Flag\" #> SAFFL #> \"Safety Population Flag\" #> BMEASIFL #> \"Response Evaluable Population Flag\" #> BEP01FL #> \"Biomarker Evaluable Population Flag\" #> AEWITHFL #> \"AE Leading to Drug Withdrawal Flag\" #> RANDDT #> \"Date of Randomization\" #> TRTSDTM #> \"Datetime of First Exposure to Treatment\" #> TRTEDTM #> \"Datetime of Last Exposure to Treatment\" #> TRT01SDTM #> \"Datetime of First Exposure to Treatment in Period 01\" #> TRT01EDTM #> \"Datetime of Last Exposure in Period 01\" #> TRT02SDTM #> \"Datetime of First Exposure to Treatment in Period 02\" #> TRT02EDTM #> \"Datetime of Last Exposure to Treatment in Period 02\" #> AP01SDTM #> \"Period 01 Start Datetime\" #> AP01EDTM #> \"Period 01 End Datetime\" #> AP02SDTM #> \"Period 02 Start Datetime\" #> AP02EDTM #> \"Period 02 End Datetime\" #> EOSSTT #> \"End of Study Status\" #> EOTSTT #> \"End of Treatment Status\" #> EOSDT #> \"End of Study Date\" #> EOSDY #> \"End of Study Relative Day\" #> DCSREAS #> \"Reason for Discontinuation from Study\" #> DTHDT #> \"Date of Death\" #> DTHCAUS #> \"Cause of Death\" #> DTHCAT #> \"Cause of Death Category\" #> LDDTHELD #> \"Elapsed Days from Last Dose to Death\" #> LDDTHGR1 #> \"Last Dose to Death - Days Elapsed Grp 1\" #> LSTALVDT #> \"Date Last Known Alive\" #> DTHADY #> \"Relative Day of Death\" #> ADTHAUT #> \"Autopsy Performed\" #> #> $row_labels #> NULL #> #> $dataname #> [1] \"ADSL\" #> #> $dataset_label #> [1] \"custom label\" #> #> $keys #> [1] \"STUDYID\" \"USUBJID\" #> #> $parent #> character(0) #>"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_binding_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets the name of the binding — get_binding_name","title":"Gets the name of the binding — get_binding_name","text":"Gets name object finding origin. Depending type object function uses different methods obtain original location. env specified object tracked substitute along sys.frames. env specified search limited specified environment.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_binding_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets the name of the binding — get_binding_name","text":"","code":"get_binding_name(object, envir)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_binding_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets the name of the binding — get_binding_name","text":"object (R object) R object envir (environment) origin object known provided precise search","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_binding_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets the name of the binding — get_binding_name","text":"character","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_binding_name.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Gets the name of the binding — get_binding_name","text":"Raises error object found environment.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_cdisc_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"","code":"get_cdisc_keys(dataname)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_cdisc_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"dataname name CDISC dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_cdisc_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"keys object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_cdisc_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"","code":"get_cdisc_keys(\"ADSL\") #> [1] \"STUDYID\" \"USUBJID\""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_children.html","id":null,"dir":"Reference","previous_headings":"","what":"Get child calls within getParseData() object — get_children","title":"Get child calls within getParseData() object — get_children","text":"Get child calls within getParseData() object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_children.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get child calls within getParseData() object — get_children","text":"","code":"get_children(pd, parent)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_children.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get child calls within getParseData() object — get_children","text":"pd (data.frame) result utils::getParseData(). parent Object parent id utils::getParseData().","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_children.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get child calls within getParseData() object — get_children","text":"Row bounded utils::getParseData() elements call pointing parent id.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code — get_code","title":"Get code — get_code","text":"Reads code specified files R6 object. reading R6: get R code stored inside object. reading files: Includes code source reading files. Method reads code without library() require() calls. Function created teal app, can used file. Get code certain files specific datasets Reads code specified files specific code chunks. Code chunks described : open chunk #code> #code ADSL> #code ADSL ADTTE> close chunk # # [1] \"XY <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\\nXYZ <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\" get_code(rd, \"XY\") #> [1] \"XY <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\" get_code(rd, \"XYZ\") #> [1] \"XYZ <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"Return lines code (side-effects) needed reproduce object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"","code":"get_code_dependency(code, names)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"code expression srcref attribute character code. names character(n) object names.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"character vector elements code calls required build side-effects influencing objects impact object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code — get_code_single","title":"Get code — get_code_single","text":"Get code specified file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get code — get_code_single","text":"","code":"get_code_single(file_path, read_sources, if_url = grepl(\"^http[s]\", file_path))"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_single.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get code — get_code_single","text":"file_path (character) path URL address file parsed read_sources (logical) whether replace source(\"path\") code lines sourced file. read_sources = TRUE changing working directory inside preprocessing allowed. if_url (logical) (optional) TRUE URL address provided","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get code — get_code_single","text":"lines (character) preprocessing code","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 method for getting a dataname(s) of\n(TealDataAbstract, (TealDatasetConnector or\nTealDataset) R6 object — get_dataname","text":"","code":"get_dataname(x) # S3 method for TealDataAbstract get_dataname(x) # S3 method for TealDatasetConnector get_dataname(x) # S3 method for TealDataset get_dataname(x) # S3 method for teal_data get_dataname(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 method for getting a dataname(s) of\n(TealDataAbstract, (TealDatasetConnector or\nTealDataset) R6 object — get_dataname","text":"x (TealDataAbstract, TealDatasetConnector TealDataset) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 method for getting a dataname(s) of\n(TealDataAbstract, (TealDatasetConnector or\nTealDataset) R6 object — get_dataname","text":"dataname (character) given name dataset(s) may contain spaces","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dataset from TealDatasetConnector — get_dataset","title":"Get dataset from TealDatasetConnector — get_dataset","text":"Get dataset TealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset from TealDatasetConnector — get_dataset","text":"","code":"get_dataset(x, dataname) # S3 method for TealDatasetConnector get_dataset(x, dataname = NULL) # S3 method for TealDataset get_dataset(x, dataname = NULL) # S3 method for TealDataAbstract get_dataset(x, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset from TealDatasetConnector — get_dataset","text":"x (TealDatasetConnector TealDatasetConnector TealDataAbstract) dataname (character) name dataset retrieved","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset from TealDatasetConnector — get_dataset","text":"(TealDataset)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get dataset from TealDatasetConnector — get_dataset","text":"See help(TealDataConnector) help(TealData) complex examples.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset from TealDatasetConnector — get_dataset","text":"","code":"# TealDatasetConnector -------- library(magrittr) pull_fun_adae <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) ADSL <- teal.data::example_cdisc_data(\"ADSL\") dc <- dataset_connector( dataname = \"ADAE\", pull_callable = pull_fun_adae, keys = get_cdisc_keys(\"ADSL\") ) if (FALSE) { load_dataset(dc) get_dataset(dc) } # TealDataset -------- ADSL <- example_cdisc_data(\"ADSL\") x <- dataset(\"ADSL\", ADSL) get_dataset(x) #> A TealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... # TealData (not containing connectors) -------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- example_cdisc_data(\\\"ADSL\\\")\" ) adae <- cdisc_dataset( dataname = \"ADAE\", x = example_cdisc_data(\"ADAE\"), code = \"library(teal.data)\\nADAE <- example_cdisc_data(\\\"ADAE\\\")\" ) rd <- teal.data:::TealData$new(adsl, adae) get_dataset(rd, \"ADSL\") #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ..."},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"","code":"get_dataset_label(x) # S3 method for TealDatasetConnector get_dataset_label(x) # S3 method for TealDataset get_dataset_label(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"x (TealDatasetConnector TealDataset) R6 object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"label (character) Label describe dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_dataset_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"","code":"fun <- callable_function(data.frame) fun$set_args(list(c1 = seq_len(10))) x <- dataset_connector( pull_callable = fun, dataname = \"ADSL\", label = \"My custom label\" ) get_dataset_label(x) #> [1] \"My custom label\" ADSL <- example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset(dataname = \"ADSL\", x = ADSL, label = \"My custom label\") get_dataset_label(ADSL_dataset) #> [1] \"My custom label\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a TealDataset objects. — get_datasets","text":"","code":"get_datasets(x) # S3 method for TealDataAbstract get_datasets(x) # S3 method for TealDatasetConnector get_datasets(x) # S3 method for TealDataset get_datasets(x) # S3 method for teal_data get_datasets(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a TealDataset objects. — get_datasets","text":"x (TealData) object containing datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a TealDataset objects. — get_datasets","text":"list TealDataset objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a TealDataset objects. — get_datasets","text":"","code":"library(magrittr) # TealData -------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), , code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) adae <- cdisc_dataset( dataname = \"ADAE\", x = teal.data::example_cdisc_data(\"ADAE\"), code = \"library(teal.data)\\nADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ) rd <- cdisc_data(adsl, adae) get_datasets(rd) #> $ADSL #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... #> #> $ADAE #> A CDISCTealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ... #> # TealDataConnector -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) adlb_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADLB\")) adlb <- cdisc_dataset_connector( dataname = \"ADLB\", pull_callable = adlb_cf, keys = get_cdisc_keys(\"ADLB\") ) rdc <- relational_data_connector( connection = data_connection(), connectors = list(adsl, adlb) ) rdc$set_ui(function(id, connection, connectors) p(\"Example UI\")) rdc$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # Note this is simplified as we are not opening a real connection here for (connector in connectors) { set_args(connector, args = list(name = input$name)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } ) } ) if (FALSE) { load_datasets(rdc) get_datasets(rdc) } # TealData -------- if (FALSE) { drc <- cdisc_data(rdc, adae) get_datasets(drc) } # TealDatasetConnector -------- adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) rdc <- cdisc_dataset_connector(\"ADSL\", adsl_cf, keys = get_cdisc_keys(\"ADSL\")) if (FALSE) { load_datasets(rdc) get_datasets(rdc) } # TealDataset -------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- example_cdisc_data(\\\"ADSL\\\")\" ) get_datasets(adsl) #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ..."},{"path":"https://insightsengineering.github.io/teal.data/reference/get_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to get join keys from a `` object — get_join_keys","title":"Function to get join keys from a `` object — get_join_keys","text":"Function get join keys `` object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to get join keys from a `` object — get_join_keys","text":"","code":"get_join_keys(data) get_join_keys(data, dataset_1, dataset_2 = NULL) <- value"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to get join keys from a `` object — get_join_keys","text":"data `` - object extract join keys dataset_1, dataset_2 (character(1)) dataset names. dataset_2 omitted, primary key dataset_1 created. value value assign","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_join_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to get join keys from a `` object — get_join_keys","text":"Either join_keys object NULL join keys","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"","code":"get_key_duplicates(dataset, keys = NULL) # S3 method for TealDataset get_key_duplicates(dataset, keys = NULL) # S3 method for data.frame get_key_duplicates(dataset, keys = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"dataset TealDataset data.frame dataset, tested keys character vector variable names dataset consisting key keys object, primary element vector variable names dataset consisting key. Optional, default: NULL","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"tibble variables consisting key row_no duplicates_count columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"information summary provides row numbers number duplicates duplicated key value.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"Raises exception function determine primary key columns tested object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"","code":"adsl <- teal.data::example_cdisc_data(\"ADSL\") # create a TealDataset with default keys rel_adsl <- cdisc_dataset(\"ADSL\", adsl) get_key_duplicates(rel_adsl) #> # A tibble: 0 × 4 #> # ℹ 4 variables: STUDYID , USUBJID , rows , n df <- as.data.frame( list(a = c(\"a\", \"a\", \"b\", \"b\", \"c\"), b = c(1, 2, 3, 3, 4), c = c(1, 2, 3, 4, 5)) ) res <- get_key_duplicates(df, keys = c(\"a\", \"b\")) # duplicated keys are in rows 3 and 4 print(res) # prints a tibble #> a b rows n #> 1 b 3 3,4 2 if (FALSE) { get_key_duplicates(df) # raises an exception, because keys are missing with no default }"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates_util.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates a duplicate keys information summary. — get_key_duplicates_util","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"Creates duplicate keys information summary.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates_util.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"","code":"get_key_duplicates_util(dataframe, keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates_util.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"dataframe dataframe keys character vector variable names consisting key data.frame","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates_util.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"data.frame duplicate keys information summary","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates_util.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"Accepts list variable names - keys, treated key data.frame argument. instance duplicated key defined two rows, values columns defined keys. Per key value duplicates returns row tibble. return table columns corresponding variable names passed keys two additional columns: rows n, provide information row numbers original dataframe, contain duplicated keys total duplicates counts.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_key_duplicates_util.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"","code":"df <- data.frame( a = c(\"a\", \"a\", \"b\", \"b\", \"c\"), b = c(1, 2, 3, 3, 4), c = c(1, 2, 3, 4, 5) ) res <- teal.data:::get_key_duplicates_util(df, keys = c(\"a\", \"b\")) print(res) # duplicated keys are in rows 3 and 4 #> a b rows n #> 1 b 3 3,4 2"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dataset primary keys — get_keys","title":"Get dataset primary keys — get_keys","text":"Get dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset primary keys — get_keys","text":"","code":"get_keys(x, ...) # S3 method for TealDataset get_keys(x, ...) # S3 method for TealDatasetConnector get_keys(x, ...) # S3 method for TealDataAbstract get_keys(x, dataname, ...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset primary keys — get_keys","text":"x object TealDataset TealDatasetConnector class ... used, support S3 dataname (character) name dataset return keys ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset primary keys — get_keys","text":"(character) vector column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset primary keys — get_keys","text":"","code":"# TealDataset -------- get_keys( dataset( \"ADSL\", teal.data::example_cdisc_data(\"ADSL\"), keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ) #> [1] \"STUDYID\" \"USUBJID\" # TealDatasetConnector -------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) get_keys( dataset_connector( \"ADSL\", pull_fun_adsl, keys = get_cdisc_keys(\"ADSL\"), ) ) #> [1] \"STUDYID\" \"USUBJID\" # TealData -------- get_keys( teal_data( dataset(\"x\", data.frame(x1 = 1:10, y1 = 11:20), keys = \"x1\"), dataset(\"y\", data.frame(x2 = 1:10, y2 = 11:20), keys = \"x2\") ), \"x\" ) #> [1] \"x1\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"","code":"get_labels(data, fill = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"data (data.frame) table extract labels fill (logical(1)) TRUE, function return variable names columns non-existent labels; otherwise return NA ","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"list two keys: dataset_labels column_labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"","code":"iris_with_labels <- iris attr(iris_with_labels, \"label\") <- \"Custom iris dataset with labels\" attr(iris_with_labels[\"Sepal.Length\"], \"label\") <- c(`Sepal.Length` = \"Sepal Length\") get_labels(iris_with_labels, fill = TRUE) #> $dataset_label #> [1] \"Custom iris dataset with labels\" #> #> $column_labels #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> \"Sepal.Length\" \"Sepal.Width\" \"Petal.Length\" \"Petal.Width\" \"Species\" #> get_labels(iris_with_labels, fill = FALSE) #> $dataset_label #> [1] \"Custom iris dataset with labels\" #> #> $column_labels #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> NA NA NA NA NA #>"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_package_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to get a file out of a package — get_package_file","title":"Function to get a file out of a package — get_package_file","text":"Function get file package","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_package_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to get a file out of a package — get_package_file","text":"","code":"get_package_file(pkg = NULL, file_name = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_package_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to get a file out of a package — get_package_file","text":"pkg (character) name package file received . file_name (character) name file received path starting base package path.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_package_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to get a file out of a package — get_package_file","text":"path file","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_package_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to get a file out of a package — get_package_file","text":"","code":"teal.data:::get_package_file(\"teal.data\", \"WORDLIST\") #> [1] \"/__w/teal.data/teal.data/teal.data/inst/WORDLIST\" teal.data:::get_package_file(\"teal.data\", \"cdisc_datasets/cdisc_datasets.yaml\") #> [1] \"/__w/teal.data/teal.data/teal.data/inst/cdisc_datasets/cdisc_datasets.yaml\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/get_raw_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve raw data — get_raw_data","text":"","code":"get_raw_data(x, dataname = NULL) # S3 method for TealDataset get_raw_data(x, dataname = NULL) # S3 method for TealDatasetConnector get_raw_data(x, dataname = NULL) # S3 method for TealDataAbstract get_raw_data(x, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_raw_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve raw data — get_raw_data","text":"x (TealDataset, TealDatasetConnector, TealDataAbstract) object dataname (character) Name dataset return raw data .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_raw_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve raw data — get_raw_data","text":"data.frame raw data inserted R6 objects. case TealDataAbstract, list data.frame can returned user specify dataname - (get_raw_data datasets).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_raw_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve raw data — get_raw_data","text":"","code":"# TealDataset --------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") x <- dataset(dataname = \"ADSL\", x = ADSL) get_raw_data(x) #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … # TealDatasetConnector --------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) dc <- dataset_connector(\"ADSL\", pull_fun_adsl) load_dataset(dc) get_raw_data(dc) #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … # TealData ---------------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) adtte <- cdisc_dataset( dataname = \"ADTTE\", x = teal.data::example_cdisc_data(\"ADTTE\"), code = \"library(teal.data)\\nADTTE <- teal.data::example_cdisc_data(\\\"ADTTE\\\")\" ) rd <- teal.data:::TealData$new(adsl, adtte) get_raw_data(rd) #> $ADSL #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … #> #> $ADTTE #> # A tibble: 2,000 × 67 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 2 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 3 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 4 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 5 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 6 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 7 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 8 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 9 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 10 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> # ℹ 1,990 more rows #> # ℹ 56 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … #> # TealDataConnector -------- library(magrittr) slice_cdisc_data <- function(dataname, n) { head(example_cdisc_data(dataname), n) } random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = slice_cdisc_data, fun_args = list(dataname = dataname), ) } open_fun <- callable_function(library) open_fun$set_args(list(package = \"teal.data\")) con <- data_connection(open_fun = open_fun) con$set_open_server( function(id, connection) { moduleServer( id = id, module = function(input, output, session) { connection$open(try = TRUE) return(invisible(connection)) } ) } ) rdc <- relational_data_connector( connection = con, connectors = list(random_data_connector(\"ADSL\"), random_data_connector(\"ADLB\")) ) rdc$set_ui( function(id, connection, connectors) { ns <- NS(id) tagList( connection$get_open_ui(ns(\"open_connection\")), numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) rdc$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection connection$get_open_server()(id = \"open_connection\", connection = connection) if (connection$is_opened()) { for (connector in connectors) { set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } } ) } ) if (FALSE) { load_datasets(rdc) get_raw_data(rdc) } # TealData (with connectors) -------- drc <- cdisc_data(rdc) if (FALSE) { get_raw_data(drc) }"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_teal_bs_theme.html","id":null,"dir":"Reference","previous_headings":"","what":"Resolve the expected bootstrap theme — get_teal_bs_theme","title":"Resolve the expected bootstrap theme — get_teal_bs_theme","text":"Resolve expected bootstrap theme","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_teal_bs_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Resolve the expected bootstrap theme — get_teal_bs_theme","text":"","code":"get_teal_bs_theme()"},{"path":"https://insightsengineering.github.io/teal.data/reference/include_js_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include JS files from /inst/js/ package directory to application header — include_js_files","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/include_js_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"","code":"include_js_files(pattern = NULL, except = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/include_js_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"pattern (character) pattern files included, passed system.file except (character) vector basename filenames excluded","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/include_js_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"HTML code includes JS files","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/include_source_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Includes source in preprocessing code lines — include_source_code","title":"Includes source in preprocessing code lines — include_source_code","text":"Includes source preprocessing code lines","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/include_source_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Includes source in preprocessing code lines — include_source_code","text":"","code":"include_source_code(lines, dir = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/include_source_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Includes source in preprocessing code lines — include_source_code","text":"lines (character) preprocessing code. dir file source called .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/include_source_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Includes source in preprocessing code lines — include_source_code","text":"lines code source text included","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/is_dag.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"Checks whether graph Directed Acyclic Graph (DAG)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/is_dag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"","code":"is_dag(graph)"},{"path":"https://insightsengineering.github.io/teal.data/reference/is_dag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"graph (named list) list node vector elements","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/is_dag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"logical(1) TRUE graph DAG; FALSE otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/is_pulled.html","id":null,"dir":"Reference","previous_headings":"","what":"Is pulled — is_pulled","title":"Is pulled — is_pulled","text":"S3 method determine dataset pulled (loaded).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/is_pulled.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Is pulled — is_pulled","text":"","code":"is_pulled(x) # S3 method for TealDatasetConnector is_pulled(x) # S3 method for TealDataset is_pulled(x) # S3 method for TealDataAbstract is_pulled(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/is_pulled.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Is pulled — is_pulled","text":"x (TealDatasetConnector, TealDataset TealDataAbstract)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/is_pulled.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Is pulled — is_pulled","text":"(logical) TRUE connector already pulled, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/is_pulled.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Is pulled — is_pulled","text":"","code":"# TealDatasetConnector -------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) x <- dataset_connector(\"ADSL\", pull_fun_adsl) is_pulled(x) #> [1] FALSE load_dataset(x) is_pulled(x) #> [1] TRUE # TealDataset -------- x <- dataset( dataname = \"XY\", x = data.frame(x = c(1, 2), y = c(\"a\", \"b\"), stringsAsFactors = FALSE), keys = \"y\", code = \"XY <- data.frame(x = c(1, 2), y = c('aa', 'bb'), stringsAsFactors = FALSE)\" ) is_pulled(x) #> [1] TRUE library(magrittr) # TealData -------- x1 <- dataset( x = teal.data::example_cdisc_data(\"ADSL\"), dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\", label = \"ADTTE dataset\" ) x2 <- dataset( x = teal.data::example_cdisc_data(\"ADTTE\"), dataname = \"ADTTE\", keys = get_cdisc_keys(\"ADTTE\"), code = \"ADTTE <- teal.data::example_cdisc_data(\\\"ADTTE\\\")\", label = \"ADTTE dataset\" ) rd <- teal_data(x1, x2) is_pulled(rd) #> [1] TRUE # TealDataConnector -------- adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) new_cf <- callable_function(function(x) { x$NEW <- 1:nrow(x) x }) new_cf$set_args(list(x = as.name(\"x\"))) new <- cdisc_dataset_connector( dataname = \"NEW\", pull_callable = new_cf, keys = get_cdisc_keys(\"ADSL\"), vars = list(x = adsl) ) rdc <- cdisc_data(adsl, new) is_pulled(rdc) #> [1] FALSE if (FALSE) { load_datasets(rdc) is_pulled(rdc) }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/join_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a relationship between a pair of datasets — join_key","text":"","code":"join_key(dataset_1, dataset_2 = dataset_1, keys)"},{"path":"https://insightsengineering.github.io/teal.data/reference/join_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a relationship between a pair of datasets — join_key","text":"dataset_1, dataset_2 (character(1)) dataset names. dataset_2 omitted, primary key dataset_1 created. keys (optionally named character) names(keys) columns dataset_1 corresponding columns dataset_2 given elements keys. unnamed, column names used datasets. element keys vector empty non-empty name, name used datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/join_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a relationship between a pair of datasets — join_key","text":"object class join_key_set passed join_keys function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/join_key.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a relationship between a pair of datasets — join_key","text":"join_key() create relationship variables pair datasets.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/join_key.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a relationship between a pair of datasets — join_key","text":"","code":"join_key(\"d1\", \"d2\", c(\"A\")) #> $d1 #> $d1$d2 #> A #> \"A\" #> #> #> attr(,\"class\") #> [1] \"join_key_set\" join_key(\"d1\", \"d2\", c(\"A\" = \"B\")) #> $d1 #> $d1$d2 #> A #> \"B\" #> #> #> attr(,\"class\") #> [1] \"join_key_set\" join_key(\"d1\", \"d2\", c(\"A\" = \"B\", \"C\")) #> $d1 #> $d1$d2 #> A C #> \"B\" \"C\" #> #> #> attr(,\"class\") #> [1] \"join_key_set\""},{"path":"https://insightsengineering.github.io/teal.data/reference/join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage relationships between datasets using join_keys — join_keys","title":"Manage relationships between datasets using join_keys — join_keys","text":"join_keys() facilitates creation retrieval relationships datasets. join_keys class extends list contains keys connecting pairs datasets. element list contains keys specific dataset. dataset can relationship (primary key) datasets. Note join_keys list symmetrical, , keys set dat1 dat2 automatically mirrored dat2 dat1.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage relationships between datasets using join_keys — join_keys","text":"","code":"## Constructor, getter and setter join_keys(...) # S3 method for default join_keys(...) # S3 method for join_keys join_keys(...) # S3 method for teal_data join_keys(...) # S3 method for TealData join_keys(...) # S3 method for join_keys [(x, i, j) # S3 method for join_keys [(x, i, j) <- value # S3 method for join_keys c(...) # S3 method for join_key_set c(...) join_keys(x) <- value # S3 method for join_keys join_keys(x) <- value # S3 method for teal_data join_keys(x) <- value # S3 method for join_keys format(x, ...) # S3 method for join_keys print(x, ...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage relationships between datasets using join_keys — join_keys","text":"... (optional) either teal_data join_keys extract join_keys, number join_key_set objects create join_keys, nothing create empty join_keys x (join_keys) empty object set new relationship pairs. x typically object join_keys class. called join_keys(x) join_keys(x) <- value can also take supported class (teal_data, join_keys) , j indices specifying elements extract replace. Index character vector, can also take numeric, logical, NULL missing. value (join_key_set list join_key_set) relationship pairs add join_keys list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/join_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Manage relationships between datasets using join_keys — join_keys","text":"join_keys object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/join_keys.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Manage relationships between datasets using join_keys — join_keys","text":"join_keys(): Returns empty join_keys object called without arguments. join_keys(join_keys): Returns . join_keys(teal_data): Returns join_keys object contained teal_data. join_keys(...): Creates new object one join_key_set parameters.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/join_keys.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Manage relationships between datasets using join_keys — join_keys","text":"x[datanames]: Returns subset join_keys object given datanames, including parent datanames symmetric mirror keys datanames result. x[, j]: Returns join keys datasets j, including implicit keys inferred relationship parent. x[, j] <- value: Assignment key pair (, j). x[] <- value: (without j parameter) supported operation join_keys. join_keys(x)[, j] <- value: Assignment join_keys object stored x, teal_data join_keys . join_keys(x) <- value: Assignment join_keys object value. value needs object class join_keys join_key_set.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/join_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage relationships between datasets using join_keys — join_keys","text":"","code":"# Creating a new join keys ---- jk <- join_keys( join_key(\"ds1\", \"ds1\", \"pk1\"), join_key(\"ds2\", \"ds2\", \"pk2\"), join_key(\"ds3\", \"ds3\", \"pk3\"), join_key(\"ds2\", \"ds1\", c(pk2 = \"pk1\")), join_key(\"ds3\", \"ds1\", c(pk3 = \"pk1\")) ) jk #> A join_keys object containing foreign keys between 3 datasets: #> ds1: [pk1] #> <-> ds2: [pk2] #> <-> ds3: [pk3] #> ds2: [pk2] #> <-> ds1: [pk1] #> ds3: [pk3] #> <-> ds1: [pk1] # Getter for join_keys --- jk[\"ds1\", \"ds2\"] #> pk1 #> \"pk2\" # Subsetting join_keys ---- jk[\"ds1\"] #> A join_keys object containing foreign keys between 1 datasets: #> ds1: [pk1] jk[1:2] #> A join_keys object containing foreign keys between 2 datasets: #> ds1: [pk1] #> <-> ds2: [pk2] #> ds2: [pk2] #> <-> ds1: [pk1] jk[c(\"ds1\", \"ds2\")] #> A join_keys object containing foreign keys between 2 datasets: #> ds1: [pk1] #> <-> ds2: [pk2] #> ds2: [pk2] #> <-> ds1: [pk1] # Setting a new primary key --- jk[\"ds4\", \"ds4\"] <- \"pk4\" jk[\"ds5\", \"ds5\"] <- \"pk5\" # Setting a single relationship pair --- jk[\"ds4\", \"ds1\"] <- c(\"pk4\" = \"pk1\") # Removing a key --- jk[\"ds5\", \"ds5\"] <- NULL # Merging multiple `join_keys` --- jk_merged <- c( jk, join_keys( join_key(\"ds4\", keys = c(\"pk4\", \"pk4_2\")), join_key(\"ds4\", \"ds3\", c(pk4_2 = \"pk3\")) ) ) # note: merge can be performed with both join_keys and join_key_set jk_merged <- c( jk_merged, join_key(\"ds5\", keys = \"pk5\"), join_key(\"ds5\", \"ds1\", c(pk5 = \"pk1\")) ) # Assigning keys via join_keys(x)[i, j] <- value ---- obj <- join_keys() # or obj <- teal_data() join_keys(obj)[\"ds1\", \"ds1\"] <- \"pk1\" join_keys(obj)[\"ds2\", \"ds2\"] <- \"pk2\" join_keys(obj)[\"ds3\", \"ds3\"] <- \"pk3\" join_keys(obj)[\"ds2\", \"ds1\"] <- c(pk2 = \"pk1\") join_keys(obj)[\"ds3\", \"ds1\"] <- c(pk3 = \"pk1\") identical(jk, join_keys(obj)) #> [1] FALSE # Setter for join_keys within teal_data ---- td <- teal_data() join_keys(td) <- jk join_keys(td)[\"ds1\", \"ds2\"] <- \"new_key\" join_keys(td) <- c(join_keys(td), join_keys(join_key(\"ds3\", \"ds2\", \"key3\"))) join_keys(td) #> A join_keys object containing foreign keys between 4 datasets: #> ds1: [pk1] #> <-> ds2: [new_key] #> <-> ds3: [pk3] #> <-> ds4: [pk4] #> ds2: [pk2] #> <-> ds1: [new_key] #> <-> ds3: [key3] #> ds3: [pk3] #> <-> ds1: [pk1] #> <-> ds2: [key3] #> ds4: [pk4] #> <-> ds1: [pk1]"},{"path":"https://insightsengineering.github.io/teal.data/reference/load_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Load data from connection — load_dataset","title":"Load data from connection — load_dataset","text":"Load data connection. Function used TealDatasetConnector TealDataset obtain data connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/load_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load data from connection — load_dataset","text":"","code":"load_dataset(x, ...) # S3 method for TealDataset load_dataset(x, ...) # S3 method for TealDatasetConnector load_dataset(x, args = NULL, try = FALSE, conn = NULL, ...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/load_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load data from connection — load_dataset","text":"x (TealDatasetConnector TealDataset) ... used, support S3 args (NULL named list) additional dynamic arguments passed function loads data. try (logical) whether perform function evaluation inside try clause conn Optional (TealDataConnection) object required pull data.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/load_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load data from connection — load_dataset","text":"x loaded dataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/load_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load data from connection — load_dataset","text":"","code":"# TealDataset -------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset(\"ADSL\", x = ADSL) load_dataset(ADSL_dataset) # TealDatasetConnector -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") load_dataset(adsl) get_dataset(adsl) #> A TealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... adae <- random_data_connector(dataname = \"ADAE\") load_dataset(adae) get_dataset(adae) #> A TealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ..."},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/load_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load datasets — load_datasets","text":"","code":"load_datasets(x, ...) # S3 method for TealDataset load_datasets(x, ...) # S3 method for TealDatasetConnector load_datasets(x, args = NULL, try = FALSE, ...) # S3 method for TealDataConnector load_datasets(x, ...) # S3 method for TealData load_datasets(x, ...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/load_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load datasets — load_datasets","text":"x (TealData, TealDataset TealDatasetConnector) ... (used) support S3 args (NULL named list) additional dynamic arguments passed function loads data. Applicable TealDatasetConnector) try (logical) whether perform function evaluation inside try clause. Applicable TealDatasetConnector)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/load_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load datasets — load_datasets","text":"executed interactive session shiny app opened load data. executed shiny application - returns shiny server module.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/load_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load datasets — load_datasets","text":"","code":"# TealDataset ------ ADSL <- teal.data::example_cdisc_data(\"ADSL\") x <- dataset(\"ADSL\", x = ADSL) load_datasets(x) # TealDatasetConnector ------ random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") load_datasets(adsl) get_dataset(adsl) #> A TealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... adae <- random_data_connector(dataname = \"ADAE\") load_datasets(adae) get_dataset(adae) #> A TealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ... # TealDataConnector -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") adrs <- random_data_connector(dataname = \"ADRS\") rdc <- cdisc_data(adsl, adrs) if (FALSE) { load_datasets(rdc) } # TealData -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") adlb <- random_data_connector(dataname = \"ADLB\") adrs <- random_data_connector(dataname = \"ADRS\") tc <- cdisc_data(adsl, adlb, adrs) if (FALSE) { load_datasets(tc) }"},{"path":"https://insightsengineering.github.io/teal.data/reference/local_cdisc_data_mixed_call.html","id":null,"dir":"Reference","previous_headings":"","what":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"(test helper) Create test data CDISC data","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/local_cdisc_data_mixed_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"","code":"local_cdisc_data_mixed_call(check = TRUE, join_keys1 = join_keys())"},{"path":"https://insightsengineering.github.io/teal.data/reference/local_cdisc_data_mixed_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"check (logical) reproducibility check - whether perform check pre-processing code included object definitions actually produces objects. check true preprocessing code empty error thrown.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/local_cdisc_data_mixed_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"CDISC data set following tables: ADSL, ADTTE ADAE","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/mae_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor of MAETealDataset — mae_dataset","text":"","code":"mae_dataset( dataname, x, label = data_label(x), code = character(0), vars = list() )"},{"path":"https://insightsengineering.github.io/teal.data/reference/mae_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor of MAETealDataset — mae_dataset","text":"dataname (character) given name dataset, contain spaces x (MultiAssayExperiment) label (character) label describe dataset code (character) character string defining code needed produce data set x vars (named list) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/mae_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor of MAETealDataset — mae_dataset","text":"","code":"# Simple example utils::data(miniACC, package = \"MultiAssayExperiment\") mae_d <- dataset(\"MAE\", miniACC) mae_d$get_dataname() #> [1] \"MAE\" mae_d$get_dataset_label() #> character(0) mae_d$get_code() #> [1] \"\" mae_d$get_raw_data() #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns #> [2] gistict: SummarizedExperiment with 198 rows and 90 columns #> [3] RPPAArray: SummarizedExperiment with 33 rows and 46 columns #> [4] Mutations: matrix with 97 rows and 90 columns #> [5] miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files"},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Mutate data by code — mutate_data","title":"Mutate data by code — mutate_data","text":"Code used mutation linked particular refers datasets. Consequence using get_code() part code returned dataset specified. method used particular call involve changing multiple datasets. Otherwise please use mutate_dataset. Execution code delayed datasets pulled (isTRUE(is_pulled)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mutate data by code — mutate_data","text":"","code":"mutate_data(x, code = character(0), script = character(0), vars = list()) # S3 method for TealDataAbstract mutate_data(x, code = character(0), script = character(0), vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mutate data by code — mutate_data","text":"x (TealDataAbstract) object. code (character) Code mutate dataset. Must contain dataset$dataname. can also object class PythonCodeClass returned python_code. script (character) file contains R Code can read using read_script. Preferred code argument. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mutate data by code — mutate_data","text":"modified x object","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mutate dataset by code — mutate_dataset","text":"","code":"mutate_dataset(x, ...) # S3 method for TealDataset mutate_dataset( x, code = character(0), script = character(0), vars = list(), ... ) # S3 method for TealDatasetConnector mutate_dataset( x, code = character(0), script = character(0), vars = list(), ... ) # S3 method for TealDataAbstract mutate_dataset( x, dataname, code = character(0), script = character(0), vars = list(), ... )"},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mutate dataset by code — mutate_dataset","text":"x (TealDataset) object. ... used, support S3 code (character) Code mutate dataset. Must contain dataset$dataname. can also object class PythonCodeClass returned python_code. script (character) file contains R Code can read using read_script. Preferred code argument. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. dataname (character)Dataname mutated.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mutate dataset by code — mutate_dataset","text":"modified x object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/mutate_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mutate dataset by code — mutate_dataset","text":"","code":"library(magrittr) ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset( dataname = \"ADSL\", x = ADSL, label = \"AdAM subject-level dataset\", code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ADSL_mutated <- ADSL_dataset %>% mutate_dataset(code = \"ADSL$new_variable <- 1\") ADSL_mutated$get_raw_data()$new_variable[1] #> [1] 1 # Use an R script to mutate the data file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"ADSL <- ADSL %>% dplyr::mutate(new_variable = new_variable * 2)\" ), con = file_example ) ADSL_mutated <- ADSL_mutated %>% mutate_dataset(script = file_example) ADSL_mutated$get_raw_data()$new_variable[1] #> [1] 2 ADSL_mutated <- ADSL_mutated %>% mutate_dataset(code = read_script(file_example)) ADSL_mutated$get_raw_data()$new_variable[1] #> [1] 4"},{"path":"https://insightsengineering.github.io/teal.data/reference/names-set-.join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"The Names of an join_keys Object — names<-.join_keys","title":"The Names of an join_keys Object — names<-.join_keys","text":"Names join_keys Object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/names-set-.join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The Names of an join_keys Object — names<-.join_keys","text":"","code":"# S3 method for join_keys names(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/reference/names-set-.join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The Names of an join_keys Object — names<-.join_keys","text":"x R object. value character vector length x, NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/new_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal constructor — new_join_keys","title":"Internal constructor — new_join_keys","text":"Internal constructor","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/new_join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal constructor — new_join_keys","text":"","code":"new_join_keys()"},{"path":"https://insightsengineering.github.io/teal.data/reference/new_join_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Internal constructor — new_join_keys","text":"empty join_keys list","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/new_teal_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize teal_data object — new_teal_data","title":"Initialize teal_data object — new_teal_data","text":"Initialize teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/new_teal_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize teal_data object — new_teal_data","text":"","code":"new_teal_data( data, code = character(0), join_keys = join_keys(), datanames = union(names(data), names(join_keys)) )"},{"path":"https://insightsengineering.github.io/teal.data/reference/new_teal_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize teal_data object — new_teal_data","text":"data (named list) List data. code (character language) code reproduce data. Accepts stores comments also. join_keys (join_keys) object datanames (character) names datasets passed data. Needed non-dataset objects needed env slot.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/parents.html","id":null,"dir":"Reference","previous_headings":"","what":"Getter and setter functions for parents attribute of join_keys — parents","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"parents() facilitates creation dependencies datasets assigning parent-child relationship. element defined list element, list(\"child\" = \"parent\").","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/parents.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"","code":"parents(x) # S3 method for join_keys parents(x) # S3 method for teal_data parents(x) parents(x) <- value # S3 method for join_keys parents(x) <- value # S3 method for teal_data parents(x) <- value parent(x, dataset_name)"},{"path":"https://insightsengineering.github.io/teal.data/reference/parents.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"x (join_keys teal_data) object contains \"parents\" information retrieve manipulate. value (named list) character vectors. dataset_name (character(1)) Name dataset query parent.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/parents.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"list character representing parents. parent(x, dataset_name) returns NULL parent exist.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/parents.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"parents(join_keys): Retrieves parents join_keys object. parents(teal_data): Retrieves parents join_keys inside teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/parents.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"parents(x) <- value: Assignment parents join_keys object. parents(join_keys) <- value: Assignment parents join_keys object. parents(teal_data) <- value: Assignment parents join_keys inside teal_data object. parent(): Getter individual parent","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/parents.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"","code":"# Get parents of join_keys --- jk <- default_cdisc_join_keys[\"ADEX\"] parents(jk) #> $ADEX #> [1] \"ADSL\" #> # Get parents of join_keys inside teal_data object --- td <- teal_data( ADSL = teal.data::rADSL, ADTTE = teal.data::rADTTE, ADRS = teal.data::rADRS, join_keys = default_cdisc_join_keys[c(\"ADSL\", \"ADTTE\", \"ADRS\")] ) parents(td) #> $ADTTE #> [1] \"ADSL\" #> #> $ADRS #> [1] \"ADSL\" #> # Assigment of parents --- jk <- join_keys( join_key(\"ds1\", \"ds2\", \"id\"), join_key(\"ds5\", \"ds6\", \"id\"), join_key(\"ds7\", \"ds6\", \"id\") ) parents(jk) <- list(ds2 = \"ds1\") # Setting individual parent-child relationship parents(jk)[\"ds6\"] <- \"ds5\" parents(jk)[\"ds7\"] <- \"ds6\" # Assigment of parents of join_keys inside teal_data object --- parents(td) <- list(\"ADTTE\" = \"ADSL\") # replace existing parents(td)[\"ADRS\"] <- \"ADSL\" # add new parent # Get individual parent --- parent(jk, \"ds2\") #> [1] \"ds1\" parent(td, \"ADTTE\") #> [1] \"ADSL\""},{"path":"https://insightsengineering.github.io/teal.data/reference/pretty_code_string.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a vector of code into a string — pretty_code_string","title":"Format a vector of code into a string — pretty_code_string","text":"Format vector code string","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/pretty_code_string.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a vector of code into a string — pretty_code_string","text":"","code":"pretty_code_string(code_vector)"},{"path":"https://insightsengineering.github.io/teal.data/reference/pretty_code_string.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a vector of code into a string — pretty_code_string","text":"code_vector (character) vector containing lines code format string.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/pretty_code_string.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a vector of code into a string — pretty_code_string","text":"(character) string containing formatted code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Python Code — python_code","title":"Python Code — python_code","text":"Create python code object directly python code script containing python code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Python Code — python_code","text":"","code":"python_code(code = character(0), script = character(0))"},{"path":"https://insightsengineering.github.io/teal.data/reference/python_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Python Code — python_code","text":"code (character) Code mutate dataset. Must contain dataset$dataname. script (character) file contains python Code can read using reticulate::py_run_script.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Python Code — python_code","text":"(PythonCodeClass) object containing python code","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_code.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Python Code — python_code","text":"Used mutate dataset connector objects python code. See mutate_dataset mutate_data details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Python Code — python_code","text":"","code":"if (FALSE) { library(reticulate) library(magrittr) # mutate dataset object random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } x <- random_data_connector(dataname = \"ADSL\") x %>% mutate_dataset(python_code(\"import pandas as pd r.ADSL = pd.DataFrame({'x': [1]})\")) x$get_code() x$pull() x$get_raw_data() # mutate data object y <- 8 tc <- cdisc_data( random_data_connector(dataname = \"ADSL\"), random_data_connector(dataname = \"ADLB\") ) tc %>% mutate_data(python_code(\"import pandas as pd r.ADSL = pd.DataFrame({'STUDYID': [r.y], 'USUBJID': [r.y]})\"), vars = list(y = y)) load_datasets(tc) # submit all ds <- tc$get_dataset(\"ADSL\") ds$get_raw_data() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/python_dataset_connector.html","id":null,"dir":"Reference","previous_headings":"","what":"Python TealDatasetConnector — python_dataset_connector","title":"Python TealDatasetConnector — python_dataset_connector","text":"Create TealDatasetConnector .py file python code supplied directly. Create CDISCTealDatasetConnector .py file python code supplied directly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Python TealDatasetConnector — python_dataset_connector","text":"","code":"python_dataset_connector( dataname, file, code, object = dataname, keys = character(0), label = character(0), mutate_code = character(0), mutate_script = character(0), vars = list(), metadata = NULL ) python_cdisc_dataset_connector( dataname, file, code, object = dataname, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", mutate_code = character(0), mutate_script = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/reference/python_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Python TealDatasetConnector — python_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) Path file location containing python script used generate object. code (character) string containing python code run using reticulate. Carefully consider indentation follow proper python syntax. object (character) name object python script assigned dataset used. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. mutate_code (character) String containing code used mutate object produced. mutate_script (character) Alternatively mutate_code - location file containing modification code. used simultaneously mutate_script. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Python TealDatasetConnector — python_dataset_connector","text":"Note addition reticulate package, support python requires existing python installation. default, reticulate attempt use location Sys.(\"python\"), however path python installation can supplied directly via reticulate::use_python. teal API delayed data requires python code script return data.frame object. , pandas package required. can installed using reticulate::py_install(\"pandas\"). Please see package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/python_dataset_connector.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Python TealDatasetConnector — python_dataset_connector","text":"Raises error passed code file passed time. using code, keep mind using reticulate delayed data, python functions access objects code must self contained. following example, function makedata() access variable x: using custom functions, function environment must entirely self contained: Additional reticulate considerations: Note using pull vars, R objects referenced python code script prefixed r.. reticulate able convert POSIXct objects. Please take extra care working datetime variables. Please read official documentation reticulate package additional features current limitations.","code":"import pandas as pd x = 1 def makedata(): return pd.DataFrame({'x': [x, 2], 'y': [3, 4]}) data = makedata() def makedata(): import pandas as pd x = 1 return pd.DataFrame({'x': [x, 2], 'y': [3, 4]}) data = makedata()"},{"path":"https://insightsengineering.github.io/teal.data/reference/python_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Python TealDatasetConnector — python_dataset_connector","text":"","code":"if (FALSE) { library(reticulate) # supply python code directly in R x <- python_dataset_connector( \"ADSL\", code = \"import pandas as pd data = pd.DataFrame({'STUDYID': [1, 2], 'USUBJID': [3, 4]})\", object = \"data\" ) x$pull() x$get_raw_data() # supply an external python script python_file <- tempfile(fileext = \".py\") writeLines( text = \"import pandas as pd data = pd.DataFrame({'STUDYID': [1, 2], 'USUBJID': [3, 4]})\", con = python_file ) x <- python_dataset_connector( \"ADSL\", file = python_file, object = \"data\", ) x$pull() x$get_raw_data() # supply pull `vars` from R y <- 8 x <- python_dataset_connector( \"ADSL\", code = \"import pandas as pd data = pd.DataFrame({'STUDYID': [r.y], 'USUBJID': [r.y]})\", object = \"data\", vars = list(y = y) ) x$pull() x$get_raw_data() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADAE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random adverse events — rADAE","title":"Random adverse events — rADAE","text":"Random adverse events","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADAE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random adverse events — rADAE","text":"","code":"rADAE"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADAE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random adverse events — rADAE","text":"object class tbl_df (inherits tbl, data.frame) 1934 rows 92 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADAE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random adverse events — rADAE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADCM.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Concomitant Medications — rADCM","title":"Random Concomitant Medications — rADCM","text":"Random Concomitant Medications","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADCM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Concomitant Medications — rADCM","text":"","code":"rADCM"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADCM.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Concomitant Medications — rADCM","text":"object class tbl_df (inherits tbl, data.frame) 3685 rows 83 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADCM.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Concomitant Medications — rADCM","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADEX.html","id":null,"dir":"Reference","previous_headings":"","what":"Random response — rADEX","title":"Random response — rADEX","text":"Random Exposure","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADEX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random response — rADEX","text":"","code":"rADEX"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADEX.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random response — rADEX","text":"object class tbl_df (inherits tbl, data.frame) 6400 rows 79 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADEX.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random response — rADEX","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADLB.html","id":null,"dir":"Reference","previous_headings":"","what":"Random lab analysis — rADLB","title":"Random lab analysis — rADLB","text":"Random lab analysis","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADLB.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random lab analysis — rADLB","text":"","code":"rADLB"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADLB.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random lab analysis — rADLB","text":"object class tbl_df (inherits tbl, data.frame) 8400 rows 102 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADLB.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random lab analysis — rADLB","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADRS.html","id":null,"dir":"Reference","previous_headings":"","what":"Random response — rADRS","title":"Random response — rADRS","text":"Random response","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADRS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random response — rADRS","text":"","code":"rADRS"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADRS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random response — rADRS","text":"object class tbl_df (inherits tbl, data.frame) 3200 rows 65 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADRS.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random response — rADRS","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADSL.html","id":null,"dir":"Reference","previous_headings":"","what":"Random patient listing — rADSL","title":"Random patient listing — rADSL","text":"Random patient listing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADSL.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random patient listing — rADSL","text":"","code":"rADSL"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADSL.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random patient listing — rADSL","text":"object class tbl_df (inherits tbl, data.frame) 400 rows 55 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADSL.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random patient listing — rADSL","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTR.html","id":null,"dir":"Reference","previous_headings":"","what":"Random data rADTR — rADTR","title":"Random data rADTR — rADTR","text":"Random data rADTR","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random data rADTR — rADTR","text":"","code":"rADTR"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTR.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random data rADTR — rADTR","text":"object class data.frame 2800 rows 76 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random data rADTR — rADTR","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTTE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Time to Event Analysis Dataset — rADTTE","title":"Random Time to Event Analysis Dataset — rADTTE","text":"Random Time Event Analysis Dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTTE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Time to Event Analysis Dataset — rADTTE","text":"","code":"rADTTE"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTTE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Time to Event Analysis Dataset — rADTTE","text":"object class tbl_df (inherits tbl, data.frame) 2000 rows 67 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADTTE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Time to Event Analysis Dataset — rADTTE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADVS.html","id":null,"dir":"Reference","previous_headings":"","what":"Random data rADVS — rADVS","title":"Random data rADVS — rADVS","text":"Random data rADVS","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADVS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random data rADVS — rADVS","text":"","code":"rADVS"},{"path":"https://insightsengineering.github.io/teal.data/reference/rADVS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random data rADVS — rADVS","text":"object class tbl_df (inherits tbl, data.frame) 16800 rows 87 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rADVS.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random data rADVS — rADVS","text":"internal","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/rds_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"","code":"rds_dataset_connector( dataname, file, keys = character(0), label = character(0), code = character(0), script = character(0), metadata = list(type = \"rds\", file = file), ... ) rds_cdisc_dataset_connector( dataname, file, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), metadata = list(type = \"rds\", file = file), ... )"},{"path":"https://insightsengineering.github.io/teal.data/reference/rds_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) path (.rds .R) contains data.frame object code source keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... (optional) additional arguments applied base::readRDS() function parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rds_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"Create TealDatasetConnector RDS file. Create CDSICTealDatasetConnector RDS file keys automatically assigned dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/rds_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"","code":"if (FALSE) { x <- rds_dataset_connector( dataname = \"ADSL\", file = \"path/to/file.RDS\" ) x$get_code() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/read_script.html","id":null,"dir":"Reference","previous_headings":"","what":"Read .R file into character — read_script","title":"Read .R file into character — read_script","text":"Comments excluded","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/read_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read .R file into character — read_script","text":"","code":"read_script(file, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/read_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read .R file into character — read_script","text":"file (character) File parsed code dataname (character) dataset name subset code chunks","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/read_script.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read .R file into character — read_script","text":"(character) vector code","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/read_script.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read .R file into character — read_script","text":"","code":"file_example <- tempfile() writeLines(c(\"x <- 2\", \"#second line comment\", \"x <- x + 2\"), file_example) read_script(file_example) #> [1] \"x <- 2\\nx <- x + 2\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/relational_data_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"","code":"relational_data_connector(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/reference/relational_data_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/relational_data_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"TealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/relational_data_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"","code":"library(magrittr) random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } open_fun <- callable_function(library) open_fun$set_args(list(package = \"teal.data\")) con <- data_connection(open_fun = open_fun) con$set_open_server( function(id, connection) { moduleServer( id = id, module = function(input, output, session) { connection$open(try = TRUE) return(invisible(connection)) } ) } ) x <- relational_data_connector( connection = con, connectors = list( random_data_connector(dataname = \"ADSL\"), random_data_connector(dataname = \"ADLB\") ) ) x$set_ui( function(id, connection, connectors) { ns <- NS(id) tagList( connection$get_open_ui(ns(\"open_connection\")), numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) x$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection connection$get_open_server()(id = \"open_connection\", connection = connection) if (connection$is_opened()) { for (connector in connectors) { set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } } ) } ) if (FALSE) { x$launch() x$get_datasets() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the lines of code needed to reproduce the object. — return_code","title":"Return the lines of code needed to reproduce the object. — return_code","text":"Return lines code needed reproduce object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the lines of code needed to reproduce the object. — return_code","text":"","code":"return_code(object, occur, cooccur, eff, parent = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the lines of code needed to reproduce the object. — return_code","text":"object character object name occur result code_dependency()$occurrence cooccur result code_dependency()$cooccurrence eff result code_dependency()$effects parent NULL numeric vector - recursive call, possible needed drop parent object indicator omit dependency cycles","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the lines of code needed to reproduce the object. — return_code","text":"numeric vector indicating lines parsed_code calls required build object numeric vector number lines input pd returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code_for_effects.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"Return lines code needed reproduce side-effects impact object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code_for_effects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"","code":"return_code_for_effects(object, calls_pd, occur, cooccur, eff)"},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code_for_effects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"object character object name calls_pd list data.frames, result get_children(utils::getParseData(), parent = 0) applied parse(text = code, keep.source = TRUE) code_dependency(code). occur result code_dependency()$occurrence cooccur result code_dependency()$cooccurrence","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/return_code_for_effects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"numeric vector indicating lines parsed_code calls required build side-effects impact object numeric vector number lines input pd returned effects.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/script_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Script TealDatasetConnector — script_dataset_connector","text":"","code":"script_dataset_connector( dataname, file, keys = character(0), label = character(0), code = character(0), script = character(0), metadata = NULL, ... ) script_cdisc_dataset_connector( dataname, file, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), metadata = NULL, ... )"},{"path":"https://insightsengineering.github.io/teal.data/reference/script_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Script TealDatasetConnector — script_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) file location containing code evaluated connector. Object obtained last call file returned connector - source(file = file)$value keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... Additional arguments applied pull function. case object code depends raw_data TealDataset, TealDatasetConnector object(s) constant value, /object(s) included. Please note vars included object local vars modified within another dataset. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/script_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Script TealDatasetConnector — script_dataset_connector","text":"Create TealDatasetConnector .R file. Create CDISCTealDatasetConnector script file keys assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/script_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Script TealDatasetConnector — script_dataset_connector","text":"","code":"if (FALSE) { x <- script_dataset_connector( dataname = \"ADSL\", file = \"path/to/script.R\", keys = get_cdisc_keys(\"ADSL\") ) x$get_code() }"},{"path":"https://insightsengineering.github.io/teal.data/reference/set_args.html","id":null,"dir":"Reference","previous_headings":"","what":"Set arguments of a CallableFunction — set_args","title":"Set arguments of a CallableFunction — set_args","text":"Set arguments CallableFunction","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/set_args.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set arguments of a CallableFunction — set_args","text":"","code":"set_args(x, args) # S3 method for CallableFunction set_args(x, args) # S3 method for CallableCode set_args(x, args) # S3 method for TealDatasetConnector set_args(x, args)"},{"path":"https://insightsengineering.github.io/teal.data/reference/set_args.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set arguments of a CallableFunction — set_args","text":"x CallableFunction TealDatasetConnector) args (NULL named list) dynamic arguments function","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/set_args.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set arguments of a CallableFunction — set_args","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/set_args.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set arguments of a CallableFunction — set_args","text":"","code":"## Using CallableFunction fun <- callable_function(example_cdisc_data) set_args(fun, list(dataname = \"ADSL\")) ## Using CallableCode code <- callable_code(\"example_cdisc_data()\") set_args(code, list(df = \"adsl\")) #> Warning: 'CallableCode' is unchangable. Ignoring arguments set by 'set_args' ## Using TealDatasetConnector ds <- dataset_connector(\"x\", pull_callable = callable_function(data.frame)) set_args(ds, list(x = 1:5, y = letters[1:5]))"},{"path":"https://insightsengineering.github.io/teal.data/reference/set_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Set dataset primary keys — set_keys","title":"Set dataset primary keys — set_keys","text":"Set dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/set_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dataset primary keys — set_keys","text":"","code":"set_keys(x, ...) # S3 method for TealDataset set_keys(x, keys, ...) # S3 method for TealDatasetConnector set_keys(x, keys, ...) # S3 method for TealDataAbstract set_keys(x, dataname, keys, ...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/set_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dataset primary keys — set_keys","text":"x object TealDataset TealDatasetConnector class ... used, support S3 keys optional, (character) vector primary keys dataname (character) name dataset set keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/set_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dataset primary keys — set_keys","text":"(character) vector column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/set_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set dataset primary keys — set_keys","text":"","code":"# TealDataset -------- set_keys( dataset( \"DF\", data.frame(ID = 1:10, x = runif(10)) ), keys = c(\"ID\") ) # TealDatasetConnector -------- pull_fun <- callable_function( function() { data.frame(ID = 1:10, x = runif(10)) } ) set_keys( dataset_connector( \"DF\", pull_fun ), keys = c(\"ID\") ) # TealData -------- set_keys( teal_data( dataset(\"x\", data.frame(x1 = 1:10, y1 = 11:20), keys = \"x1\"), dataset(\"y\", data.frame(x2 = 1:10, y2 = 11:20), keys = \"x2\") ), \"x\", c(\"x1\", \"y1\") )"},{"path":"https://insightsengineering.github.io/teal.data/reference/teal.data-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.data: Reproducible data model for teal applications — teal.data-package","title":"teal.data: Reproducible data model for teal applications — teal.data-package","text":"package extends teal applications module stores data relationships (keys) reproducible code. Package offers also load data files, databases easily extendable another data sources.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/teal.data-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.data: Reproducible data model for teal applications — teal.data-package","text":"Maintainer: Dawid Kaledkowski dawid.kaledkowski@roche.com Authors: Pawel Rucki pawel.rucki@roche.com Mahmoud Hallal mahmoud.hallal@roche.com Nikolas Burkoff Maciej Nasinski Konrad Pagacz Junlue Zhao contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Reproducible data. — teal_data-class","title":"Reproducible data. — teal_data-class","text":"Reproducible data container class. Inherits code tracking behavior teal.code::qenv.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reproducible data. — teal_data-class","text":"class provides isolated environment store process data code recorded. environment, code, data set names, data joining keys stored respective slots. slots never accessed directly, use provided get/set functions. code evaluated teal_data, messages warnings stored respective slots. errors raised, qenv.error object returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Reproducible data. — teal_data-class","text":"env (environment) environment containing data sets possibly auxiliary variables Access variables get_var() [[[]. setter provided. Evaluate code add variables @env. code (character) representing code necessary reproduce contents @env. Access get_code(). setter provided. Evaluate code append code slot. id (integer) random identifier assigned line code @code. Used internally. warnings (character) warnings output evaluating code. warnings (character) warnings raised evaluating code. Access get_warnings(). messages (character) messages raised evaluating code. join_keys (join_keys) object specifying joining keys data sets @env. Access modify join_keys(). datanames (character) vector names data sets @env. Used internally distinguish auxiliary variables. Access modify datanames().","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Data — teal_data","title":"Teal Data — teal_data","text":"Universal function pass data teal application.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Data — teal_data","text":"","code":"teal_data( ..., join_keys = teal.data::join_keys(), code = character(0), check = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Data — teal_data","text":"... (TealDataConnector, TealDataset, TealDatasetConnector, ) Either 1) object Teal* class, deprecated removed next release, 2) number objects provided name = value pairs, available version 0.4.0. join_keys (join_keys) single (join_key_set) (optional) object dataset column relationships used joining. empty joins pairs objects code (character, language) code reproduce datasets. check (logical) reproducibility check - whether perform check pre-processing code included object definitions actually produces objects. check true preprocessing code empty error thrown.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Data — teal_data","text":"old data classes provided (TealDataset TealDatasetConnector, TealDataConnector), TealData object. Otherwise teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Data — teal_data","text":"","code":"teal_data(x1 = iris, x2 = mtcars) #> [L] #> Parent: #> Bindings: #> • x1: [L] #> • x2: [L]"},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Load TealData object from a file — teal_data_file","title":"Load TealData object from a file — teal_data_file","text":"Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealData object from a file — teal_data_file","text":"","code":"teal_data_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealData object from a file — teal_data_file","text":"path (connection) (character) string giving pathname file URL read . \"\" indicates connection stdin. code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealData object from a file — teal_data_file","text":"TealData object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/teal_data_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealData object from a file — teal_data_file","text":"","code":"# simple example file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) x1 <- dataset(dataname = \\\"IRIS\\\", x = iris, code = \\\"IRIS <- iris\\\") x2 <- dataset(dataname = \\\"MTCARS\\\", x = mtcars, code = \\\"MTCARS <- mtcars\\\") teal_data(x1, x2)\" ), con = file_example ) teal_data_file(file_example, code = character(0)) #> A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (150 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa #> ... #> --> Element 2: #> A TealDataset object containing the following data.frame (32 rows and 11 columns): #> mpg cyl disp hp drat wt qsec vs am gear carb #> Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 #> Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 #> Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 #> Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 #> Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 #> Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 #> ..."},{"path":"https://insightsengineering.github.io/teal.data/reference/text_to_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Create call from string — text_to_call","title":"Create call from string — text_to_call","text":"Create call string","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/text_to_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create call from string — text_to_call","text":"","code":"text_to_call(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/text_to_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create call from string — text_to_call","text":"x (character) string containing code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/text_to_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create call from string — text_to_call","text":"(call) object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/to_relational_data.html","id":null,"dir":"Reference","previous_headings":"","what":"S3 generic for to_relational_data function. — to_relational_data","title":"S3 generic for to_relational_data function. — to_relational_data","text":"function takes object converts TealData object, primary data object use teal applications.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/to_relational_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 generic for to_relational_data function. — to_relational_data","text":"","code":"to_relational_data(data)"},{"path":"https://insightsengineering.github.io/teal.data/reference/to_relational_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 generic for to_relational_data function. — to_relational_data","text":"data TealDataset, TealDatasetConnector, data.frame, MultiAssayExperiment, list function returning named list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/to_relational_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 generic for to_relational_data function. — to_relational_data","text":"TealData object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/to_relational_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S3 generic for to_relational_data function. — to_relational_data","text":"Passing TealData function leaves object unchanged.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/to_relational_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 generic for to_relational_data function. — to_relational_data","text":"","code":"to_relational_data(head(iris)) #> A TealData object containing 1 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa to_relational_data(dataset(\"IRIS\", head(iris))) #> A TealData object containing 1 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa to_relational_data(list(iris = head(iris), mtcars = head(mtcars))) #> A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa #> --> Element 2: #> A TealDataset object containing the following data.frame (6 rows and 11 columns): #> mpg cyl disp hp drat wt qsec vs am gear carb #> Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 #> Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 #> Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 #> Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 #> Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 #> Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 d_connector <- dataset_connector(\"iris\", callable_function(function() head(iris))) d_connector$pull() to_relational_data(d_connector) #> A TealData object containing 1 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDatasetConnector object, named iris, containing a TealDataset object that has been loaded/pulled: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa"},{"path":"https://insightsengineering.github.io/teal.data/reference/topological_sort.html","id":null,"dir":"Reference","previous_headings":"","what":"Topological graph sort — topological_sort","title":"Topological graph sort — topological_sort","text":"Graph list node contains vector child nodes returned list, parents appear children.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/topological_sort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Topological graph sort — topological_sort","text":"","code":"topological_sort(graph)"},{"path":"https://insightsengineering.github.io/teal.data/reference/topological_sort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Topological graph sort — topological_sort","text":"graph (named list) list node vector elements","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/topological_sort.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Topological graph sort — topological_sort","text":"Implementation Kahn algorithm modification maintain order input elements.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/topological_sort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Topological graph sort — topological_sort","text":"","code":"teal.data:::topological_sort(list(A = c(), B = c(\"A\"), C = c(\"B\"), D = c(\"A\"))) #> [[1]] #> [1] \"A\" #> #> [[2]] #> [1] \"B\" #> #> [[3]] #> [1] \"C\" #> #> [[4]] #> [1] \"D\" #> teal.data:::topological_sort(list(D = c(\"A\"), A = c(), B = c(\"A\"), C = c(\"B\"))) #> [[1]] #> [1] \"A\" #> #> [[2]] #> [1] \"D\" #> #> [[3]] #> [1] \"B\" #> #> [[4]] #> [1] \"C\" #> teal.data:::topological_sort(list(D = c(\"A\"), B = c(\"A\"), C = c(\"B\"), A = c())) #> [[1]] #> [1] \"A\" #> #> [[2]] #> [1] \"D\" #> #> [[3]] #> [1] \"B\" #> #> [[4]] #> [1] \"C\" #>"},{"path":"https://insightsengineering.github.io/teal.data/reference/update_join_keys_to_primary.html","id":null,"dir":"Reference","previous_headings":"","what":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","title":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","text":"Add primary keys join_keys dataset self","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/update_join_keys_to_primary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","text":"","code":"update_join_keys_to_primary(data_objects, x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/update_join_keys_to_primary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","text":"data_objects (list) TealDataset, TealDatasetConnector TealDataConnector objects x (join_keys) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/update_keys_given_parents.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"Updates keys datasets based parents.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/update_keys_given_parents.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"","code":"update_keys_given_parents(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/update_keys_given_parents.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"x (join_keys) object update keys.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/update_keys_given_parents.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/used_in_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Whether an object is used inside a function within a call — used_in_function","title":"Whether an object is used inside a 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used_in_function","text":"logical(1).","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/validate_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","title":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","text":"validate metadata list length one atomic entries (NULL)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/validate_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","text":"","code":"validate_metadata(metadata)"},{"path":"https://insightsengineering.github.io/teal.data/reference/validate_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"validate metadata as a list of length one atomic 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Added backstop missing reticulate package teal.data Python vignette.","code":""},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"miscellaneous-0-2-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.2.0","text":"Modified teal.Dataset$print method less cluttered output. Transferred data hashing step TealDataset MAETealDataset teal. Removed CDISCTealData class updated TealData account removed functionality. Added datasets parents information JoinKeys class. Updated cdisc_data teal_data wrappers handle join_keys creation updating instead CDISCTealData TealData. 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Removed rtables dependency package.","code":""}] +[{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. 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Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: _. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: __. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Join Keys","text":"teal.data package provides way define primary keys dataset establish relationships datasets. dataset can characterized : Columns constituting primary key Merge keys, analogous SQL foreign keys Typically, application developer specifies keys manually. However, datasets following ADaM standard, teal.data can automatically assign keys using default_cdisc_join_keys object. Refer section “Joining Keys ADaM Datasets” details using object select specific datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"uses-of-join_keys-class-in-teal-applications","dir":"Articles","previous_headings":"Overview","what":"Uses of join_keys class in teal applications","title":"Join Keys","text":"primary function join_keys teal applications facilitate seamless merging datasets using teal.transform. Additionally, plays role data filtering using Filter Panel teal application. filters applied (parent) dataset also applied children.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"anatomy-of-join-keys","dir":"Articles","previous_headings":"","what":"Anatomy of Join Keys","title":"Join Keys","text":"join_keys object contains information foreign/primary keys multiple datasets. key represented pair datasets (name reference) named character vector encodes match column name two datasets. addition, foreign key also contains parent-child attribute used “Filter Panel” mentioned . new join_keys can created empty defining initial set primary foreign keys. initial object can extended adding/modifying/removing keys establishing parent-child relationships datasets. join_keys function used constructor getter. getter used retrieve join_keys contained objects, teal_data. constructor used specify keys join_keys(...) collection multiple join_key entries: dataset_1, dataset_2: names datasets (dataset_2 dataset_1, creates primary key) key (optional): named vector column names Note join keys assumed symmetric, .e., join_key(\"ds1\", \"ds2\", c(\"ds1_col\" = \"ds2_col\")) establishes relationship “x” “y” vice versa.","code":"library(teal.data) jk <- join_keys( join_key(\"ds1\", keys = \"col_1\"), # ds1: [col_1] join_key(\"ds2\", keys = c(\"col_1\", \"col_2\")), # ds2: [col_1, col_2] join_key(\"ds3\", keys = c(\"col_1\", \"col_3\")), # ds3: [col_1, col_3] join_key(\"ds1\", \"ds2\", keys = \"col_1\"), # ds1 <--> ds2 join_key(\"ds1\", \"ds3\", keys = \"col_1\"), # ds1 <--> ds3 join_key(\"ds4\", \"ds5\", keys = c(\"col_4\" = \"col_5\")) # ds4 <--> ds5 ) # The parent of ds2 and ds3 is ds1 # converts relationship to child-parent # ds1 <--> ds2 becomes ds1 <-- ds2 # ds1 <--> ds3 becomes ds1 <-- ds3 parents(jk) <- list(ds2 = \"ds1\", ds3 = \"ds1\") jk"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"accessing-and-modifying-keys","dir":"Articles","previous_headings":"","what":"Accessing and Modifying keys","title":"Join Keys","text":"subset operator 2 indices used retrieve primary/foreign keys join_keys. indices must string. Note symmetry ds4 ds5 relationship: 1 argument used operator return join_keys object filtered accordingly. Modifying adding key uses notation assignment operator <-. symmetric relationship created automatically. Assigning NULL value delete relationship.","code":"# Using the jk object defined on \"Anatomy of Join Keys\" jk ## A join_keys object containing foreign keys between 5 datasets: ## ds1: [col_1] ## <-- ds2: [col_1] ## <-- ds3: [col_1] ## ds2: [col_1, col_2] ## --> ds1: [col_1] ## --* (implicit via parent with): ds3 ## ds3: [col_1, col_3] ## --> ds1: [col_1] ## --* (implicit via parent with): ds2 ## ds4: [no primary keys] ## <-> ds5: [col_5] ## ds5: [no primary keys] ## <-> ds4: [col_4] # Getting primary key of \"ds1\" jk[\"ds1\", \"ds1\"] ## col_1 ## \"col_1\" # Getting foreign keys between \"ds4\" and \"ds5\" jk[\"ds4\", \"ds5\"] ## col_4 ## \"col_5\" jk[\"ds5\", \"ds4\"] ## col_5 ## \"col_4\" jk[\"ds5\", \"ds4\"] ## col_5 ## \"col_4\" # Using the jk object defined on \"Anatomy of Join Keys\" jk ## A join_keys object containing foreign keys between 5 datasets: ## ds1: [col_1] ## <-- ds2: [col_1] ## <-- ds3: [col_1] ## ds2: [col_1, col_2] ## --> ds1: [col_1] ## --* (implicit via parent with): ds3 ## ds3: [col_1, col_3] ## --> ds1: [col_1] ## --* (implicit via parent with): ds2 ## ds4: [no primary keys] ## <-> ds5: [col_5] ## ds5: [no primary keys] ## <-> ds4: [col_4] # Getting primary key of \"ds1\" jk[\"ds1\"] ## A join_keys object containing foreign keys between 1 datasets: ## ds1: [col_1] # Adding a new ds5 <-> ds1 key jk[\"ds5\", \"ds1\"] <- \"a_column\" # Removing an existing key jk[\"ds4\", \"ds5\"] <- NULL"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"join-keys-relationships","dir":"Articles","previous_headings":"","what":"Join Keys Relationships","title":"Join Keys","text":"2 types relationships encoded join_keys described following sections. primary foreign keys created explicitly using join_key function. Additionally, join_keys object detects implicit relationships two datasets share foreign keys parent dataset, . implicit relationships available just like another foreign key can used merge datasets, despite defined user.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"primary-key-with-teal_data","dir":"Articles","previous_headings":"Join Keys Relationships","what":"Primary Key with teal_data","title":"Join Keys","text":"using teal_data function, simplest method define join keys use join_keys argument. can specify column(s) dataset (together) uniquely identify rows dataset. can extend previous example define primary keys multiple datasets:","code":"library(teal.data) td_pk <- within( teal_data(), ds1 <- dplyr::mutate(iris, id = factor(dplyr::row_number())) ) datanames(td_pk) <- \"ds1\" join_keys(td_pk) <- join_keys(join_key(\"ds1\", keys = \"id\")) join_keys(td_pk) ## A join_keys object containing foreign keys between 1 datasets: ## ds1: [id] library(teal.data) td_pk <- within( td_pk, { ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2)) ds3 <- data.frame(V = 5:14, N = 4) } ) datanames(td_pk) <- c(datanames(td_pk), \"ds2\", \"ds3\") join_keys(td_pk)[\"ds2\", \"ds2\"] <- c(\"V\", \"W\") join_keys(td_pk)[\"ds3\", \"ds3\"] <- c(\"V\", \"W\") join_keys(td_pk) ## A join_keys object containing foreign keys between 3 datasets: ## ds1: [id] ## ds2: [V, W] ## ds3: [V, W]"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"foreign-keys-with-teal_data","dir":"Articles","previous_headings":"Join Keys Relationships","what":"Foreign Keys with teal_data","title":"Join Keys","text":"passing multiple datasets teal_data function, dataset relationships set using join_keys join_key used merge datasets together within teal apps. users familiar SQL database schema, relationships symmetric strict SQL foreign key relationships teal validate whether values inserted foreign key columns present parent table. example:","code":"library(teal.data) td_fk <- within( teal_data(), { ds1 <- data.frame(X = 1:10, Y = 21:30, Z = 1:10) ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2)) ds3 <- data.frame(V = 5:14, N = 4) } ) datanames(td_fk) <- c(\"ds1\", \"ds2\", \"ds3\") join_keys(td_fk) <- join_keys( # Primary keys join_key(\"ds1\", keys = c(\"X\")), join_key(\"ds2\", keys = c(\"V\", \"W\")), join_key(\"ds3\", keys = c(\"V\")), # Foreign keys join_key(\"ds2\", \"ds1\", c(\"W\" = \"X\")), join_key(\"ds3\", \"ds2\", c(\"V\" = \"V\")) ) # The parent of ds2 and ds3 is ds1 parents(td_fk) <- list(ds2 = \"ds1\", ds3 = \"ds2\") join_keys(td_fk) ## A join_keys object containing foreign keys between 3 datasets: ## ds1: [X] ## <-- ds2: [W] ## ds2: [V, W] ## --> ds1: [X] ## <-- ds3: [V] ## ds3: [V] ## --> ds2: [V]"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"implicit-relationships","dir":"Articles","previous_headings":"Join Keys Relationships","what":"Implicit Relationships","title":"Join Keys","text":"Two datasets share common foreign keys parent dataset implicit relationship modeled accessible join_keys. special inferred relationship existing join_keys need explicitly defined can seamlessly accessible just foreign key. foreign key can overwritten. implicit relationships can used merge 2 datasets together, just defined manually. Note definition contains join_key \"ds2\" <-> \"ds4\"","code":"library(teal.data) td <- within( teal_data(), { ds1 <- data.frame(X = 1:10, Y = 21:30, Z = 1:10) ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2)) ds3 <- data.frame(V = 5:14, N = 4) ds4 <- data.frame(V = 5:14, R = rnorm(10)) } ) datanames(td) <- c(\"ds1\", \"ds2\", \"ds3\", \"ds4\") join_keys(td) <- join_keys( # Primary keys join_key(\"ds1\", keys = c(\"X\")), join_key(\"ds2\", keys = c(\"V\", \"W\")), join_key(\"ds3\", keys = c(\"V\")), join_key(\"ds4\", keys = c(\"V\")), # Foreign keys join_key(\"ds2\", \"ds1\", c(\"W\" = \"X\")), join_key(\"ds3\", \"ds2\", c(\"V\" = \"V\")), join_key(\"ds4\", \"ds1\", c(\"V\" = \"X\")) ) # The parent of ds2 and ds3 is ds1 parents(td) <- list(ds2 = \"ds1\", ds3 = \"ds2\", ds4 = \"ds1\") join_keys(td) ## A join_keys object containing foreign keys between 4 datasets: ## ds1: [X] ## <-- ds2: [W] ## <-- ds4: [V] ## ds2: [V, W] ## --> ds1: [X] ## <-- ds3: [V] ## --* (implicit via parent with): ds4 ## ds3: [V] ## --> ds2: [V] ## ds4: [V] ## --> ds1: [X] ## --* (implicit via parent with): ds2 join_keys(td)[\"ds2\", \"ds4\"] ## W ## \"V\""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/join-keys.html","id":"join-keys-in-adam-datasets","dir":"Articles","previous_headings":"","what":"Join Keys in ADaM Datasets","title":"Join Keys","text":"teal.data provides set default join keys (primary foreign) datasets named according ADaM standard. stored default_cdisc_join_keys. default keys required users can select smaller set datasets subsetting (example: default_cdisc_join_keys[c(\"ADSL\", \"ADTTE\")]). Please note, every element selected, parent also returned (one) well pair-wise relationships resulting selection.","code":"names(default_cdisc_join_keys) |> sort() ## [1] \"ADAE\" \"ADAETTE\" \"ADCM\" \"ADCSSRS\" \"ADDV\" \"ADEG\" ## [7] \"ADEQ5D5L\" \"ADEX\" \"ADHY\" \"ADLB\" \"ADMH\" \"ADQLQC\" ## [13] \"ADQS\" \"ADRS\" \"ADSAFTTE\" \"ADSL\" \"ADSUB\" \"ADTTE\" ## [19] \"ADVS\" default_cdisc_join_keys ## A join_keys object containing foreign keys between 19 datasets: ## ADSL: [STUDYID, USUBJID] ## <-- ADAE: [STUDYID, USUBJID] ## <-- ADEG: [STUDYID, USUBJID] ## <-- ADTTE: [STUDYID, USUBJID] ## <-- ADAETTE: [STUDYID, USUBJID] ## <-- ADCM: [STUDYID, USUBJID] ## <-- ADEX: [STUDYID, USUBJID] ## <-- ADLB: [STUDYID, USUBJID] ## <-- ADMH: [STUDYID, USUBJID] ## <-- ADQS: [STUDYID, USUBJID] ## <-- ADRS: [STUDYID, USUBJID] ## <-- ADSAFTTE: [STUDYID, USUBJID] ## <-- ADVS: [STUDYID, USUBJID] ## <-- ADDV: [STUDYID, USUBJID] ## <-- ADSUB: [STUDYID, USUBJID] ## <-- ADHY: [STUDYID, USUBJID] ## <-- ADQLQC: [STUDYID, USUBJID] ## <-- ADCSSRS: [STUDYID, USUBJID] ## <-- ADEQ5D5L: [STUDYID, USUBJID] ## ADAE: [STUDYID, USUBJID, ASTDTM, AETERM, AESEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADEG: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADAETTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADCM: [STUDYID, USUBJID, ASTDTM, CMSEQ, ATC1CD, ATC2CD, ATC3CD, ATC4CD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADEX: [STUDYID, USUBJID, PARCAT1, PARAMCD, AVISITN, ASTDTM, EXSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADLB: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADMH: [STUDYID, USUBJID, ASTDTM, MHSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADQS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADSAFTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADVS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADDV: [STUDYID, USUBJID, ASTDT, DVTERM, DVSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADSUB: [STUDYID, USUBJID, PARAMCD, AVISITN, ADTM, SRCSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L ## ADHY: [STUDYID, USUBJID, PARAMCD, AVISITN, ADTM, SRCSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADQLQC, ADCSSRS, ADEQ5D5L ## ADQLQC: [STUDYID, USUBJID, PARCAT1N, PARAMCD, BASETYPE, AVISITN, ATPTN, ADTM, QSSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADCSSRS, ADEQ5D5L ## ADCSSRS: [STUDYID, USUBJID, PARAMCD, BASETYPE, AVISITN, DTYPE, ADTM] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADEQ5D5L ## ADEQ5D5L: [STUDYID, USUBJID, PARCAT1N, PARAMCD, BASETYPE, AVISITN, ATPTN, ADTM, QSSEQ] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS default_cdisc_join_keys[\"ADSL\"] ## A join_keys object containing foreign keys between 1 datasets: ## ADSL: [STUDYID, USUBJID] default_cdisc_join_keys[\"ADTTE\"] ## A join_keys object containing foreign keys between 2 datasets: ## ADSL: [STUDYID, USUBJID] ## <-- ADTTE: [STUDYID, USUBJID] ## ADTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] default_cdisc_join_keys[c(\"ADSL\", \"ADTTE\", \"ADRS\")] ## A join_keys object containing foreign keys between 3 datasets: ## ADSL: [STUDYID, USUBJID] ## <-- ADTTE: [STUDYID, USUBJID] ## <-- ADRS: [STUDYID, USUBJID] ## ADTTE: [STUDYID, USUBJID, PARAMCD] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADRS ## ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT] ## --> ADSL: [STUDYID, USUBJID] ## --* (implicit via parent with): ADTTE"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/preprocessing-delayed-data.html","id":"processing-dependencies","dir":"Articles","previous_headings":"","what":"Processing dependencies","title":"Pre-processing Delayed Data","text":"may required generate delayed data object dependent delayed object constant value. , creating delayed data object ’s possible supply additional variables accessed data loading (pull) using additional arguments ...: ’s also possible supply additional variables creating object using mutate_dataset function. also required creating object depends another delayed data object: possible provide code Data level. However, always return code used generate datasets object: better approach supply code Dataset level. ensures code accessed dataset level contains snippets pertains : Related idea, delayed data object needs supplied code needed reproduce data. can provided Dataset level Data level. comparison two approaches:","code":"get_code(adsl) ## [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\\nADSL$SEX <- as.factor(ADSL$SEX)\" pull_fun_adae <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- dataset_connector( dataname = \"ADAE\", pull_callable = pull_fun_adae, keys = get_cdisc_keys(\"ADAE\") ) get_code(adae) ## [1] \"ADAE <- teal.data::example_cdisc_data(dataname = \\\"ADAE\\\")\" last_run <- Sys.Date() # constant value stored as a variable in the current session adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) %>% mutate_dataset(\"ADSL$last_run <- last_run\", vars = list(last_run = last_run)) cat(get_code(adsl)) ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## last_run <- structure(19696, class = \"Date\") ## ADSL$last_run <- last_run # compared to evaluating the variable at the time of loading adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) %>% mutate_dataset(\"last_run <- Sys.Date()\\nADSL$last_run <- last_run\") adsl %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## last_run <- Sys.Date() ## ADSL$last_run <- last_run adsl <- teal.data::example_cdisc_data(\"ADSL\") adae_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = adae_cf, keys = get_cdisc_keys(\"ADAE\") ) %>% mutate_dataset(\"ADAE$n <- nrow(ADSL)\") cat(get_code(adae)) # the code returned by `adae` is not sufficient to reproduce `adae` ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) adae_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = adae_cf, keys = get_cdisc_keys(\"ADAE\") ) %>% mutate_dataset(\"ADAE$n <- nrow(ADSL)\", vars = list(ADSL = adsl)) cat(get_code(adae)) # this code can be run independently ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE$n <- nrow(ADSL) adsl_adae <- cdisc_data( adsl, adae ) %>% mutate_data(\"ADAE$avg_age <- mean(ADAE$AGE)\") # the output for all 3 are the same adsl_adae %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(dataname = \"ADAE\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(dataname = \"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae <- cdisc_data( adsl, adae %>% mutate_dataset(\"ADAE$avg_age <- mean(ADAE$AGE)\") ) adsl_adae %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(\"ADAE\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") ## ADAE <- teal.data::example_cdisc_data(dataname = \"ADAE\") ## ADAE$n <- nrow(ADSL) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) ## ADAE$avg_age <- mean(ADAE$AGE) adsl_adae %>% get_code(\"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") adsl <- teal.data::example_cdisc_data(\"ADSL\") # no reproducible code provided cdisc_dataset(\"ADSL\", adsl) %>% get_code() %>% cat() # provide the code to reproduce the data: cdisc_dataset(\"ADSL\", adsl, code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) %>% get_code() ## [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" # it's possible to supply the code at the `Data` level: adae <- teal.data::example_cdisc_data(\"ADAE\") adsl_adae <- cdisc_data( cdisc_dataset(\"ADSL\", adsl), cdisc_dataset(\"ADAE\", adae), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\\nADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ) adsl_adae %>% get_code() %>% cat() ## ADSL <- teal.data::example_cdisc_data(\"ADSL\") ## ADAE <- teal.data::example_cdisc_data(\"ADAE\") # but it's not possible then to access the code at a `Dataset` level: adsl_adae %>% get_code(\"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(\"ADSL\") ## ADAE <- teal.data::example_cdisc_data(\"ADAE\") # this can be avoided by storing the code like so: adsl_adae <- cdisc_data( cdisc_dataset(\"ADSL\", adsl, code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\"), cdisc_dataset(\"ADAE\", adae, code = \"ADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\") ) adsl_adae %>% get_code(\"ADSL\") %>% cat() ## ADSL <- teal.data::example_cdisc_data(\"ADSL\")"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/articles/reproducibility.html","id":"mechanism","dir":"Articles","previous_headings":"Reproducibility check","what":"Mechanism","title":"Reproducibility check","text":"teal.data classes accumulate raw data accept boolean check argument, e.g. teal_data. boolean flag indicates whether teal performs validation data passed TealData object launch teal application. validation compares raw data passed class dataset returned code stored class. E.g.: check() method called launch can invoked directly returns TRUE raw data passed teal_data matches return value code stored class. returns error comparison fails NULL check = FALSE passed teal_data. Find teal_data() documentation.","code":"library(teal.data) iris_ds <- dataset(\"iris\", iris, code = \"iris <- iris\") data <- teal_data(iris_ds, check = TRUE) ## Warning: The `data_objects` argument of `teal_data()` should use data directly. Using ## TealDatasetConnector and TealDataset is deprecated. Find more information on ## https://github.com/insightsengineering/teal/discussions/945 as of teal.data ## 0.3.1. ## This warning is displayed once every 8 hours. ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was ## generated. data$check() ## [1] TRUE # throws an error: data <- teal_data(dataset(\"iris\", iris, code = \"iris <- mtcars\"), check = TRUE) ## Error in x$check_reproducibility(): Reproducibility check failed. data <- teal_data(dataset(\"iris\", iris, code = \"iris <- mtcars\"), check = FALSE) # returns NULL even though the code does not match the raw data data$check() ## NULL"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/reproducibility.html","id":"final-considerations","dir":"Articles","previous_headings":"Reproducibility check","what":"Final considerations","title":"Reproducibility check","text":"_connector objects accept raw data input therefore checked even check = TRUE used.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Introduction to teal.data","text":"teal.data package enables teal application developers convert data format can used inside teal applications.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data.html","id":"quick-start","dir":"Articles","previous_headings":"Introduction","what":"Quick Start","title":"Introduction to teal.data","text":"creating ADaM clinical trial data please use cdisc_data cdisc_dataset functions: general data use teal_data dataset functions:","code":"library(teal.data) # create some dummy data adsl <- teal.data::example_cdisc_data(\"ADSL\") adtte <- teal.data::example_cdisc_data(\"ADTTE\") my_data <- cdisc_data( ADSL = adsl, ADTTE = adtte ) my_general_data <- teal_data( iris = iris, mtcars = mtcars )"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data.html","id":"additional-functionality","dir":"Articles","previous_headings":"Introduction","what":"Additional functionality","title":"Introduction to teal.data","text":"teal.data package provides many features help specify data: Specifying ADaM data Specifying MultiAssayExperiment data Specifying general relational data Specifying relationships datasets Dynamically loading data (DDL) Pre-processing data Pre-processing DDL data Checking reproducibility Using python create data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal.data-with-python.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"teal.data with Python","text":"possible use Python code (via reticulate package) create teal dataset. python_dataset_connector allows seamless integration teal application Python package(s) required access/create data. recommend thorough understanding reticulate package (see ) using Python functionality described .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal.data-with-python.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"teal.data with Python","text":"section show simple example Python code can used create teal dataset. example require Python environment pandas installed. See details install Python packages. first load packages: Next define Python code want use create dataset. example, demonstration purposes create trivial dataset easily done directly R. Note use variable num_rows needs passed Python code R. Next create python_dataset_connector object. Finally can test code pulling data R:","code":"library(reticulate) # may need to be installed if not available # reticulate function to call to install the pandas package if not installed: py_install(\"pandas\") library(teal.data) python_code <- \"import pandas as pd data = pd.DataFrame({\\\"id\\\" : range(r.num_rows), \\\"val\\\" : range(r.num_rows)})\" x <- python_dataset_connector( dataname = \"DATA\", # the teal dataset name code = python_code, # the code used to generate the dataset object = \"data\", # the object in the Python code to be converted to a data.frame for the teal dataset keys = \"id\", # the key for teal dataset object vars = list(num_rows = 5L) # any variables passed from R into Python (note this could be an R variable) ) x$pull() print(x)"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal.data-with-python.html","id":"reproducibility","dir":"Articles","previous_headings":"Further Concerns","what":"Reproducibility","title":"teal.data with Python","text":"order ensure reproducibility generating teal datasets using Python necessary use reproducible Python environment (example using virtualenv conda) see details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal.data-with-python.html","id":"deployment","dir":"Articles","previous_headings":"Further Concerns","what":"Deployment","title":"teal.data with Python","text":"Python interpreter (Python environment described ) need available deploying app. recommend following example see can done.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/testing-delayed-data.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Examining Delayed Data Objects","text":"delayed data object created described Delayed Data Objects, teal.data provides useful set functions examine object outside shiny application, .e. global environment. exhaustive list functions: basic function get_dataname returns name dataset datasets delayed data object: delayed data objects described also contain launch method can used test data loading screen: also pull method test data can loaded without launching shiny app. See Delayed Data Advanced. Alternatively teal.data provides load_dataset function <...>Dataset<...> objects used pull data without launching delayed loading screen, load_datasetsfunction <...>Data<...> objects launches delayed loading screen used pull datasets connection. loading data, can checked data successfully pulled using is_pulled function:","code":"library(teal.data) library(magrittr) adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) get_dataname(adsl) # \"ADSL\" ## [1] \"ADSL\" adae_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = adae_cf, keys = get_cdisc_keys(\"ADAE\") ) delayed_data <- cdisc_data(adsl, adae) ## Warning: The `data_objects` argument of `teal_data()` should use data directly. Using ## TealDatasetConnector and TealDataset is deprecated. Find more information on ## https://github.com/insightsengineering/teal/discussions/945 as of teal.data ## 0.3.1. ## ℹ The deprecated feature was likely used in the teal.data package. ## Please report the issue at ## . ## This warning is displayed once every 8 hours. ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was ## generated. get_dataname(delayed_data) # \"ADSL\" \"ADAE\" ## [1] \"ADSL\" \"ADAE\" if (interactive()) { delayed_data$launch() } if (interactive()) { load_datasets(delayed_data) } is_pulled(delayed_data) ## [1] FALSE"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/testing-delayed-data.html","id":"aside-loading-page-ui","dir":"Articles","previous_headings":"Overview","what":"Aside: Loading page UI","title":"Examining Delayed Data Objects","text":"possible set default values boxes loading page using set_ui_input method:","code":"adae$set_ui_input(function(ns) { list(numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 5)) })"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/testing-delayed-data.html","id":"testing-data-loading-continued","dir":"Articles","previous_headings":"Overview","what":"Testing data loading continued","title":"Examining Delayed Data Objects","text":"data loaded, ’s also possible access individual dataset objects using get_dataset function, <...>Data<...> objects, retrieve dataset objects using get_datasets function: Note connector loaded, result dataset object: view raw dataframe object, use get_raw_data function: get_code function called check processing code expected (reproducibility). See section pre-processing Delayed Data specify additional code instructions transform delayed data also added output get_code.","code":"lapply(delayed_data$get_items(), function(item) item$pull()) # return a particular dataset by name get_dataset(delayed_data, dataname = \"ADSL\") # or return all datasets load_datasets(delayed_data) get_datasets(delayed_data) # \"CDISCTealDatasetConnector\" \"TealDatasetConnector\" \"R6\" class(adsl) ## [1] \"CDISCTealDatasetConnector\" \"TealDatasetConnector\" ## [3] \"R6\" # \"CDISCTealDataset\" \"TealDataset\" \"R6\" class(get_dataset(adsl)) ## [1] \"CDISCTealDataset\" \"TealDataset\" \"R6\" # for a single <...>Dataset<..> object head(get_raw_data(adsl), 2) ## # A data frame: 2 × 55 ## STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL ## * ## 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y ## 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N ## # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , ## # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , ## # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , ## # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , ## # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , ## # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , ## # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , … # or for a <...>Data<...> object containing multiple datasets, specify the name of the dataset of interest raw <- get_raw_data(delayed_data, \"ADSL\") head(raw, 2) ## # A data frame: 2 × 55 ## STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL ## * ## 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y ## 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N ## # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , ## # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , ## # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , ## # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , ## # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , ## # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , ## # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , … # note the raw data is now just a regular R table class(raw) ## [1] \"tbl_df\" \"tbl\" \"data.frame\" get_code(delayed_data) ## [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\\nADAE <- teal.data::example_cdisc_data(dataname = \\\"ADAE\\\")\""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/testing-delayed-data.html","id":"aside-piping-functions","dir":"Articles","previous_headings":"Overview","what":"Aside: Piping functions","title":"Examining Delayed Data Objects","text":"examples covered basic piping, natural sequence loading inspection delayed data object. reason, magrittr pipe %>% works well many pre-processing tasks. Since functions modify (operate ) objects given , need assign result. introduction pipes, refer documentation %>% resources pipes.","code":"library(teal.data) library(magrittr) adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) %>% mutate_dataset(\"ADSL$TRTDUR <- round(as.numeric(ADSL$TRTEDTM - ADSL$TRTSDTM), 1)\") %>% load_dataset() %>% get_raw_data() %>% head(n = 2) ## # A data frame: 2 × 56 ## STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL ## * ## 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y ## 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N ## # ℹ 45 more variables: INVID , INVNAM , ARM , ARMCD , ## # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , ## # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , ## # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , ## # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , ## # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , ## # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , …"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Creating Delayed Data Classes (Advanced)","text":"teal.data provides several ways include datasets shiny applications. Normally, one develops application way data available app starts. always involves passing data.frame objects using cdisc_data teal_data functions shiny application. way building app applicable data physically available app created. Including data shiny app global objects means fixed won’t change throughout life application session. possible scenario data may available creation initialization application. data need loaded shiny application initialized, may also involve entering user name password credentials via shiny UI components. Delayed data loading applications involves specifying metadata stores information needed pull data right source. delayed data loading applications, main app loads user prompted data loading UI. means delayed data applications can two-staged: Data loading app Main app","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-key-definitions","dir":"Articles","previous_headings":"","what":"Key definitions","title":"Creating Delayed Data Classes (Advanced)","text":"following general descriptions main classes teal.data package. TealDataset contains physical data form single data.frame plus reproducible code. TealDatasetConnector contains instructions obtain single TealDataset object. TealDataConnection opens closes connections (remote data sources). TealDataConnector contains arbitrary many TealDatasetConnector objects optionally one TealDataConnection object. TealData contains arbitrary many TealDataset, TealDatasetConnector / TealDataConnector objects. exception TealDataConnection, classes CDISC equivalent, e.g. TealData -> CDISCTealData.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-callablefunction","dir":"Articles","previous_headings":"Creating an app > Callable","what":"CallableFunction","title":"Creating Delayed Data Classes (Advanced)","text":"class won’t used often developers ’s essential connectors store execute R functions feature get code reproduce function calls. example object class CallableFunction created runs example_cdisc_data function arguments specified user. ’s also possible execute fun$run() function arguments added fly named list. Dynamic arguments won’t reflected reproducible code, consequences places - get back later stages documentation. CallableFunction can also depend R objects example function depends ADSL. function can executed specific environment can copy objects needed execute call. include objects function call, one use $assign_to_env() copy object $set_args(list(ADSL = .name(ADSL))) link object function argument.","code":"library(teal.data) #> Loading required package: shiny # initialize object fun <- callable_function(fun = teal.data::example_cdisc_data) # set arguments to function fun$set_args(list(dataname = \"ADSL\")) # execute function with arguments set df <- fun$run() head(df, 2) #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 14.424934 #> 2 C: Combination B: Placebo C: Combination Asia C S1 4.055463 #> BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 MEDIUM Y Y Y Y N 2019-02-22 2019-02-24 11:09:25 #> 2 LOW Y Y N N Y 2019-02-26 2019-02-26 09:05:10 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-12 04:28:08 2019-02-24 11:09:25 2021-02-11 22:28:08 #> 2 2022-02-26 03:05:10 2019-02-26 09:05:10 2021-02-25 21:05:10 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-11 22:28:08 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2021-02-25 21:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 DISCONTINUED #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-12 1084 DEATH 2022-03-06 ADVERSE EVENT ADVERSE EVENT #> 2 COMPLETED 2022-02-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT #> 1 22 <=30 2022-03-06 1105 Yes #> 2 NA 2022-03-17 NA # check reproducible code cat(fun$get_call()) #> teal.data::example_cdisc_data(dataname = \"ADSL\") # initialize object fun <- callable_function(fun = teal.data::example_cdisc_data) # add arguments on the fly df <- fun$run(args = list(dataname = \"ADAE\")) head(df, 2) #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM ARM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe A: Drug X #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe A: Drug X #> ARMCD ACTARM ACTARMCD TRT01P TRT01A TRT02P TRT02A #> 1 ARM A A: Drug X ARM A A: Drug X A: Drug X B: Placebo A: Drug X #> 2 ARM A A: Drug X ARM A A: Drug X A: Drug X B: Placebo A: Drug X #> REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL #> 1 South America B S2 6.462991 LOW Y Y Y N #> 2 South America B S2 6.462991 LOW Y Y Y N #> AEWITHFL RANDDT TRTSDTM TRTEDTM #> 1 N 2020-11-03 2020-11-04 04:08:58 2022-02-20 03:33:55 #> 2 N 2020-11-03 2020-11-04 04:08:58 2022-02-20 03:33:55 #> TRT01SDTM TRT01EDTM TRT02SDTM #> 1 2020-11-04 04:08:58 2021-02-19 21:33:55 2021-02-19 21:33:55 #> 2 2020-11-04 04:08:58 2021-02-19 21:33:55 2021-02-19 21:33:55 #> TRT02EDTM AP01SDTM AP01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> AP02SDTM AP02EDTM EOSSTT EOTSTT EOSDT #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED DISCONTINUED 2022-02-20 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED DISCONTINUED 2022-02-20 #> EOSDY DCSREAS DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 #> 1 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT 24 <=30 #> 2 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT 24 <=30 #> LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM AELLT #> 1 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 llt B.2.1.2.1 #> 2 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 llt D.1.1.4.2 #> AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV AESER #> 1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE N #> 2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE N #> AEACN AEREL AEOUT AESDTH AESCONG AESDISAB AESHOSP #> 1 DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y N #> 2 DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y N #> AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM AENDTM ASTDY #> 1 N N Y Y 2021-04-15 04:08:58 2021-10-04 04:08:58 162 #> 2 N N Y N 2021-05-19 04:08:58 2021-10-31 04:08:58 196 #> AENDY LDOSEDTM LDRELTM AETOXGR SMQ01NAM SMQ02NAM SMQ01SC #> 1 334 2020-11-07 09:05:04 228663.896 3 #> 2 361 2021-05-17 07:21:09 2687.814 3 #> SMQ02SC CQ01NAM ANL01FL AERELNST AEACNOTH #> 1 Y NONE PROCEDURE/SURGERY #> 2 Y CONCURRENT ILLNESS MEDICATION # dynamic arguments not reflected in the call cat(fun$get_call()) #> teal.data::example_cdisc_data() adsl_raw <- teal.data::example_cdisc_data(dataname = \"ADSL\") fun <- callable_function(fun = function(adsl) { adsl_2 <- adsl adsl_2$new_col <- TRUE adsl_2 }) # copy adsl to CallableFunction environment fun$assign_to_env(\"adsl\", adsl_raw) # set arguments fun$set_args(args = list(adsl = as.name(\"adsl\"))) # execute function df <- fun$run() head(df, 2) #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 14.424934 #> 2 C: Combination B: Placebo C: Combination Asia C S1 4.055463 #> BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 MEDIUM Y Y Y Y N 2019-02-22 2019-02-24 11:09:25 #> 2 LOW Y Y N N Y 2019-02-26 2019-02-26 09:05:10 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-12 04:28:08 2019-02-24 11:09:25 2021-02-11 22:28:08 #> 2 2022-02-26 03:05:10 2019-02-26 09:05:10 2021-02-25 21:05:10 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-11 22:28:08 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2021-02-25 21:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 DISCONTINUED #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-12 1084 DEATH 2022-03-06 ADVERSE EVENT ADVERSE EVENT #> 2 COMPLETED 2022-02-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT new_col #> 1 22 <=30 2022-03-06 1105 Yes TRUE #> 2 NA 2022-03-17 NA TRUE # get R code fun$get_call() #> [1] \"(function(adsl) {\\n adsl_2 <- adsl\\n adsl_2$new_col <- TRUE\\n adsl_2\\n})(adsl = adsl)\""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-callablecode","dir":"Articles","previous_headings":"Creating an app","what":"CallableCode","title":"Creating Delayed Data Classes (Advanced)","text":"simpler version Callable class CallableCode. Similar CallableFunction, CallableCode stores code can evaluated using run() isn’t able use dynamic arguments make code general. CallableCode also allows assignment objects environment. CallableCode can contain multiple lines (commands) code also allows library calls. Please note objects assigned independent environment can’t modified locked immediately. means CallableCode created allowed make changes x1.","code":"code <- callable_code( \"library(teal.data) ADTTE <- teal.data::example_cdisc_data(\\\"ADTTE\\\") ADTTE$x1 <- x1 ADTTE <- dplyr::filter(ADTTE, PARAMCD %in% c('EFS', 'OS'))\" ) # examine call cat(code$get_call()) #> library(teal.data) #> ADTTE <- teal.data::example_cdisc_data(\"ADTTE\") #> ADTTE$x1 <- x1 #> ADTTE <- dplyr::filter(ADTTE, PARAMCD %in% c(\"EFS\", \"OS\")) # assign x1 to environment (otherwise code would run with error as x1 would not be defined) code$assign_to_env(\"x1\", 1) # evaluate call df <- code$run() head(df$x1, 2) #> [1] 1 1"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-tealdataset-base-class-which-cdisctealdataset-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealDataset (base class which CDISCTealDataset inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"TealDataset R6 class keeps data.frame raw_data slot. One can create TealDataset including data.frame setting data attributes. example first create adsl put data.frame cdisc_dataset function. Together data.frame one also provide dataname optional code reproduce data reproducibility required. Note cdisc_dataset returns object CDISCTealDataset, needed CDISC analysis. object created contains previously defined attributes can extracted.","code":"library(magrittr) adsl_raw <- teal.data::example_cdisc_data(\"ADSL\") %>% head(3) adsl_dataset <- cdisc_dataset( dataname = \"ADSL\", x = adsl_raw, code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\") %>% head(3)\" ) # check if code is reproducible get_dataname(adsl_dataset) #> [1] \"ADSL\" # get label get_dataset_label(adsl_dataset) #> [1] \"Subject Level Analysis Dataset\" # get reproducible code get_code(adsl_dataset) #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\") %>% head(3)\" # get data.frame get_raw_data(adsl_dataset) #> # A tibble: 3 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-CH… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-CH… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-RU… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , #> # AP01SDTM , AP01EDTM , AP02SDTM , AP02EDTM , … # get keys (i.e. the primary keys of the dataset) adsl_dataset$get_keys() #> [1] \"STUDYID\" \"USUBJID\""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-tealdatasetconnector-base-class-which-cdisctealdatasetconnector-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealDatasetConnector (base class which CDISCTealDatasetConnector inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"TealDatasetConnector contains Callable object obtain single TealDataset object. code chunk , connector created based example_cdisc_data function. Initially, adsl_conn doesn’t contain data. Attempting fetch unavailable data produce error. Data can loaded using load_dataset() function. data loaded, adsl_conn contains reproducible code also code pull data. TealDatasetConnector also allows variables passed Callable object may depend . code adsl_raw object - created - added CallableFunction. properly link ADSL argument function inside CallableFunction object raw data adsl_raw several parameters match: .name(\"dummy_name\") must value name \"ADSL\" - set_args(list(ADSL = .name(\"dummy_name\"))) dummy_name must linked raw data adsl_raw - vars = list(dummy_name = adsl_raw) name ADSL fixed name argument function inside CallableFunction. name dummy_name free valid R name. TealDatasetConnector like delayed data objects contains launch method can used obtain data using shiny application. function can used check objects specified correctly investigate potential mistakes. default shiny app won’t render inputs datasets specify . set inputs use $set_ui_input(), passing UI module function, ns argument (shiny namespace ID object). example , callable_function object contains two arguments, ADSL n. ADSL given n entered shiny app launch method called.","code":"adsl_conn <- dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"Subject-Level Analysis Dataset\" ) # get raw data try(get_raw_data(adsl_conn)) #> Error : 'ADSL' has not been pulled yet #> - please use `load_dataset()` first. # execution/reproducible code get_code(adsl_conn) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" # pull data load_dataset(adsl_conn) # get raw data get_raw_data(adsl_conn) #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … # here we use the general dataset_connector function which pulls an object of type TealDataset # there is also a cdisc_dataset_connector function which pulls an object of type CDISCTealDataset adsl_2 <- dataset_connector( dataname = \"ADSL_2\", pull_callable = callable_function(fun = function(ADSL) ADSL_2 <- ADSL) %>% # nolint set_args(list(ADSL = as.name(\"dummy_name\"))), keys = get_cdisc_keys(\"ADSL\"), label = \"Example label\", vars = list(dummy_name = adsl_raw) ) load_dataset(adsl_2) adsl_3 <- dataset_connector( dataname = \"ADSL_3\", pull_callable = callable_function(fun = function(ADSL, n) ADSL_3 <- head(ADSL, n)) %>% # nolint set_args(list(ADSL = as.name(\"ADSL\"))), keys = get_cdisc_keys(\"ADSL\"), label = \"Example label\", vars = list(ADSL = adsl_raw) ) adsl_3$set_ui_input(function(ns) { list( numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1) ) }) if (interactive()) { adsl_3$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-tealdataconnection","dir":"Articles","previous_headings":"Creating an app","what":"TealDataConnection","title":"Creating Delayed Data Classes (Advanced)","text":"Objects class responsible set connection remote data sources. TealDataConnection opens closes connections calling CallableFunction appropriate arguments. Note app pulls data remote source, outputs change even code data remote source changes. shiny applications, connection arguments need linked inputs, TealDataConnection contains module. Developers can customize UI inputs open connection using set_open_ui() specify relevant server function using set_open_server(). ’s important keep mind server module needs connection argument open() close() needed.","code":"open_fun <- callable_function(data.frame) # define opening function open_fun$set_args(list(x = 1:5)) # define fixed arguments to opening function close_fun <- callable_function(sum) # define closing function close_fun$set_args(list(x = 1:5)) # define fixed arguments to closing function ping_fun <- callable_function(function() TRUE) x <- data_connection( ping_fun = ping_fun, # define ping function open_fun = open_fun, # define opening function close_fun = close_fun # define closing function )"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-tealdataconnector-base-class-which-cdisctealdataconnector-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealDataConnector (base class which CDISCTealDataConnector inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"class combines multiple TealDatasetConnector (CDISCTealDatasetConnector) single TealDataConnection object. creates module manage connection load data. create two TealDatasetConnector objects TealDataConnection object combine together TealDataConnector object. object created can used pull data obtain code. combines code pull datasets preceded open connection code followed close connection code. Please note TealDataConnector doesn’t limit kind connectors set within, one must aware rather contain similar connectors (.e. calling functions share arguments). example, execute data$set_pull_args(args = list(n = 5)), argument set connectors. case connector contains CallableFunction doesn’t n formals fail. CallableCode can’t hold additional arguments ’s fixed ignore every arguments set set_pull_args. default TealDataConnector creates simple shiny module without inputs arguments callable_function connectors. means , opening, closing, pulling datasets done default arguments. However, users can easily extend module using set_ui() set_server() specify UI server function . general rule creating modules callback server UI possible, server module executed submit button clicked. see set_preopen_server TealDataConnection object slight relaxation rule. extend app interface adding text input passed scda function. UI created conn connectors object server module requires connectors connection objects additional arguments. Executing data$launch() open shiny application prompts user input load data. Remember data can loaded . run code data$pull() please reinitialize connectors, connection data object running code .","code":"# create TealDatasetConnectors slice_example_cdisc_data <- function(dataname, n) { teal.data::example_cdisc_data(dataname) %>% head(n) } adsl <- dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(slice_example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"Subject-Level Analysis Dataset\" ) adsl_3 <- dataset_connector( dataname = \"ADSL_3\", pull_callable = callable_function(fun = function(ADSL, n = 5) { # nolint ADSL_3 <- head(ADSL, n) # nolint }) %>% set_args(list(ADSL = as.name(\"ADSL\"))), keys = get_cdisc_keys(\"ADSL\"), label = \"Example label\", vars = list(ADSL = adsl) ) adsl_3$set_ui_input(function(ns) { list( numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1) ) }) connectors <- list(adsl, adsl_3) # create connection open_fun <- callable_function(fun = library) open_fun$set_args(list(package = \"teal.data\")) conn <- teal.data:::TealDataConnection$new(open_fun = open_fun) # nolint # create TealDataConnector data <- teal.data:::TealDataConnector$new( connection = conn, connectors = connectors ) cat(get_code(data)) #> library(package = \"teal.data\") #> ADSL <- (function(dataname, n) { #> teal.data::example_cdisc_data(dataname) %>% head(n) #> })(dataname = \"ADSL\") #> ADSL_3 <- (function(ADSL, n = 5) { #> ADSL_3 <- head(ADSL, n) #> })(ADSL = ADSL) # pull ADSL and ADSL_3 data$set_pull_args(args = list(n = 5)) data$pull() data$set_ui( function(id, ...) { ns <- NS(id) tagList( conn$get_open_ui(ns(\"open_connection\")), textInput(ns(\"name\"), p(\"Choose\", code(\"name\")), value = \"latest\"), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) data$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection if (!is.null(connection$get_open_server())) { connection$get_open_server()( id = \"open_connection\", connection = connection ) } for (connector in connectors) { # set_args before to return them in the code (fixed args) set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } ) } ) if (interactive()) { data$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-tealdata-base-class-which-cdisctealdata-inherits-from","dir":"Articles","previous_headings":"Creating an app","what":"TealData (base class which CDISCTealData inherits from)","title":"Creating Delayed Data Classes (Advanced)","text":"TealData manages TealDataset, TealDatasetConnector / TealDataConnector objects. CDISCTealData equivalent object creating apps analyze CDISC data. objects created using teal_data cdisc_data respectively. using teal package objects passed data argument init. One can combine multiple delayed data objects using [teal|cdisc]_data functions include shiny application. TealData gathers objects sets combined UI shiny inputs objects. code chunk specified four dataset connectors, works arbitrary many objects combination classes TealDataset, TealDatasetConnector / TealDataConnector. TealData also contains launch() method investigate data set correctly. However, TealData lacks pull() method. Reproducible code attached data object combined code components, one can also extract code single dataset specifying dataname argument. Developers can also extract datasets connectors included TealData.","code":"data <- cdisc_data( cdisc_dataset( dataname = \"ADSL\", teal.data::example_cdisc_data(dataname = \"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" ), cdisc_dataset( dataname = \"ADTTE\", teal.data::example_cdisc_data(\"ADTTE\"), code = \"ADTTE <- teal.data::example_cdisc_data(dataname = \\\"ADTTE\\\")\" ) ) #> Warning: The `data_objects` argument of `teal_data()` should use data directly. Using #> TealDatasetConnector and TealDataset is deprecated. Find more information on #> https://github.com/insightsengineering/teal/discussions/945 as of teal.data #> 0.3.1. #> ℹ The deprecated feature was likely used in the teal.data package. #> Please report the issue at #> . #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was #> generated. # nolint start example_cdisc_dataset_connector <- function(dataname) { cdisc_dataset_connector( dataname = dataname, pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = dataname)), keys = get_cdisc_keys(dataname), label = sprintf(\"%s connector\", dataname) ) } adsl <- example_cdisc_dataset_connector(\"ADSL\") adae <- example_cdisc_dataset_connector(\"ADAE\") advs <- example_cdisc_dataset_connector(\"ADVS\") adtte <- example_cdisc_dataset_connector(\"ADTTE\") data <- cdisc_data(adsl, adae, advs, adtte) # nolint end if (interactive()) { data$launch() } get_code(data) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\\nADAE <- teal.data::example_cdisc_data(dataname = \\\"ADAE\\\")\\nADVS <- teal.data::example_cdisc_data(dataname = \\\"ADVS\\\")\\nADTTE <- teal.data::example_cdisc_data(dataname = \\\"ADTTE\\\")\" get_code(data, dataname = \"ADSL\") #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" get_code(data, dataname = \"ADTTE\") #> [1] \"ADTTE <- teal.data::example_cdisc_data(dataname = \\\"ADTTE\\\")\" # if you launched the shiny app and pressed the submit button above to load the data, # then these 4 lines do not need to be run adsl$pull() adae$pull() advs$pull() adtte$pull() # get loaded datasets data$get_datasets() # get single dataset data$get_dataset(dataname = \"ADSL\") # get data and dataset connectors data$get_connectors() # get all datasets/connectors data$get_items()"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-data-modification","dir":"Articles","previous_headings":"Creating an app","what":"Data modification","title":"Creating Delayed Data Classes (Advanced)","text":"modify single dataset one use mutate_dataset specifying code argument code single character script location script file. case delayed data, pre-processing code passed mutate_dataset run data becomes available. get_code() function returns loading code CallableFunction mutation code provided using mutate_dataset. mutate_dataset can also used TealData objects applies code dataset specified dataname. important, TealData can track call affects particular dataset. Check code , create data containing two datasets using cdisc_data function. can still use mutate_dataset object contains multiple datasets, one requirement - one needs specify dataname. Afterwards, one can extract reproducible code data affects particular dataname. One can also pipe multiple mutate_dataset calls applied different datasets. Sometimes code one object can depend another, case can link way link TealDatasetConnector objects. object code dependent another, ADTTE depends ADSL , get_code return everything need executed reproduce dataset. Using mutate_dataset creates tree calls, can subset dataname, developers can also use mutate_data function doesn’t require dataname specified. mutate_data used, code single dataset possible subset, instead code datasets returned.","code":"adsl <- cdisc_dataset( dataname = \"ADSL\", teal.data::example_cdisc_data(dataname = \"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" ) %>% mutate_dataset(code = \"ADSL$x1 <- 1\") cat(get_code(adsl)) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 data <- cdisc_data(adsl, adtte) %>% mutate_dataset(code = \"ADSL$x3 <- 3\", dataname = \"ADSL\") # get reproducible code of all datasets cat(get_code(data)) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 # get ADSL reproducible code cat(get_code(data, dataname = \"ADSL\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADSL$x3 <- 3 data <- mutate_dataset(data, code = \"ADTTE$x4 <- 4\", dataname = \"ADTTE\") %>% mutate_dataset(code = \"ADSL <- dplyr::filter(ADSL, SEX == 'F')\", dataname = \"ADSL\") cat(get_code(data, \"ADSL\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADSL$x3 <- 3 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") # note that the code for ADTTE below does not contain any mention of ADSL cat(get_code(data, \"ADTTE\")) #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADTTE$x4 <- 4 data <- mutate_dataset( data, code = \"ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID)\", dataname = \"ADTTE\", vars = list(ADSL = adsl) # vars = list( = )) ) %>% mutate_dataset(\"ADSL$var_created_after <- NA\", dataname = \"ADSL\") # note that the code that defines ADSL is now part of the code of ADTTE below cat(get_code(data, dataname = \"ADTTE\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 #> ADTTE$x4 <- 4 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") #> ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID) # moreover, note that the code inserted to the mutate_dataset after the pipe was not included. data <- mutate_data(data, code = \" ADSL$x3 <- 3 proxy_var <- 4 ADTTE$x4 <- proxy_var \" ) # single dataset code is not possible to obtain anymore cat(adsl_code <- get_code(data, \"ADSL\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 #> ADTTE$x4 <- 4 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") #> ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID) #> ADSL$var_created_after <- NA #> ADSL$x3 <- 3 #> proxy_var <- 4 #> ADTTE$x4 <- proxy_var cat(adtte_code <- get_code(data, \"ADTTE\")) #> ADSL <- teal.data::example_cdisc_data(dataname = \"ADSL\") #> ADSL$x1 <- 1 #> ADTTE <- teal.data::example_cdisc_data(dataname = \"ADTTE\") #> ADSL$x3 <- 3 #> ADTTE$x4 <- 4 #> ADSL <- dplyr::filter(ADSL, SEX == \"F\") #> ADTTE <- filter(ADTTE, USUBJID %in% ADSL$USUBJID) #> ADSL$var_created_after <- NA #> ADSL$x3 <- 3 #> proxy_var <- 4 #> ADTTE$x4 <- proxy_var # TRUE as.character(adsl_code) == as.character(adtte_code) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-advanced.html","id":"section-teal-data-in-a-shiny-app","dir":"Articles","previous_headings":"Creating an app","what":"teal.data in a shiny app","title":"Creating Delayed Data Classes (Advanced)","text":"","code":"# nolint start library(teal.data) library(magrittr) slice_example_cdisc_data <- function(dataname, n) { teal.data::example_cdisc_data(dataname) %>% head(n) } adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(slice_example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADSL connector\" ) adrs <- cdisc_dataset_connector( dataname = \"ADRS\", pull_callable = callable_function(slice_example_cdisc_data) %>% set_args(list(dataname = \"ADRS\")), keys = get_cdisc_keys(\"ADRS\"), label = \"ADRS connector\" ) x <- dataset(\"x\", data.frame(x = 1, b = 2), code = \"x <- data.frame(x = 1, b = 2)\") data <- teal_data(adsl, adrs, x) shinyApp( ui = fluidPage( shinyjs::useShinyjs(), titlePanel(\"Delayed data loading\"), sidebarLayout( sidebarPanel(data$get_ui(\"data\"), uiOutput(\"dataset\")), mainPanel(tableOutput(\"dist_plot\")) ) ), server = function(input, output, session) { data_reactive <- data$get_server()(\"data\") observeEvent(data_reactive(), ignoreNULL = TRUE, { shinyjs::hide(\"data-delayed_data\") }) output$dataset <- renderUI({ req(data_reactive()) datanames <- names(get_raw_data(data_reactive())) radioButtons(\"dataname\", \"Select dataname\", datanames, datanames[1]) }) output$dist_plot <- renderTable({ req(input$dataname) dataset <- get_raw_data(data_reactive())[[input$dataname]] head(dataset) }) } ) # nolint end"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-basic.html","id":"basic-understanding","dir":"Articles","previous_headings":"","what":"Basic understanding","title":"Using Delayed Data Loading (Basic)","text":"Delayed data objects R objects contain instructions acquire data. practice, pass DDL objects instructions teal application can launch teal app first pull data afterwards. main difference DDL object non-DDL object data available immediately creating non-DDL object. contrast, data DDL object available construction, pulling (executing instructions stored object).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-basic.html","id":"key-concepts","dir":"Articles","previous_headings":"Basic understanding","what":"Key concepts","title":"Using Delayed Data Loading (Basic)","text":"TealDatasetConnector object used pull single delayed data set teal app. Connectors pull data proprietary data storage included package. TealDataConnector object used pull set delayed data sets teal app share common connection (see Delayed Data Loading definition connection object). cdisc_data function takes set TealDataConnector, TealDatasetConnector / cdisc_datasets (non-delayed datasets) create TealData object used create teal applications.","code":"# nolint start library(teal.data) # generalized function to create delayed data from code - see package help for other connectors x <- code_dataset_connector( dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) # nolint end # nolint start library(teal.data) library(magrittr) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADSL connector\" ) adae <- cdisc_dataset_connector( dataname = \"ADAE\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADAE connector\" ) adsl_adae <- relational_data_connector( connection = data_connection(), connectors = list(adsl, adae) ) # nolint end # nolint start # create a TealDatasetConnector for ADVS library(teal.data) library(magrittr) advs <- cdisc_dataset_connector( dataname = \"ADVS\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADVS\")), keys = get_cdisc_keys(\"ADVS\"), label = \"ADVS connector\" ) # use cdisc_data() to create a `DDL` object delayed_data <- cdisc_data(adsl_adae, advs) ## Warning: The `data_objects` argument of `teal_data()` should use data directly. Using ## TealDatasetConnector and TealDataset is deprecated. Find more information on ## https://github.com/insightsengineering/teal/discussions/945 as of teal.data ## 0.3.1. ## ℹ The deprecated feature was likely used in the teal.data package. ## Please report the issue at ## . ## This warning is displayed once every 8 hours. ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was ## generated. # nolint end"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-basic.html","id":"constructors","dir":"Articles","previous_headings":"Basic understanding","what":"Constructors","title":"Using Delayed Data Loading (Basic)","text":"list constructors available teal.data create TealDataset delayed TealDatasetConnector objects: Notes: xyz_dataset_connector functions equivalent xyz_cdisc_dataset_connector function (example rds_cdisc_dataset_connector) specifies additional dataset metadata. cdisc_data standard function used create data object used within teal apps standard CDISC study data. general teal_data function can used allow arbitrary relational data used within teal apps.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-basic.html","id":"dataset-dependencies","dir":"Articles","previous_headings":"Basic understanding","what":"Dataset dependencies","title":"Using Delayed Data Loading (Basic)","text":"datasets passed teal_data cdisc_data pulled order inputted. datasets depend datasets available placed later argument list:","code":"# nolint start library(teal.data) library(magrittr) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")), keys = get_cdisc_keys(\"ADSL\"), label = \"ADSL connector\" ) adsl_2 <- code_cdisc_dataset_connector(\"ADSL_2\", code = \"head(ADSL, 5)\", keys = get_cdisc_keys(\"ADSL\"), ADSL = adsl ) # launch method will be able to load the data as adsl will be pulled first cdisc_data(adsl, adsl_2) ## A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): ## --> Element 1: ## A CDISCTealDatasetConnector object, named ADSL, containing a TealDataset object that has not been loaded/pulled ## --> Element 2: ## A CDISCTealDatasetConnector object, named ADSL_2, containing a TealDataset object that has not been loaded/pulled # launch method will not be able to load the data as adae is pulled first but it depends on adsl cdisc_data(adsl_2, adsl) ## A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): ## --> Element 1: ## A CDISCTealDatasetConnector object, named ADSL_2, containing a TealDataset object that has not been loaded/pulled ## --> Element 2: ## A CDISCTealDatasetConnector object, named ADSL, containing a TealDataset object that has not been loaded/pulled # nolint end"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/using-delayed-data-basic.html","id":"suggested-development-workflow","dir":"Articles","previous_headings":"","what":"Suggested development workflow","title":"Using Delayed Data Loading (Basic)","text":"following workflow facilitates building teal apps DDL minimizing debugging overhead. Run teal app configured without delayed data verify app starts expected. Replace cdisc_dataset functions appropriate TealDatasetConnector objects. Add preprocessing code (see Delayed Data Advanced preprocessing documentation) verify running newly created object’s $launch method. First, include just single module verify teal app starts loads expected data. , add rest modules one one, replacing dataset calls strings iteratively verify app functions expected.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dawid Kaledkowski. Author, maintainer. Pawel Rucki. Author. Mahmoud Hallal. Author. Nikolas Burkoff. Author. Maciej Nasinski. Author. Konrad Pagacz. Author. Junlue Zhao. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kaledkowski D, Rucki P, Hallal M, Burkoff N, Nasinski M, Pagacz K, Zhao J (2023). teal.data: Data Model 'teal' Applications. R package version 0.3.0.9016, https://github.com/insightsengineering/teal.data/, https://insightsengineering.github.io/teal.data/main/.","code":"@Manual{, title = {teal.data: Data Model for 'teal' Applications}, author = {Dawid Kaledkowski and Pawel Rucki and Mahmoud Hallal and Nikolas Burkoff and Maciej Nasinski and Konrad Pagacz and Junlue Zhao}, year = {2023}, note = {R package version 0.3.0.9016, https://github.com/insightsengineering/teal.data/}, url = {https://insightsengineering.github.io/teal.data/main/}, }"},{"path":"https://insightsengineering.github.io/teal.data/main/index.html","id":"tealdata","dir":"","previous_headings":"","what":"Data Model for teal Applications","title":"Data Model for teal Applications","text":"package used create data needed teal applications. data can : Independent data frames CDISC data (clinical trial reporting) Relational data MultiAssayExperiment objects package provides: mechanism pulling data existing systems ability mutate (.e. pre-process) data record operations used create data enable reproducibility","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Data Model for teal Applications","text":"Alternatively, might want use development version available r-universe.","code":"# stable versions install.packages('teal.data', repos = c('https://insightsengineering.r-universe.dev', getOption('repos'))) # install.packages(\"pak\") pak::pak(\"insightsengineering/teal.data@*release\") # beta versions install.packages('teal.data', repos = c('https://pharmaverse.r-universe.dev', getOption('repos'))) # install.packages(\"pak\") pak::pak(\"insightsengineering/teal.data\")"},{"path":"https://insightsengineering.github.io/teal.data/main/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Data Model for teal Applications","text":"understand use package, please refer Introduction teal.data article, provides multiple examples code implementation. showcase example usage","code":"library(teal.data) # quick start for clinical trial data adsl <- teal.data::example_cdisc_data(\"ADSL\") adtte <- teal.data::example_cdisc_data(\"ADTTE\") my_data <- cdisc_data( cdisc_dataset(\"ADSL\", adsl), cdisc_dataset(\"ADTTE\", adtte) ) # quick start for general data my_general_data <- teal_data( dataset(\"iris\", iris), dataset(\"mtcars\", mtcars) ) # reproducibility check data <- teal_data(dataset(\"iris\", iris, code = \"iris <- mtcars\"), check = TRUE) #> Error in x$check_reproducibility() : Reproducibility check failed. # code extraction iris2 <- iris[1:6, ] iris2_data <- teal_data(dataset(\"iris2\", iris2, code = \"iris2 <- iris[1:6, ]\")) iris2_data$get_code() #> \"iris2 <- iris[1:6, ]\""},{"path":"https://insightsengineering.github.io/teal.data/main/index.html","id":"getting-help","dir":"","previous_headings":"","what":"Getting help","title":"Data Model for teal Applications","text":"encounter bug feature request - please file issue. questions, discussions staying date, please use “teal” channel pharmaverse slack workspace.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/pull_request_template.html","id":null,"dir":"","previous_headings":"","what":"Pull Request","title":"Pull Request","text":"Fixes #nnn","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"Class manages TealDatasetConnector specify additional dynamic arguments open/close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"super-classes","dir":"Reference","previous_headings":"","what":"Super classes","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"teal.data::TealDataAbstract -> teal.data::TealDataConnector -> CDISCTealDataConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"teal.data::TealDataAbstract$check() teal.data::TealDataAbstract$check_reproducibility() teal.data::TealDataAbstract$execute_mutate() teal.data::TealDataAbstract$get_check() teal.data::TealDataAbstract$get_check_result() teal.data::TealDataAbstract$get_code() teal.data::TealDataAbstract$get_datanames() teal.data::TealDataAbstract$get_dataset() teal.data::TealDataAbstract$get_datasets() teal.data::TealDataAbstract$get_items() teal.data::TealDataAbstract$is_pulled() teal.data::TealDataAbstract$mutate_dataset() teal.data::TealDataAbstract$reassign_datasets_vars() teal.data::TealDataAbstract$set_check() teal.data::TealDataAbstract$set_pull_code() teal.data::TealDataConnector$get_code_class() teal.data::TealDataConnector$get_connection() teal.data::TealDataConnector$get_preopen_server() teal.data::TealDataConnector$get_server() teal.data::TealDataConnector$get_ui() teal.data::TealDataConnector$is_failed() teal.data::TealDataConnector$launch() teal.data::TealDataConnector$mutate() teal.data::TealDataConnector$print() teal.data::TealDataConnector$pull() teal.data::TealDataConnector$set_preopen_server() teal.data::TealDataConnector$set_pull_args() teal.data::TealDataConnector$set_server() teal.data::TealDataConnector$set_ui()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"CDISCTealDataConnector$new() CDISCTealDataConnector$get_parent() CDISCTealDataConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"Create new CDISCTealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"","code":"CDISCTealDataConnector$new(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"method-get-parent-","dir":"Reference","previous_headings":"","what":"Method get_parent()","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"Get datasets parent names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"","code":"CDISCTealDataConnector$get_parent()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"(named list) dataset name corresponding parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"","code":"CDISCTealDataConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — CDISCTealDataConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"data.frame object can stored inside object. difference compared TealDataset class parent field indicates name parent dataset. Note parent field might empty (.e. character(0)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"teal.data::TealDataset -> CDISCTealDataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"teal.data::TealDataset$check() teal.data::TealDataset$check_keys() teal.data::TealDataset$get_character_colnames() teal.data::TealDataset$get_code() teal.data::TealDataset$get_code_class() teal.data::TealDataset$get_colnames() teal.data::TealDataset$get_column_labels() teal.data::TealDataset$get_dataname() teal.data::TealDataset$get_datanames() teal.data::TealDataset$get_dataset() teal.data::TealDataset$get_dataset_label() teal.data::TealDataset$get_factor_colnames() teal.data::TealDataset$get_keys() teal.data::TealDataset$get_metadata() teal.data::TealDataset$get_mutate_code_class() teal.data::TealDataset$get_mutate_vars() teal.data::TealDataset$get_ncol() teal.data::TealDataset$get_nrow() teal.data::TealDataset$get_numeric_colnames() teal.data::TealDataset$get_raw_data() teal.data::TealDataset$get_row_labels() teal.data::TealDataset$get_rownames() teal.data::TealDataset$get_var_r6() teal.data::TealDataset$get_vars() teal.data::TealDataset$is_mutate_delayed() teal.data::TealDataset$is_pulled() teal.data::TealDataset$mutate() teal.data::TealDataset$print() teal.data::TealDataset$reassign_datasets_vars() teal.data::TealDataset$set_code() teal.data::TealDataset$set_dataset_label() teal.data::TealDataset$set_keys() teal.data::TealDataset$set_vars()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"CDISCTealDataset$new() CDISCTealDataset$recreate() CDISCTealDataset$get_attrs() CDISCTealDataset$get_parent() CDISCTealDataset$set_parent() CDISCTealDataset$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Create new object CDISCTealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$new( dataname, x, keys, parent, code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys (character) vector primary keys parent optional, (character) parent dataset name code (character) character string defining code needed produce data set x label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"method-recreate-","dir":"Reference","previous_headings":"","what":"Method recreate()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Recreate dataset current attributes useful way access class initialize method basing class object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$recreate( dataname = self$get_dataname(), x = self$get_raw_data(), keys = self$get_keys(), parent = self$get_parent(), code = private$code, label = self$get_dataset_label(), vars = list(), metadata = self$get_metadata() )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys (character) vector primary keys parent optional, (character) parent dataset name code (character) character string defining code needed produce data set x label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"new object CDISCTealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"method-get-attrs-","dir":"Reference","previous_headings":"","what":"Method get_attrs()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Get dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$get_attrs()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"(named list) dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"method-get-parent-","dir":"Reference","previous_headings":"","what":"Method get_parent()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Get parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$get_parent()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"(character) indicating parent dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"method-set-parent-","dir":"Reference","previous_headings":"","what":"Method set_parent()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"Set parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$set_parent(parent)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"parent (character) indicating parent dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"CDISCTealDataset$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class representing a dataset with parent attribute — CDISCTealDataset","text":"","code":"x <- cdisc_dataset( dataname = \"XYZ\", x = data.frame(x = c(1, 2), y = c(\"a\", \"b\"), stringsAsFactors = FALSE), keys = \"y\", parent = \"ABC\", code = \"XYZ <- data.frame(x = c(1, 2), y = c('aa', 'bb'), stringsAsFactors = FALSE)\", metadata = list(type = \"example\") ) x$ncol #> NULL x$get_code() #> [1] \"XYZ <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\" x$get_dataname() #> [1] \"XYZ\" x$get_keys() #> [1] \"y\" x$get_parent() #> [1] \"ABC\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Objects class store connection function fetch single dataset. difference compared TealDatasetConnector parent field indicates name parent dataset. Note parent field might empty (.e. character(0)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"teal.data::TealDatasetConnector -> CDISCTealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"teal.data::TealDatasetConnector$check() teal.data::TealDatasetConnector$get_code() teal.data::TealDatasetConnector$get_code_class() teal.data::TealDatasetConnector$get_dataname() teal.data::TealDatasetConnector$get_datanames() teal.data::TealDatasetConnector$get_dataset() teal.data::TealDatasetConnector$get_dataset_label() teal.data::TealDatasetConnector$get_error_message() teal.data::TealDatasetConnector$get_keys() teal.data::TealDatasetConnector$get_pull_args() teal.data::TealDatasetConnector$get_pull_callable() teal.data::TealDatasetConnector$get_raw_data() teal.data::TealDatasetConnector$get_server() teal.data::TealDatasetConnector$get_ui() teal.data::TealDatasetConnector$get_var_r6() teal.data::TealDatasetConnector$is_failed() teal.data::TealDatasetConnector$is_mutate_delayed() teal.data::TealDatasetConnector$is_pulled() teal.data::TealDatasetConnector$launch() teal.data::TealDatasetConnector$mutate() teal.data::TealDatasetConnector$print() teal.data::TealDatasetConnector$reassign_datasets_vars() teal.data::TealDatasetConnector$set_args() teal.data::TealDatasetConnector$set_dataset_label() teal.data::TealDatasetConnector$set_keys() teal.data::TealDatasetConnector$set_ui_input()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"CDISCTealDatasetConnector$new() CDISCTealDatasetConnector$get_parent() CDISCTealDatasetConnector$pull() CDISCTealDatasetConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Create new TealDatasetConnector object. Set pulling function CallableFunction returns data.frame, e.g. reading function creating fly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$new( dataname, pull_callable, keys, parent, code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys (character) vector dataset primary keys column names parent optional, (character) parent dataset name code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script label (character) Label describe dataset. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"method-get-parent-","dir":"Reference","previous_headings":"","what":"Method get_parent()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Get parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$get_parent()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"(character) indicating parent dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"method-pull-","dir":"Reference","previous_headings":"","what":"Method pull()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"Pull data Read create data using pull_callable specified constructor.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$pull(args = NULL, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"args (NULL named list) additional dynamic arguments pull function. args can omitted pull_callable constructor already contains necessary arguments pull data. One can try execute pull_callable directly x$pull_callable$run() get code using x$pull_callable$get_code(). args specified pull used temporary get data saved code. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"self invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"","code":"CDISCTealDatasetConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CDISCTealDatasetConnector.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CDISCTealDatasetConnector class of objects — CDISCTealDatasetConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/Callable.html","id":null,"dir":"Reference","previous_headings":"","what":"A Callable class of objects — Callable","title":"A Callable class of objects — Callable","text":"Object stores function name arguments. Methods get call run .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/Callable.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A Callable class of objects — Callable","text":"Callable$new() Callable$assign_to_env() Callable$run() Callable$is_failed() Callable$get_error_message() Callable$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/Callable.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A Callable class of objects — Callable","text":"Create new CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/Callable.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A Callable class of objects — Callable","text":"","code":"Callable$new(env)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/Callable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A Callable class of objects — Callable","text":"env (environment) environment call evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/Callable.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A Callable class of objects — Callable","text":"new CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/Callable.html","id":"method-assign-to-env-","dir":"Reference","previous_headings":"","what":"Method assign_to_env()","title":"A Callable class of objects — Callable","text":"Assigns x <- value object env. 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Class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"Code Class — CodeClass","text":"code (list) Derive code dataset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Code Class — CodeClass","text":"CodeClass$new() CodeClass$append() CodeClass$set_code() CodeClass$get_code() CodeClass$eval() CodeClass$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Code Class — CodeClass","text":"CodeClass constructor","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$new( code = character(0), dataname = character(0), deps = character(0) )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"code (character) vector code text set dataname optional, (character) vector datanames assign code . empty code considered \"global\" deps optional, (character) vector datanames given code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"object class CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"method-append-","dir":"Reference","previous_headings":"","what":"Method append()","title":"Code Class — CodeClass","text":"Append CodeClass object given CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$append(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"x (CodeClass) object appended","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"changed CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"method-set-code-","dir":"Reference","previous_headings":"","what":"Method set_code()","title":"Code Class — CodeClass","text":"Set code form character","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$set_code(code, dataname = character(0), deps = character(0))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"code (character) vector code text set dataname optional, (character) vector datanames assign code . empty code considered \"global\" deps optional, (character) vector datanames given code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"changed CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"Code Class — CodeClass","text":"Get code given data names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$get_code(dataname = NULL, deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"dataname optional, (character) vector datanames code extracted. NULL get code data names deparse optional, (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"character list calls","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"method-eval-","dir":"Reference","previous_headings":"","what":"Method eval()","title":"Code Class — CodeClass","text":"Evaluates internal code within given environment","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$eval(envir = new.env(parent = parent.env(.GlobalEnv)))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"envir (environment) environment code evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"Code Class — CodeClass","text":"invisibly NULL","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Code Class — CodeClass","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Code Class — CodeClass","text":"","code":"CodeClass$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code Class — CodeClass","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/CodeClass.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Code Class — CodeClass","text":"","code":"cc <- teal.data:::CodeClass$new() cc$set_code(c(\"foo <- function() {1}\", \"foo2 <- function() {2}\")) cc$get_code() #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\" cc$get_code(deparse = FALSE) #> [[1]] #> foo <- function() { #> 1 #> } #> #> [[2]] #> foo2 <- function() { #> 2 #> } #> cc$set_code(c(\"DF <- data.frame(x = 1:10)\", \"DF$y <- 1\"), \"DF\") cc$set_code(\"DF$a <- foo()\", \"DF\") # dependent dataset cc$set_code(c(\"DF2 <- data.frame(x2 = 1:10)\", \"DF2$y2 <- DF$y\"), \"DF2\", deps = \"DF\") cc$set_code(\"baz <- function() {2}\") cc$set_code(\"DF2$a <- baz()\", \"DF2\") cc$get_code() #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\\nDF <- data.frame(x = 1:10)\\nDF$y <- 1\\nDF$a <- foo()\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$y2 <- DF$y\\nbaz <- function() {\\n 2\\n}\\nDF2$a <- baz()\" cc$get_code(\"DF\") #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\\nDF <- data.frame(x = 1:10)\\nDF$y <- 1\\nDF$a <- foo()\" cc$get_code(\"DF2\") #> [1] \"foo <- function() {\\n 1\\n}\\nfoo2 <- function() {\\n 2\\n}\\nDF <- data.frame(x = 1:10)\\nDF$y <- 1\\nDF$a <- foo()\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$y2 <- DF$y\\nbaz <- function() {\\n 2\\n}\\nDF2$a <- baz()\" x1 <- teal.data:::CodeClass$new() x1$set_code(\"DF <- data.frame(x = 1:10)\", \"DF\") x1$get_code() #> [1] \"DF <- data.frame(x = 1:10)\" x2 <- teal.data:::CodeClass$new() x2$set_code(c(\"DF2 <- data.frame(x2 = 1:10)\", \"DF2$x2 <- DF$x\"), \"DF2\", deps = \"DF\") x2$get_code() #> [1] \"DF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x <- teal.data:::CodeClass$new() x$append(x1) x$append(x2) x$get_code() #> [1] \"DF <- data.frame(x = 1:10)\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x$get_code(\"DF\") #> [1] \"DF <- data.frame(x = 1:10)\" x$get_code(\"DF2\") #> [1] \"DF <- data.frame(x = 1:10)\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x$get_code(c(\"DF\", \"DF2\")) #> [1] \"DF <- data.frame(x = 1:10)\\nDF2 <- data.frame(x2 = 1:10)\\nDF2$x2 <- DF$x\" x3 <- teal.data:::CodeClass$new() x3$set_code(\"DF3 <- data.frame(x3 = 1:10) \", \"DF3\") x3$get_code() #> [1] \"DF3 <- data.frame(x3 = 1:10)\" x$append(x3) x$get_code(\"DF3\") #> [1] \"DF3 <- data.frame(x3 = 1:10)\" # mutation simulation x$set_code(\"DF3$x <- foo(DF$x)\", \"DF3\", deps = \"DF\") x$get_code(\"DF3\") #> [1] \"DF <- data.frame(x = 1:10)\\nDF3 <- data.frame(x3 = 1:10)\\nDF3$x <- foo(DF$x)\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"MultiAssayExperiment object can stored inside MAETealDataset. attributes like colnames, dimension column names specific type automatically derived.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"teal.data::TealDataset -> MAETealDataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"teal.data::TealDataset$get_attrs() teal.data::TealDataset$get_character_colnames() teal.data::TealDataset$get_code() teal.data::TealDataset$get_code_class() teal.data::TealDataset$get_dataname() teal.data::TealDataset$get_datanames() teal.data::TealDataset$get_dataset() teal.data::TealDataset$get_dataset_label() teal.data::TealDataset$get_factor_colnames() teal.data::TealDataset$get_keys() teal.data::TealDataset$get_metadata() teal.data::TealDataset$get_mutate_code_class() teal.data::TealDataset$get_mutate_vars() teal.data::TealDataset$get_numeric_colnames() teal.data::TealDataset$get_raw_data() teal.data::TealDataset$get_row_labels() teal.data::TealDataset$get_var_r6() teal.data::TealDataset$get_vars() teal.data::TealDataset$is_mutate_delayed() teal.data::TealDataset$is_pulled() teal.data::TealDataset$mutate() teal.data::TealDataset$reassign_datasets_vars() teal.data::TealDataset$recreate() teal.data::TealDataset$set_code() teal.data::TealDataset$set_dataset_label() teal.data::TealDataset$set_keys() teal.data::TealDataset$set_vars()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"MAETealDataset$new() MAETealDataset$check() MAETealDataset$check_keys() MAETealDataset$get_colnames() MAETealDataset$get_column_labels() MAETealDataset$get_ncol() MAETealDataset$get_nrow() MAETealDataset$get_rownames() MAETealDataset$print() MAETealDataset$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Create new object MAETealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$new( dataname, x, keys = character(0), code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"dataname (character) given name dataset may contain spaces x (MultiAssayExperiment) keys optional, (character) vector primary keys code (character CodeClass) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order. label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Check determine raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$check()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"TRUE dataset generated evaluating get_code() code identical raw data, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-check-keys-","dir":"Reference","previous_headings":"","what":"Method check_keys()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Check keys specified correctly dataset. Set keys distinguish unique rows character(0).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$check_keys(keys = private$.keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"keys optional, (character) vector primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-get-colnames-","dir":"Reference","previous_headings":"","what":"Method get_colnames()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Derive column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-get-column-labels-","dir":"Reference","previous_headings":"","what":"Method get_column_labels()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Derive column labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_column_labels()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-get-ncol-","dir":"Reference","previous_headings":"","what":"Method get_ncol()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Get number columns data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_ncol()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-get-nrow-","dir":"Reference","previous_headings":"","what":"Method get_nrow()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Get number rows data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_nrow()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-get-rownames-","dir":"Reference","previous_headings":"","what":"Method get_rownames()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Derive row names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$get_rownames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"Prints MAETealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"","code":"MAETealDataset$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/MAETealDataset.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a MultiAssayExperiment object with its attributes — MAETealDataset","text":"deep Whether make deep clone.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"teal.data::CodeClass -> PythonCodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"teal.data::CodeClass$append() teal.data::CodeClass$get_code() teal.data::CodeClass$initialize() teal.data::CodeClass$set_code()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"PythonCodeClass$eval() PythonCodeClass$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"method-eval-","dir":"Reference","previous_headings":"","what":"Method eval()","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"Evaluates internal code within environment","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"","code":"PythonCodeClass$eval( vars = list(), dataname = NULL, envir = new.env(parent = parent.env(.GlobalEnv)) )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"vars (named list) additional pre-requisite vars execute code dataname (character) name data frame object returned envir (environment) environment code evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"data.frame containing mutated dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"","code":"PythonCodeClass$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/PythonCodeClass.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A CallablePythonCode class of objects — PythonCodeClass","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Class manages TealDataConnector, TealDatasetConnector TealDataset objects aggregate one collection. Class also decides whether launch app initialize teal application.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"teal.data::TealDataAbstract -> TealData","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"teal.data::TealDataAbstract$check() teal.data::TealDataAbstract$check_reproducibility() teal.data::TealDataAbstract$execute_mutate() teal.data::TealDataAbstract$get_check() teal.data::TealDataAbstract$get_check_result() teal.data::TealDataAbstract$get_code() teal.data::TealDataAbstract$get_code_class() teal.data::TealDataAbstract$get_datanames() teal.data::TealDataAbstract$get_dataset() teal.data::TealDataAbstract$get_datasets() teal.data::TealDataAbstract$is_pulled() teal.data::TealDataAbstract$mutate() teal.data::TealDataAbstract$mutate_dataset() teal.data::TealDataAbstract$reassign_datasets_vars() teal.data::TealDataAbstract$set_check() teal.data::TealDataAbstract$set_pull_code()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"TealData$new() TealData$copy() TealData$print() TealData$get_connectors() TealData$get_items() TealData$get_join_keys() TealData$get_parents() TealData$get_ui() TealData$get_server() TealData$launch() TealData$mutate_join_keys() TealData$check_metadata() TealData$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Create new object TealData class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$new(..., check = FALSE, join_keys = teal.data::join_keys())"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"... (TealDataConnector, TealDataset, TealDatasetConnector) objects check (logical) reproducibility check - whether evaluated preprocessing code gives objects provided arguments. Check run flag true preprocessing code empty. join_keys (join_keys) single (join_key_set) (optional) object dataset column relationships used joining. empty empty join_keys object passed default.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-copy-","dir":"Reference","previous_headings":"","what":"Method copy()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Creates copy object keeping valid references TealDataset TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$copy(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"deep (logical(1)) argument passed clone method. TRUE deep copy made","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"self invisible","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Prints TealData.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-get-connectors-","dir":"Reference","previous_headings":"","what":"Method get_connectors()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get data connectors.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_connectors()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"(list) TealDatasetConnector TealDataConnector objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-get-items-","dir":"Reference","previous_headings":"","what":"Method get_items()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get datasets dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_items(dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"dataname (character value) name dataset connector returned. NULL, connectors returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"list datasets connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-get-join-keys-","dir":"Reference","previous_headings":"","what":"Method get_join_keys()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get join keys two datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_join_keys(dataset_1 = NULL, dataset_2 = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"dataset_1 (character) name first dataset. dataset_2 (character) name second dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"(character) named character vector x names(x) columns dataset_1 values (x) corresponding join keys dataset_2 character(0) relationship","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-get-parents-","dir":"Reference","previous_headings":"","what":"Method get_parents()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"returns parents list datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_parents()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"named (list) parents datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-get-ui-","dir":"Reference","previous_headings":"","what":"Method get_ui()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get shiny-module UI render necessary app derive TealDataConnector object's data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"id (character) item ID shiny module","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"shiny ui function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-get-server-","dir":"Reference","previous_headings":"","what":"Method get_server()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Get shiny-module server render necessary app derive TealDataConnector object's data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$get_server()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"shiny server module.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Launch app allows run user-interfaces TealDataConnector TealDatasetConnector modules piece mainly used debugging.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$launch()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-mutate-join-keys-","dir":"Reference","previous_headings":"","what":"Method mutate_join_keys()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Change join_keys given pair dataset names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$mutate_join_keys(dataset_1, dataset_2, val)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"dataset_1, dataset_2 (character) datasets join_keys returned val (named character) column names used join","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-check-metadata-","dir":"Reference","previous_headings":"","what":"Method check_metadata()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"Check consistency datasets join_keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$check_metadata()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"raise error invisible TRUE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"TealData$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage multiple TealDataConnector, TealDatasetConnector and TealDataset objects. — TealData","text":"","code":"adsl_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADSL\")) adlb_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADLB\")) adrs_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADRS\")) adtte_cf <- callable_function(teal.data::example_cdisc_data)$set_args(list(dataname = \"ADTTE\")) x1 <- cdisc_dataset_connector(\"ADSL\", adsl_cf, keys = get_cdisc_keys(\"ADSL\")) x2 <- cdisc_dataset_connector(\"ADRS\", adrs_cf, keys = get_cdisc_keys(\"ADRS\")) x3 <- cdisc_dataset( dataname = \"ADAE\", x = teal.data::example_cdisc_data(\"ADAE\"), code = \"library(teal.data)\\nADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ) x4 <- cdisc_dataset_connector(\"ADTTE\", adtte_cf, keys = get_cdisc_keys(\"ADTTE\")) tc <- teal.data:::TealData$new(x1, x2, x3, x4) tc$get_datanames() #> [1] \"ADSL\" \"ADRS\" \"ADAE\" \"ADTTE\" if (FALSE) { tc$launch() get_datasets(tc) # equivalent to tc$get_datasets() tc$get_dataset(\"ADAE\") tc$check() } x <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) x2 <- cdisc_dataset_connector(\"ADTTE\", adtte_cf, keys = get_cdisc_keys(\"ADTTE\")) tc <- teal.data:::TealData$new(x, x2) if (FALSE) { # This errors as we have not pulled the data # tc$get_datasets() # pull the data and then we can get the datasets tc$launch() tc$get_datasets() get_raw_data(tc) }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":null,"dir":"Reference","previous_headings":"","what":"TealDataAbstract class — TealDataAbstract","title":"TealDataAbstract class — TealDataAbstract","text":"Abstract class containing code handling set datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"TealDataAbstract class — TealDataAbstract","text":"id String used create unique GUI elements","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"TealDataAbstract class — TealDataAbstract","text":"TealDataAbstract$new() TealDataAbstract$check() TealDataAbstract$check_reproducibility() TealDataAbstract$execute_mutate() TealDataAbstract$get_check_result() TealDataAbstract$get_code() TealDataAbstract$get_code_class() TealDataAbstract$get_datanames() TealDataAbstract$get_dataset() TealDataAbstract$get_datasets() TealDataAbstract$get_items() TealDataAbstract$get_check() TealDataAbstract$is_pulled() TealDataAbstract$mutate() TealDataAbstract$mutate_dataset() TealDataAbstract$set_check() TealDataAbstract$set_pull_code() TealDataAbstract$reassign_datasets_vars() TealDataAbstract$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"TealDataAbstract class — TealDataAbstract","text":"create TealDataAbstract object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$new()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"throws error","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"TealDataAbstract class — TealDataAbstract","text":"Check object raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$check()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"NULL check step disabled TRUE datasets generated evaluating get_code() code identical raw data, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-check-reproducibility-","dir":"Reference","previous_headings":"","what":"Method check_reproducibility()","title":"TealDataAbstract class — TealDataAbstract","text":"Execute check() raise error reproducible.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$check_reproducibility()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"error code reproducible else invisibly nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-execute-mutate-","dir":"Reference","previous_headings":"","what":"Method execute_mutate()","title":"TealDataAbstract class — TealDataAbstract","text":"Execute mutate code. Using mutate_data(set).TealDataAbstract cause instant execution, mutate_code delayed can evaluated using method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$execute_mutate()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-check-result-","dir":"Reference","previous_headings":"","what":"Method get_check_result()","title":"TealDataAbstract class — TealDataAbstract","text":"Get result reproducibility check","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_check_result()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"NULL check called yet, TRUE / FALSE otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"TealDataAbstract class — TealDataAbstract","text":"Get code datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_code(dataname = NULL, deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character) dataname NULL datasets deparse (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"(character) vector code generate datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"TealDataAbstract class — TealDataAbstract","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_code_class(only_pull = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"only_pull (logical value) TRUE code pull datasets returned without mutate code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-datanames-","dir":"Reference","previous_headings":"","what":"Method get_datanames()","title":"TealDataAbstract class — TealDataAbstract","text":"Get names datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_datanames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"character vector names datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-dataset-","dir":"Reference","previous_headings":"","what":"Method get_dataset()","title":"TealDataAbstract class — TealDataAbstract","text":"Get TealDataset object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_dataset(dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character value) name dataset returned. NULL, datasets returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"TealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-datasets-","dir":"Reference","previous_headings":"","what":"Method get_datasets()","title":"TealDataAbstract class — TealDataAbstract","text":"Get list TealDataset objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_datasets()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"list TealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-items-","dir":"Reference","previous_headings":"","what":"Method get_items()","title":"TealDataAbstract class — TealDataAbstract","text":"Get datasets dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_items(dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character value) name dataset connector returned. NULL, connectors returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"list datasets connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-get-check-","dir":"Reference","previous_headings":"","what":"Method get_check()","title":"TealDataAbstract class — TealDataAbstract","text":"data data subjected reproducibility check","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$get_check()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"logical","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-is-pulled-","dir":"Reference","previous_headings":"","what":"Method is_pulled()","title":"TealDataAbstract class — TealDataAbstract","text":"Check dataset already pulled.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$is_pulled()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"TealDataAbstract class — TealDataAbstract","text":"Mutate data code. Code used mutation linked particular refers datasets. Consequence using get_code() part code returned specified dataset. method used particular call involve changing multiple datasets. Otherwise please use mutate_dataset. Execution mutate_code delayed datasets pulled (isTRUE(is_pulled)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$mutate(code, vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"code (character) Code mutate dataset. Must contain dataset$dataname vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"self invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-mutate-dataset-","dir":"Reference","previous_headings":"","what":"Method mutate_dataset()","title":"TealDataAbstract class — TealDataAbstract","text":"Mutate dataset code. Execution mutate_code delayed datasets pulled (isTRUE(is_pulled)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$mutate_dataset(dataname, code, vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"dataname (character) Dataname mutated code (character) Code mutate dataset. Must contain dataset$dataname vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"self invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-set-check-","dir":"Reference","previous_headings":"","what":"Method set_check()","title":"TealDataAbstract class — TealDataAbstract","text":"Set reproducibility check","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$set_check(check = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"check (logical) whether perform reproducibility check.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-set-pull-code-","dir":"Reference","previous_headings":"","what":"Method set_pull_code()","title":"TealDataAbstract class — TealDataAbstract","text":"Set pull code","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$set_pull_code(code)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"code (character value) code reproduce data TealDataset objects. set dataset code set already.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"TealDataAbstract class — TealDataAbstract","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-reassign-datasets-vars-","dir":"Reference","previous_headings":"","what":"Method reassign_datasets_vars()","title":"TealDataAbstract class — TealDataAbstract","text":"Reassign vars TealDataset TealDatasetConnector objects keep valid reference deep cloning example TealDatasetConnector dependency TealDataset, TealDataset reassigned inside TealDatasetConnector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$reassign_datasets_vars()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"TealDataAbstract class — TealDataAbstract","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"TealDataAbstract class — TealDataAbstract","text":"","code":"TealDataAbstract$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataAbstract.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"TealDataAbstract class — TealDataAbstract","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":null,"dir":"Reference","previous_headings":"","what":"A TealDataConnection class of objects — TealDataConnection","title":"A TealDataConnection class of objects — TealDataConnection","text":"Objects class store connection data source. can database server connection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A TealDataConnection class of objects — TealDataConnection","text":"TealDataConnection$new() TealDataConnection$finalize() TealDataConnection$is_opened() TealDataConnection$is_failed() TealDataConnection$launch() TealDataConnection$open() TealDataConnection$get_conn() TealDataConnection$get_open_call() TealDataConnection$get_open_error_message() TealDataConnection$get_preopen_server() TealDataConnection$get_open_server() TealDataConnection$get_open_ui() TealDataConnection$is_open_failed() TealDataConnection$set_open_args() TealDataConnection$set_preopen_server() TealDataConnection$set_open_server() TealDataConnection$set_open_ui() TealDataConnection$close() TealDataConnection$get_close_call() TealDataConnection$get_close_error_message() TealDataConnection$get_close_server() TealDataConnection$is_close_failed() TealDataConnection$set_close_args() TealDataConnection$set_close_ui() TealDataConnection$set_close_server() TealDataConnection$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Create new TealDataConnection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$new( open_fun = NULL, close_fun = NULL, ping_fun = NULL, if_conn_obj = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"open_fun (CallableFunction) function open connection close_fun (CallableFunction) function close connection ping_fun (CallableFunction) function ping connection if_conn_obj optional, (logical) whether store conn object returned opening connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"new TealDataConnection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-finalize-","dir":"Reference","previous_headings":"","what":"Method finalize()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Finalize method closing connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$finalize()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"NULL","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-is-opened-","dir":"Reference","previous_headings":"","what":"Method is_opened()","title":"A TealDataConnection class of objects — TealDataConnection","text":"connection opened open connection successfully evaluated","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_opened()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) connection open","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-is-failed-","dir":"Reference","previous_headings":"","what":"Method is_failed()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Check connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_failed()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) TRUE connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Run simple application uses ui server fields open connection. Useful debugging","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$launch()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"object represents app","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-open-","dir":"Reference","previous_headings":"","what":"Method open()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Open connection. Note connection already opened nothing.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$open(args = NULL, silent = FALSE, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"args (NULL named list) additional arguments set previously silent (logical) whether convert \"missing function\" errors messages try (logical) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"returns self successful connection already opened. open_fun fails, app returns error form shinyjs::alert (try = TRUE) breaks app (try = FALSE)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-conn-","dir":"Reference","previous_headings":"","what":"Method get_conn()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get internal connection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_conn()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"connection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-open-call-","dir":"Reference","previous_headings":"","what":"Method get_open_call()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get executed open connection call","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_call(deparse = TRUE, args = NULL, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"deparse (logical) whether return deparsed form call args (NULL named list) additional arguments set previously silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-open-error-message-","dir":"Reference","previous_headings":"","what":"Method get_open_error_message()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get error message last connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_error_message()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(character) text error message character(0) last connection successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-preopen-server-","dir":"Reference","previous_headings":"","what":"Method get_preopen_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get shiny server module prior opening connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_preopen_server()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(function) shiny server prior opening connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-open-server-","dir":"Reference","previous_headings":"","what":"Method get_open_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get shiny server module open connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_server()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(function) shiny server open connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-open-ui-","dir":"Reference","previous_headings":"","what":"Method get_open_ui()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get Shiny module inputs open connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_open_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"id character shiny element id","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(function) shiny UI set arguments open connection function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-is-open-failed-","dir":"Reference","previous_headings":"","what":"Method is_open_failed()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Check open connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_open_failed()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) TRUE open connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-set-open-args-","dir":"Reference","previous_headings":"","what":"Method set_open_args()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set open connection function argument","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_open_args(args, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"args (NULL named list) values list names argument names silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-set-preopen-server-","dir":"Reference","previous_headings":"","what":"Method set_preopen_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set pre-open connection server function function called submit button hit.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_preopen_server(preopen_module)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"preopen_module (function) shiny module server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-set-open-server-","dir":"Reference","previous_headings":"","what":"Method set_open_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set open connection server function function called submit button hit. possibility specify dynamic ui server function executed hitting submit button.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_open_server(open_module)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"open_module (function) shiny module server function load data connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-set-open-ui-","dir":"Reference","previous_headings":"","what":"Method set_open_ui()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set open connection UI function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_open_ui(open_module)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"open_module (function) shiny module function. Inputs specified ui passed server module defined set_open_server method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-16","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-close-","dir":"Reference","previous_headings":"","what":"Method close()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$close(silent = FALSE, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"silent (logical) whether convert \"missing function\" errors messages try (logical) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-17","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"returns (self) successful. unsuccessful evaluation depends try argument: try = TRUE returns error, try = FALSE otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-close-call-","dir":"Reference","previous_headings":"","what":"Method get_close_call()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get executed close connection call","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_close_call(deparse = TRUE, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"deparse (logical) whether return deparsed form call silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-18","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-close-error-message-","dir":"Reference","previous_headings":"","what":"Method get_close_error_message()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get error message last connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_close_error_message()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-19","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(character) text error message character(0) last connection successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-get-close-server-","dir":"Reference","previous_headings":"","what":"Method get_close_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Get shiny server module close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$get_close_server()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-20","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"server function close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-is-close-failed-","dir":"Reference","previous_headings":"","what":"Method is_close_failed()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Check close connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$is_close_failed()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-21","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(logical) TRUE close connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-set-close-args-","dir":"Reference","previous_headings":"","what":"Method set_close_args()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set close connection function argument","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_close_args(args, silent = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"args (named list) values list names argument names silent (logical) whether convert \"missing function\" errors messages","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-22","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-set-close-ui-","dir":"Reference","previous_headings":"","what":"Method set_close_ui()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set close connection UI function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_close_ui(close_module)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"close_module (function) shiny module function. Inputs specified ui passed server module defined set_close_server method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-23","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-set-close-server-","dir":"Reference","previous_headings":"","what":"Method set_close_server()","title":"A TealDataConnection class of objects — TealDataConnection","text":"Set close-connection server function function called submit button hit. possibility specify dynamic ui server function executed hitting submit button.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$set_close_server(close_module)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"close_module (function) shiny module server function load data connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"returns-24","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDataConnection class of objects — TealDataConnection","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A TealDataConnection class of objects — TealDataConnection","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"TealDataConnection$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDataConnection class of objects — TealDataConnection","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnection.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDataConnection class of objects — TealDataConnection","text":"","code":"open_fun <- callable_function(data.frame) # define opening function open_fun$set_args(list(x = 1:5)) # define fixed arguments to opening function close_fun <- callable_function(sum) # define closing function close_fun$set_args(list(x = 1:5)) # define fixed arguments to closing function ping_fun <- callable_function(function() TRUE) x <- data_connection( # define connection ping_fun = ping_fun, # define ping function open_fun = open_fun, # define opening function close_fun = close_fun # define closing function ) x$set_open_args(args = list(y = letters[1:5])) # define additional arguments if necessary x$open() # call opening function x$get_open_call() # check reproducible R code #> [1] \"data.frame(x = 1:5, y = c(\\\"a\\\", \\\"b\\\", \\\"c\\\", \\\"d\\\", \\\"e\\\"))\" # get data from connection via TealDataConnector$get_dataset() if (FALSE) { x$open(args = list(x = 1:5, y = letters[1:5])) # able to call opening function with arguments x$close() # call closing function }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Class manages TealDatasetConnector specify additional dynamic arguments open/close connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"teal.data::TealDataAbstract -> TealDataConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"teal.data::TealDataAbstract$check() teal.data::TealDataAbstract$check_reproducibility() teal.data::TealDataAbstract$execute_mutate() teal.data::TealDataAbstract$get_check() teal.data::TealDataAbstract$get_check_result() teal.data::TealDataAbstract$get_code() teal.data::TealDataAbstract$get_datanames() teal.data::TealDataAbstract$get_dataset() teal.data::TealDataAbstract$get_datasets() teal.data::TealDataAbstract$get_items() teal.data::TealDataAbstract$is_pulled() teal.data::TealDataAbstract$mutate_dataset() teal.data::TealDataAbstract$reassign_datasets_vars() teal.data::TealDataAbstract$set_check() teal.data::TealDataAbstract$set_pull_code()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"TealDataConnector$new() TealDataConnector$print() TealDataConnector$get_connection() TealDataConnector$get_code_class() TealDataConnector$get_server() TealDataConnector$get_preopen_server() TealDataConnector$get_ui() TealDataConnector$set_pull_args() TealDataConnector$set_ui() TealDataConnector$set_server() TealDataConnector$set_preopen_server() TealDataConnector$pull() TealDataConnector$launch() TealDataConnector$mutate() TealDataConnector$is_failed() TealDataConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Create new TealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$new(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Prints TealDataConnector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-get-connection-","dir":"Reference","previous_headings":"","what":"Method get_connection()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Get connection data source","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_connection()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"connector's connection","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_code_class()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-get-server-","dir":"Reference","previous_headings":"","what":"Method get_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"get server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_server()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-get-preopen-server-","dir":"Reference","previous_headings":"","what":"Method get_preopen_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"get preopen server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_preopen_server()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-get-ui-","dir":"Reference","previous_headings":"","what":"Method get_ui()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Get Shiny module inputs TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$get_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"id character shiny element id","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"ui function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-set-pull-args-","dir":"Reference","previous_headings":"","what":"Method set_pull_args()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set argument pull_fun","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_pull_args(args)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"args (named list) arguments values separate list elements named argument name. arguments passed dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-set-ui-","dir":"Reference","previous_headings":"","what":"Method set_ui()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set connector UI function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_ui(f)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"f (function) shiny module function. Inputs specified ui passed server module defined set_server method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-set-server-","dir":"Reference","previous_headings":"","what":"Method set_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set connector server function function called submit button hit. possibility specify dynamic ui server function executed hitting submit button.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_server(f)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"f (function) shiny module server function load data connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-set-preopen-server-","dir":"Reference","previous_headings":"","what":"Method set_preopen_server()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Set connector pre-open server function function called submit button hit.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$set_preopen_server(f)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"f (function) shiny module server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-pull-","dir":"Reference","previous_headings":"","what":"Method pull()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Load data TealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$pull(con_args = NULL, args = NULL, try = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"con_args (NULL named list) additional dynamic arguments connection function. args passed TealDatasetConnector object evaluate CallableFunction assigned dataset. args null default set arguments used, otherwise call executed arguments (arguments set ignored). pull function update reproducible call, just evaluate function. args (NULL named list) additional dynamic arguments pull dataset. args passed TealDatasetConnector object evaluate CallableFunction assigned dataset. args null default set arguments used, otherwise call executed arguments (arguments set ignored). pull function update reproducible call, just evaluate function. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"(self) invisibly chaining. order get data please use get_datasets method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Run simple application uses ui server fields pull data connection. Useful debugging","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$launch()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"object represents app","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Mutate data code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$mutate(...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"... parameters inherited TealDataAbstract.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Informational message use mutate_data() TealDataConnectors.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-is-failed-","dir":"Reference","previous_headings":"","what":"Method is_failed()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"Check pull connection failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$is_failed()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"TRUE pull connection failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"TealDataConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataConnector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage multiple and TealDatasetConnector of the same type. — TealDataConnector","text":"","code":"library(magrittr) #> #> Attaching package: ‘magrittr’ #> The following objects are masked from ‘package:testthat’: #> #> equals, is_less_than, not random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } open_fun <- callable_function(library) open_fun$set_args(list(package = \"teal.data\")) con <- data_connection(open_fun = open_fun) con$set_open_server( function(id, connection) { moduleServer( id = id, module = function(input, output, session) { connection$open(try = TRUE) return(invisible(connection)) } ) } ) x <- teal.data:::TealDataConnector$new( connection = con, connectors = list( random_data_connector(dataname = \"ADSL\"), random_data_connector(dataname = \"ADLB\") ) ) x$set_ui( function(id, connection, connectors) { ns <- NS(id) tagList( connection$get_open_ui(ns(\"open_connection\")), numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) x$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection connection$get_open_server()(id = \"open_connection\", connection = connection) if (connection$is_opened()) { for (connector in connectors) { set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } } ) } ) if (FALSE) { x$launch() x$get_datasets() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 Class representing a dataset with its attributes — TealDataset","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"data.frame object can stored inside object. attributes like colnames, dimension column names specific type automatically derived.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"raw_data data.frame behind R6 class data data.frame behind R6 class var_names column names data","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TealDataset$new() TealDataset$recreate() TealDataset$print() TealDataset$get_dataset() TealDataset$get_attrs() TealDataset$get_raw_data() TealDataset$get_numeric_colnames() TealDataset$get_character_colnames() TealDataset$get_factor_colnames() TealDataset$get_colnames() TealDataset$get_column_labels() TealDataset$get_ncol() TealDataset$get_nrow() TealDataset$get_rownames() TealDataset$get_row_labels() TealDataset$get_dataname() TealDataset$get_datanames() TealDataset$get_dataset_label() TealDataset$get_keys() TealDataset$get_metadata() TealDataset$get_var_r6() TealDataset$reassign_datasets_vars() TealDataset$set_dataset_label() TealDataset$set_keys() TealDataset$set_vars() TealDataset$set_code() TealDataset$get_code() TealDataset$get_code_class() TealDataset$get_mutate_code_class() TealDataset$get_vars() TealDataset$get_mutate_vars() TealDataset$is_mutate_delayed() TealDataset$mutate() TealDataset$check() TealDataset$check_keys() TealDataset$is_pulled() TealDataset$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Create new object TealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$new( dataname, x, keys = character(0), code = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys optional, (character) Vector primary keys code (character) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order. label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-recreate-","dir":"Reference","previous_headings":"","what":"Method recreate()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Recreate TealDataset current attributes.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$recreate( dataname = self$get_dataname(), x = self$get_raw_data(), keys = self$get_keys(), code = private$code, label = self$get_dataset_label(), vars = list(), metadata = self$get_metadata() )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"dataname (character) given name dataset may contain spaces x (data.frame) keys optional, (character) Vector primary keys code (character) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order. label (character) Label describe dataset vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) Field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"new object TealDataset class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Prints TealDataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-dataset-","dir":"Reference","previous_headings":"","what":"Method get_dataset()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Performs delayed mutate calls returning self.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_dataset()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"dataset (TealDataset)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-attrs-","dir":"Reference","previous_headings":"","what":"Method get_attrs()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_attrs()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(named list) dataset attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-raw-data-","dir":"Reference","previous_headings":"","what":"Method get_raw_data()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive raw data frame inside object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_raw_data()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"data.frame","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-numeric-colnames-","dir":"Reference","previous_headings":"","what":"Method get_numeric_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive names numeric columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_numeric_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-character-colnames-","dir":"Reference","previous_headings":"","what":"Method get_character_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive names character columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_character_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-factor-colnames-","dir":"Reference","previous_headings":"","what":"Method get_factor_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive names factor columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_factor_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-colnames-","dir":"Reference","previous_headings":"","what":"Method get_colnames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_colnames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-column-labels-","dir":"Reference","previous_headings":"","what":"Method get_column_labels()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive column labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_column_labels()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-ncol-","dir":"Reference","previous_headings":"","what":"Method get_ncol()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get number columns data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_ncol()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-nrow-","dir":"Reference","previous_headings":"","what":"Method get_nrow()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get number rows data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_nrow()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"numeric vector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-rownames-","dir":"Reference","previous_headings":"","what":"Method get_rownames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive row names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_rownames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-row-labels-","dir":"Reference","previous_headings":"","what":"Method get_row_labels()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive row labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_row_labels()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-dataname-","dir":"Reference","previous_headings":"","what":"Method get_dataname()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive name formerly called dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_dataname()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character name dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-datanames-","dir":"Reference","previous_headings":"","what":"Method get_datanames()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_datanames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character name dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-dataset-label-","dir":"Reference","previous_headings":"","what":"Method get_dataset_label()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Derive label former called datalabel","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_dataset_label()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-16","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"character label dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-keys-","dir":"Reference","previous_headings":"","what":"Method get_keys()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get primary keys dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_keys()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-17","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(character vector) dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-metadata-","dir":"Reference","previous_headings":"","what":"Method get_metadata()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get metadata dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_metadata()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-18","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(named list)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-var-r-","dir":"Reference","previous_headings":"","what":"Method get_var_r6()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get list dependencies TealDataset TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_var_r6()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-19","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-reassign-datasets-vars-","dir":"Reference","previous_headings":"","what":"Method reassign_datasets_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Overwrites TealDataset TealDatasetConnector dependencies TealDataset found datasets. Reassignment refers provided datasets, vars remains .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$reassign_datasets_vars(datasets)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"datasets (named list TealDataset(s) TealDatasetConnector(s)) objects valid pointers.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Reassign vars object keep references date deep clone. Update done based objects passed datasets argument. Overwrites dependencies names matching names objects passed datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-20","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"NULL invisible","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"test_dataset <- teal.data:::TealDataset$new( dataname = \"iris\", x = iris, vars = list(dep = teal.data:::TealDataset$new(\"iris2\", iris)) ) test_dataset$reassign_datasets_vars( list(iris2 = teal.data:::TealDataset$new(\"iris2\", head(iris))) )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-set-dataset-label-","dir":"Reference","previous_headings":"","what":"Method set_dataset_label()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Set label dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_dataset_label(label)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"label (character) Label describe dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-21","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-set-keys-","dir":"Reference","previous_headings":"","what":"Method set_keys()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Set new keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_keys(keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"keys optional, (character) Vector primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-22","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-set-vars-","dir":"Reference","previous_headings":"","what":"Method set_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Adds variables code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_vars(vars)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"vars (named list) contains R object code depends ","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-23","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-set-code-","dir":"Reference","previous_headings":"","what":"Method set_code()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Sets reproducible code","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$set_code(code)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"code (character) character string defining code needed produce data set x. initialize() recreate() accept code CodeClass also needed preserve code uniqueness correct order.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-24","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get code get data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-26","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_code(deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"deparse (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-25","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-27","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_code_class(nodeps = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"nodeps (logical(1)) whether CodeClass contain code dependent vars mutate","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-26","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-mutate-code-class-","dir":"Reference","previous_headings":"","what":"Method get_mutate_code_class()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-28","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_mutate_code_class()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-27","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-vars-","dir":"Reference","previous_headings":"","what":"Method get_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal vars object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-29","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_vars()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-28","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-get-mutate-vars-","dir":"Reference","previous_headings":"","what":"Method get_mutate_vars()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Get internal mutate_vars object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-30","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$get_mutate_vars()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-29","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-is-mutate-delayed-","dir":"Reference","previous_headings":"","what":"Method is_mutate_delayed()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Whether mutate code delayed evaluation.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-31","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$is_mutate_delayed()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-30","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"logical","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Mutate dataset code","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-32","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$mutate(code, vars = list(), force_delay = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"code (CodeClass) (character) R expressions executed vars named list R objects code depends execute force_delay (logical) used containing TealDatasetConnector object Either code script must provided, .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-31","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Check determine raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-33","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$check()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-32","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TRUE dataset generated evaluating get_code() code identical raw data, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-check-keys-","dir":"Reference","previous_headings":"","what":"Method check_keys()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Check keys specified correctly dataset. Set keys distinguish unique rows character(0).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-34","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$check_keys(keys = private$.keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"keys optional, (character) Vector primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-33","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-is-pulled-","dir":"Reference","previous_headings":"","what":"Method is_pulled()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"Check dataset already pulled.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-35","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$is_pulled()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"returns-34","dir":"Reference","previous_headings":"","what":"Returns","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"TRUE dataset already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"usage-36","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"TealDataset$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 Class representing a dataset with its attributes — TealDataset","text":"","code":"## ------------------------------------------------ ## Method `TealDataset$reassign_datasets_vars` ## ------------------------------------------------ test_dataset <- teal.data:::TealDataset$new( dataname = \"iris\", x = iris, vars = list(dep = teal.data:::TealDataset$new(\"iris2\", iris)) ) test_dataset$reassign_datasets_vars( list(iris2 = teal.data:::TealDataset$new(\"iris2\", head(iris))) )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":null,"dir":"Reference","previous_headings":"","what":"A TealDatasetConnector class of objects — TealDatasetConnector","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Objects class store connection function fetch single dataset. Note specific connection types, object class TealDataConnection must provided. Data can pulled via pull method accessed directly dataset active binding. Pulled data inherits class TealDataset","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TealDatasetConnector$new() TealDatasetConnector$print() TealDatasetConnector$get_dataname() TealDatasetConnector$get_datanames() TealDatasetConnector$get_dataset_label() TealDatasetConnector$get_keys() TealDatasetConnector$get_code() TealDatasetConnector$get_code_class() TealDatasetConnector$get_pull_args() TealDatasetConnector$get_dataset() TealDatasetConnector$get_error_message() TealDatasetConnector$get_pull_callable() TealDatasetConnector$get_raw_data() TealDatasetConnector$get_var_r6() TealDatasetConnector$reassign_datasets_vars() TealDatasetConnector$set_dataset_label() TealDatasetConnector$set_keys() TealDatasetConnector$pull() TealDatasetConnector$set_args() TealDatasetConnector$mutate() TealDatasetConnector$is_failed() TealDatasetConnector$is_pulled() TealDatasetConnector$is_mutate_delayed() TealDatasetConnector$check() TealDatasetConnector$set_ui_input() TealDatasetConnector$get_ui() TealDatasetConnector$get_server() TealDatasetConnector$launch() TealDatasetConnector$clone()","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Create new TealDatasetConnector object. Set pulling function CallableFunction returns data.frame MultiAssayExperiment, e.g. reading function creating fly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$new( dataname, pull_callable, keys = character(0), label = character(0), code = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Prints TealDatasetConnector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$print(...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"... additional arguments printing method","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"invisibly self","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-dataname-","dir":"Reference","previous_headings":"","what":"Method get_dataname()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_dataname()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-1","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-datanames-","dir":"Reference","previous_headings":"","what":"Method get_datanames()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_datanames()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-2","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character dataname dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-dataset-label-","dir":"Reference","previous_headings":"","what":"Method get_dataset_label()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get label dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_dataset_label()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-3","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character dataset label","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-keys-","dir":"Reference","previous_headings":"","what":"Method get_keys()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get primary keys dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_keys()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-4","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character vector dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-code-","dir":"Reference","previous_headings":"","what":"Method get_code()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get code get data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_code(deparse = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"deparse (logical) whether return deparsed form call","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-5","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"optionally deparsed call object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-code-class-","dir":"Reference","previous_headings":"","what":"Method get_code_class()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get internal CodeClass object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_code_class()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-6","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"CodeClass","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-pull-args-","dir":"Reference","previous_headings":"","what":"Method get_pull_args()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Derive arguments connector pull ","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_pull_args()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-7","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"list pull function fixed arguments","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-dataset-","dir":"Reference","previous_headings":"","what":"Method get_dataset()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_dataset()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-8","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"dataset (TealDataset)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-error-message-","dir":"Reference","previous_headings":"","what":"Method get_error_message()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get error message last pull","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_error_message()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-9","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"character object error message character(0) last pull successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-pull-callable-","dir":"Reference","previous_headings":"","what":"Method get_pull_callable()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get pull function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_pull_callable()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-10","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"CallableFunction","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-raw-data-","dir":"Reference","previous_headings":"","what":"Method get_raw_data()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get raw data dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_raw_data()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-11","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"data.frame MultiAssayExperiment data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-var-r-","dir":"Reference","previous_headings":"","what":"Method get_var_r6()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get list dependencies TealDataset TealDatasetConnector objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_var_r6()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-12","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"list","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-reassign-datasets-vars-","dir":"Reference","previous_headings":"","what":"Method reassign_datasets_vars()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Reassign vars object keep references date deep clone. Update done based objects passed datasets argument. Reassignment refers provided datasets, vars remains .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$reassign_datasets_vars(datasets)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"datasets (named list TealDataset(s) TealDatasetConnector(s)) objects valid pointers.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-13","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"NULL invisible","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-set-dataset-label-","dir":"Reference","previous_headings":"","what":"Method set_dataset_label()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Set label dataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_dataset_label(label)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"label (character) Label describe dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-14","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-set-keys-","dir":"Reference","previous_headings":"","what":"Method set_keys()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Set new keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_keys(keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"keys optional, (character) vector dataset primary keys column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-15","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-pull-","dir":"Reference","previous_headings":"","what":"Method pull()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Pull data (metadata Callable) Read create data using pull_callable specified constructor.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$pull(args = NULL, try = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"args (NULL named list) additional dynamic arguments pull function. args can omitted pull_callable constructor already contains necessary arguments pull data. One can try execute pull_callable directly x$pull_callable$run() get code using x$pull_callable$get_code(). args specified pull used temporary get data saved code. try (logical value) whether perform function evaluation inside try clause","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-16","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) successful.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-set-args-","dir":"Reference","previous_headings":"","what":"Method set_args()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Set arguments pulling function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_args(args)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"args (NULL named list) dynamic arguments function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-17","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-mutate-","dir":"Reference","previous_headings":"","what":"Method mutate()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Dispatcher either eager delayed mutate methods Either code script must provided, .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$mutate(code, vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-18","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-is-failed-","dir":"Reference","previous_headings":"","what":"Method is_failed()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check pull failed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$is_failed()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-19","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TRUE pull failed, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-is-pulled-","dir":"Reference","previous_headings":"","what":"Method is_pulled()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check dataset already pulled.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$is_pulled()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-20","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TRUE connector already pulled, else FALSE","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-is-mutate-delayed-","dir":"Reference","previous_headings":"","what":"Method is_mutate_delayed()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check dataset mutations delayed","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$is_mutate_delayed()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-21","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"logical","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-check-","dir":"Reference","previous_headings":"","what":"Method check()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Check determine raw data reproducible get_code() code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$check()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-22","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"TRUE always connectors avoid evaluating code multiple times.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-set-ui-input-","dir":"Reference","previous_headings":"","what":"Method set_ui_input()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Sets shiny UI according given inputs. Inputs must provide scalar (length 1) variables.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$set_ui_input(inputs = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"inputs (function) shiny module UI function single argument ns. function needs return list shiny inputs inputId wrapped function ns. inputId must match exactly argument name set. See example. Nested lists allowed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-23","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"(self) invisibly chaining.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) \\dontrun{ ds$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-ui-","dir":"Reference","previous_headings":"","what":"Method get_ui()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get shiny ui function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_ui(id)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"id (character) namespace id","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-24","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"shiny UI given namespace id","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-get-server-","dir":"Reference","previous_headings":"","what":"Method get_server()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Get shiny server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-26","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$get_server()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-25","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"shiny server function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-launch-","dir":"Reference","previous_headings":"","what":"Method launch()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Launches shiny app.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-27","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$launch()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"returns-26","dir":"Reference","previous_headings":"","what":"Returns","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"Shiny app","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) \\dontrun{ ds$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"objects class cloneable method.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"usage-28","dir":"Reference","previous_headings":"","what":"Usage","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"TealDatasetConnector$clone(deep = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"deep Whether make deep clone.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealDatasetConnector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A TealDatasetConnector class of objects — TealDatasetConnector","text":"","code":"## ------------------------------------------------ ## Method `TealDatasetConnector$set_ui_input` ## ------------------------------------------------ ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) if (FALSE) { ds$launch() } ## ------------------------------------------------ ## Method `TealDatasetConnector$launch` ## ------------------------------------------------ ds <- dataset_connector(\"xyz\", pull_callable = callable_function(data.frame)) ds$set_ui_input( function(ns) { list(sliderInput(ns(\"colA\"), \"Select value for colA\", min = 0, max = 10, value = 3), sliderInput(ns(\"colB\"), \"Select value for colB\", min = 0, max = 10, value = 7)) } ) if (FALSE) { ds$launch() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/all.equal.join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":".equal(target, current) utility compare join_keys objects target current testing near equality.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/all.equal.join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":"","code":"# S3 method for equal.join_keys all(target, current, ...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/all.equal.join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":"target R object. current R object, compared target. ... arguments different methods. used join_keys.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/all.equal.join_keys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Test if Two Objects are (Nearly) Equal — all.equal.join_keys","text":"different, comparison still made extent, report differences returned. use .equal directly expressions—either use isTRUE(.equal(....)) identical appropriate. parents attribute comparison tolerates NULL empty lists find difference. list containing relationships treated like map ignores entries NULL exist.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/as_cdisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"","code":"as_cdisc( x, parent = if (identical(get_dataname(x), \"ADSL\")) character(0) else \"ADSL\" ) # S3 method for TealDataset as_cdisc( x, parent = if (identical(get_dataname(x), \"ADSL\")) character(0) else \"ADSL\" ) # S3 method for TealDatasetConnector as_cdisc( x, parent = if (identical(get_dataname(x), \"ADSL\")) character(0) else \"ADSL\" )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/as_cdisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"x object TealDataset TealDatasetConnector class parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/as_cdisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"(CDISCTealDataset CDISCTealDatasetConnector) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/as_cdisc.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"Convert TealDataset(Connector) object CDISCTealDataset(Connector) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/as_cdisc.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"passed CDISC-flavored object returns unmodified object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/as_cdisc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a TealDataset(Connector) object to a CDISCTealDataset(Connector) object — as_cdisc","text":"","code":"# TealDataset -------- as_cdisc( dataset( \"ADSL\", teal.data::example_cdisc_data(\"ADSL\"), keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ) #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... as_cdisc( dataset( \"ADAE\", teal.data::example_cdisc_data(\"ADAE\"), keys = get_cdisc_keys(\"ADAE\"), code = \"ADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ), parent = \"ADSL\" ) #> A CDISCTealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ... # TealDatasetConnector -------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) as_cdisc( dataset_connector( \"ADSL\", pull_fun_adsl, keys = get_cdisc_keys(\"ADSL\") ) ) #> A CDISCTealDatasetConnector object, named ADSL, containing a TealDataset object that has not been loaded/pulled pull_fun_adae <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) as_cdisc( dataset_connector( \"ADAE\", pull_fun_adae, keys = get_cdisc_keys(\"ADAE\") ), parent = \"ADSL\" ) #> A CDISCTealDatasetConnector object, named ADAE, containing a TealDataset object that has not been loaded/pulled"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/assert_compatible_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to assert if two key sets contain incompatible keys — assert_compatible_keys","title":"Helper function to assert if two key sets contain incompatible keys — assert_compatible_keys","text":"return TRUE compatible, throw error otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/assert_compatible_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to assert if two key sets contain incompatible keys — assert_compatible_keys","text":"","code":"assert_compatible_keys(join_key_1, join_key_2)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/assert_parent_child.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function checks the parent-child relations are valid — assert_parent_child","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"Helper function checks parent-child relations valid","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/assert_parent_child.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"","code":"assert_parent_child(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/assert_parent_child.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"x (join_keys) object assert validity relations","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/assert_parent_child.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function checks the parent-child relations are valid — assert_parent_child","text":"join_keys invisibly","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/build_cdisc_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","title":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","text":"Helper method build default_cdisc_join_keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/build_cdisc_join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","text":"","code":"build_cdisc_join_keys(default_cdisc_keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/build_cdisc_join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper method to build default_cdisc_join_keys — build_cdisc_join_keys","text":"default_cdisc_keys (list) default definition primary foreign keys CDISC datasets","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Create CallableCode object — callable_code","title":"Create CallableCode object — callable_code","text":"Create CallableCode object execute specific code get reproducible call.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create CallableCode object — callable_code","text":"","code":"callable_code(code)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create CallableCode object — callable_code","text":"code (character) string containing R code reproduce desired object. Please aware objects assigned temporary environment locked means modified.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create CallableCode object — callable_code","text":"CallableCode object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create CallableCode object — callable_code","text":"","code":"cf <- callable_code(code = \"mtcars\") cf$run() #> mpg cyl disp hp drat wt qsec vs am gear carb #> Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 #> Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 #> Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 #> Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 #> Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 #> Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 #> Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 #> Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 #> Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 #> Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 #> Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 #> Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 #> Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 #> Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 #> Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 #> Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 #> Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 #> Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 #> Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 #> Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 #> Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 #> Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 #> AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 #> Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 #> Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 #> Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 #> Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 #> Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 #> Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 #> Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 #> Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 #> Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 cf$get_call() #> [1] \"mtcars\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Create CallableFunction object — callable_function","title":"Create CallableFunction object — callable_function","text":"Create CallableFunction object execute specific function get reproducible call.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_function.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create CallableFunction object — callable_function","text":"","code":"callable_function(fun)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_function.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create CallableFunction object — callable_function","text":"fun (function) R function, directly name character string.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_function.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create CallableFunction object — callable_function","text":"CallableFunction object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/callable_function.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create CallableFunction object — callable_function","text":"","code":"cf <- callable_function(fun = stats::median) cf$set_args(list(x = 1:10, na.rm = FALSE)) cf$run() #> [1] 5.5 cf$get_call() #> [1] \"stats::median(x = 1:10, na.rm = FALSE)\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Data input for teal app — cdisc_data","title":"Data input for teal app — cdisc_data","text":"Function wrapper around teal_data() guesses join_keys given datasets whose names match ADAM datasets names.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data input for teal app — cdisc_data","text":"","code":"cdisc_data( ..., join_keys = teal.data::default_cdisc_join_keys[names(rlang::list2(...))], code = character(0), check = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data input for teal app — cdisc_data","text":"... (TealDataConnector, TealDataset, TealDatasetConnector, ) Either 1) object Teal* class, deprecated removed next release, 2) number objects provided name = value pairs, available version 0.4.0. join_keys (join_keys) single (join_key_set) (optional) object datasets column names used joining. empty automatically derived basing intersection datasets primary keys. ADAM datasets automatically derived. code (character, language) code reproduce datasets. check (logical) reproducibility check - whether perform check pre-processing code included object definitions actually produces objects. check true preprocessing code empty error thrown.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data input for teal app — cdisc_data","text":"TealData object TealDataset TealDatasetConnector, TealDataConnector provided, teal_data object otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data input for teal app — cdisc_data","text":"function checks keys added data sets","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data input for teal app — cdisc_data","text":"","code":"data <- cdisc_data( join_keys = join_keys( join_key(\"ADSL\", \"ADTTE\", c(\"STUDYID\" = \"STUDYID\", \"USUBJID\" = \"USUBJID\")) ) ) data <- within(data, { ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADTTE <- teal.data::example_cdisc_data(\"ADTTE\") })"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"","code":"cdisc_data_connector(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"CDISCTealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor of CDISCTealDataConnector objects. — cdisc_data_connector","text":"","code":"adsl_cf <- callable_function( function() as.data.frame(as.list(setNames(nm = get_cdisc_keys(\"ADSL\")))) ) adae_cf <- callable_function( function() as.data.frame(as.list(setNames(nm = get_cdisc_keys(\"ADAE\")))) ) adsl <- cdisc_dataset_connector( \"ADSL\", adsl_cf, keys = get_cdisc_keys(\"ADSL\"), parent = character(0) ) adae <- cdisc_dataset_connector( \"ADAE\", adae_cf, keys = get_cdisc_keys(\"ADAE\"), parent = \"ADSL\" ) data <- cdisc_data_connector( connection = data_connection(open_fun = callable_function(function() \"open function\")), connectors = list(adsl, adae) )"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealData object from a file — cdisc_data_file","text":"","code":"cdisc_data_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealData object from a file — cdisc_data_file","text":"path (connection) (character) string giving pathname file URL read . \"\" indicates connection stdin. code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealData object from a file — cdisc_data_file","text":"TealData object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_data_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealData object from a file — cdisc_data_file","text":"","code":"file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"# code> ADSL <- teal.data::example_cdisc_data('ADSL') ADTTE <- teal.data::example_cdisc_data('ADTTE') cdisc_data( cdisc_dataset(\\\"ADSL\\\", ADSL), cdisc_dataset(\\\"ADTTE\\\", ADTTE), code = \\\"ADSL <- teal.data::example_cdisc_data('ADSL') ADTTE <- teal.data::example_cdisc_data('ADTTE')\\\", check = FALSE ) # Warning: `cdisc_data_file()` was deprecated in teal.data 0.1.3. #> ℹ Please use `teal_data_file()` instead. #> Warning: The `data_objects` argument of `teal_data()` should use data directly. Using #> TealDatasetConnector and TealDataset is deprecated. Find more information on #> https://github.com/insightsengineering/teal/discussions/945 as of teal.data #> 0.3.1. #> ℹ The deprecated feature was likely used in the teal.data package. #> Please report the issue at #> . #> A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... #> --> Element 2: #> A CDISCTealDataset object containing the following data.frame (2000 rows and 67 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 2 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 3 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 4 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 5 AB12345 AB12345-BRA-1-id-105 id-105 BRA-1 38 YEARS M #> 6 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 2 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 3 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 4 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 5 BLACK OR AFRICAN AMERICAN HISPANIC OR LATINO BRA N INV ID BRA-1 #> 6 WHITE NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 6 Dr. BRA-1 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 ITTFL #> 1 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 2 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 3 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 4 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 5 C: Combination A: Drug X South America B S1 4.156914 MEDIUM Y #> 6 B: Placebo A: Drug X South America B S2 6.462991 LOW Y #> SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 2 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 3 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 4 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 5 Y Y Y N 2020-03-08 2020-03-08 05:39:28 #> 6 Y Y N N 2020-11-03 2020-11-04 04:08:58 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 2 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 3 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 4 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 5 2022-02-14 20:58:26 2020-03-08 05:39:28 2021-02-14 14:58:26 #> 6 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 2 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 3 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 4 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 5 2021-02-14 14:58:26 2022-02-14 20:58:26 2020-03-08 05:39:28 #> 6 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 2 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 3 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 4 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 5 2021-02-14 14:58:26 2021-02-14 14:58:26 2022-02-14 20:58:26 DISCONTINUED #> 6 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS #> 1 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 2 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 3 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 4 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 5 DISCONTINUED 2022-02-14 709 PROTOCOL VIOLATION #> 6 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT #> DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ TTESEQ #> 1 NA 2022-03-09 NA 4 4 #> 2 NA 2022-03-09 NA 2 2 #> 3 NA 2022-03-09 NA 3 3 #> 4 NA 2022-03-09 NA 1 1 #> 5 NA 2022-03-09 NA NA NA #> 6 ADVERSE EVENT 24 <=30 2022-03-16 496 Yes 2 2 #> PARAM PARAMCD AVAL AVALU ADTM #> 1 Duration of Confirmed Response CRSD 1273.8498 DAYS 2021-05-27 05:39:28 #> 2 Event Free Survival EFS 135.9787 DAYS 2020-09-25 05:39:28 #> 3 Overall Survival OS 1759.8678 DAYS 2020-11-25 05:39:28 #> 4 Progression Free Survival PFS 241.1912 DAYS 2020-03-30 05:39:28 #> 5 Total Number of Exacerbations TNE 1.0000 COUNT #> 6 Duration of Confirmed Response CRSD 544.5728 DAYS 2021-10-05 04:08:58 #> ADY CNSR EVNTDESC CNSDTDSC lgTMATRSK #> 1 445 1 Last Date Known To Be Alive End of AE Reporting Period NA #> 2 201 0 Death NA #> 3 262 0 Death NA #> 4 22 0 Disease Progression NA #> 5 NA 1 End of AE Reporting Period -2.802988 #> 6 335 0 Death NA #> ..."},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a new object of CDISCTealDataset class — cdisc_dataset","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"Function creates CDISCTealDataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"","code":"cdisc_dataset( dataname, x, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0) else \"ADSL\", label = data_label(x), code = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"dataname (character) given name dataset, contain spaces x (data.frame MultiAssayExperiment) object dataset created keys optional, (character) vector primary keys parent (character, optional) parent dataset name label (character) label describe dataset code (character) character string defining code needed produce data set x vars (named list) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"(CDISCTealDataset) dataset connected metadata","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a new object of CDISCTealDataset class — cdisc_dataset","text":"","code":"ADSL <- example_cdisc_data(\"ADSL\") cdisc_dataset(\"ADSL\", ADSL, metadata = list(type = \"teal.data\")) #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ..."},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"","code":"cdisc_dataset_connector( dataname, pull_callable, keys, parent = if (identical(dataname, \"ADSL\")) character(0) else \"ADSL\", label = character(0), code = character(0), script = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys optional, (character) vector dataset primary keys column names parent (character, optional) parent dataset name label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"new CDISCTealDatasetConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a new CDISCTealDatasetConnector object — cdisc_dataset_connector","text":"Create CDISCTealDatasetConnector callable_function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Load CDISCTealDataset object from a file — cdisc_dataset_file","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"","code":"cdisc_dataset_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"path (character) string giving pathname file read . code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"(CDISCTealDataset) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/cdisc_dataset_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load CDISCTealDataset object from a file — cdisc_dataset_file","text":"","code":"# simple example file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) cdisc_dataset(dataname = \\\"ADSL\\\", x = teal.data::example_cdisc_data(\\\"ADSL\\\"), code = \\\"ADSL <- teal.data::example_cdisc_data('ADSL')\\\")\" ), con = file_example ) x <- cdisc_dataset_file(file_example, code = character(0)) get_code(x) #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_ellipsis.html","id":null,"dir":"Reference","previous_headings":"","what":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"Ellipsis, ..., needed part method arguments allow arguments different generic's arguments pass check(). Hence, ..., always empty. function check condition.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_ellipsis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"","code":"check_ellipsis(..., stop = FALSE, allowed_args = character(0))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_ellipsis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"... literally just ... stop TRUE raise error; FALSE output warning message allowed_args character vector naming arguments allowed .... allow unnamed arguments, let \"\" one elements character vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_ellipsis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"NULL ... empty","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_ellipsis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Ensure the ellipsis, ..., in method arguments are empty — check_ellipsis","text":"","code":"method.class <- function(a, b, c, ...) { check_ellipsis(...) } method.class <- function(a, b, c, ...) { check_ellipsis(..., allowed_args = c(\"y\", \"z\")) }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_pkg_quietly.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if package can be loaded — check_pkg_quietly","title":"Check if package can be loaded — check_pkg_quietly","text":"Check package can loaded","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_pkg_quietly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if package can be loaded — check_pkg_quietly","text":"","code":"check_pkg_quietly(pckg, msg)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_pkg_quietly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if package can be loaded — check_pkg_quietly","text":"pckg character package name. msg character error message display package available.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_pkg_quietly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if package can be loaded — check_pkg_quietly","text":"Error invisible NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_simple_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Whether the variable name is good to use within Show R Code — check_simple_name","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"Spaces problematic variables must escaped backticks. Also, start number R may silently make valid changing . Therefore, allow alphanumeric characters underscores. first character name must alphabetic character can followed alphanumeric characters.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_simple_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"","code":"check_simple_name(name)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_simple_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"name character, single vector name check","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/check_simple_name.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Whether the variable name is good to use within Show R Code — check_simple_name","text":"","code":"teal.data:::check_simple_name(\"aas2df\") teal.data:::check_simple_name(\"ADSL\") teal.data:::check_simple_name(\"ADSLmodified\") teal.data:::check_simple_name(\"ADSL_2\") teal.data:::check_simple_name(\"a1\") # the following fail if (FALSE) { teal.data:::check_simple_name(\"1a\") teal.data:::check_simple_name(\"ADSL.modified\") teal.data:::check_simple_name(\"ADSL_modified\") teal.data:::check_simple_name(\"a1...\") }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Code TealDatasetConnector — code_dataset_connector","text":"","code":"code_dataset_connector( dataname, code, keys = character(0), label = character(0), mutate_code = character(0), mutate_script = character(0), metadata = NULL, ... ) code_cdisc_dataset_connector( dataname, code, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), mutate_code = character(0), metadata = NULL, ... )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Code TealDatasetConnector — code_dataset_connector","text":"dataname (character) given name dataset may contain spaces code (character) String containing code produce object. code must end call object. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. mutate_code (character) String containing code used mutate object produced. mutate_script (character) Alternatively mutate_code - location file containing modification code. used simultaneously mutate_script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... Additional arguments applied pull function. case object code depends raw_data TealDataset, TealDatasetConnector object(s) constant value, /object(s) included. Please note vars included object local vars modified within another dataset. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Code TealDatasetConnector — code_dataset_connector","text":"Create TealDatasetConnector string code. Create CDISCTealDatasetConnector string code keys assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Code TealDatasetConnector — code_dataset_connector","text":"","code":"x <- code_dataset_connector( dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\"); ADSL\" ) x$get_code() #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\\nADSL <- ADSL\" mutate_dataset(x, code = \"ADSL$new_variable <- 1\") x$get_code() #> [1] \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\\nADSL <- ADSL\\nADSL$new_variable <- 1\" file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"seed <- 1; ADSL <- radsl(cached = TRUE, seed = seed)\\nADSL\" ), con = file_example ) y <- code_dataset_connector( dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = paste0(readLines(file_example), collapse = \"\\n\") )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dependency.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Object Dependencies Structure Within Parsed Code — code_dependency","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"function constructs dependency structure identifies relationships objects parsed code. helps understand objects needed recreate specific object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dependency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"","code":"code_dependency(code, object_names)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dependency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"code expression srcref attribute character code. object_names (character(n)) vector containing names existing objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dependency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"list three components: occurrence: named list object names names existing objects, element numeric vector indicating calls object appears. cooccurrence: list length number calls parsed_code (parsed_code = parse(text = code) code input character parsed_code = code expression input. contains NULL values co-occurrence objects character vector indicating co-occurrence objects specific parsed_code call element. character vector, first element name dependent object, rest influencing objects. effects: named list object names names existing objects, element numeric vector indicating calls effect object. side-effects pointing object, element NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_dependency.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create Object Dependencies Structure Within Parsed Code — code_dependency","text":"function assumes object relationships established using <-, =, -> assignment operators. support object creation methods like assign <<-, non-standard-evaluation methods. specify relationships side-effects objects, can use comment tag # @linksto object_name end line side-effect occurs.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_exclude.html","id":null,"dir":"Reference","previous_headings":"","what":"Exclude from code — code_exclude","title":"Exclude from code — code_exclude","text":"Excludes lines code. possible exclude one line ended # nocode","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_exclude.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Exclude from code — code_exclude","text":"","code":"code_exclude(lines, exclude_comments, file_path)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/code_exclude.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Exclude from code — code_exclude","text":"lines (character) preprocessing code. exclude_comments (logical) whether exclude commented-lines code. Lines excluded ended # nocode. multiple line exclusions one enclose ignored block code # nocode> # Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> NA NA NA NA NA col_labels(x) <- paste(\"label for\", names(iris)) col_labels(x) #> Sepal.Length Sepal.Width Petal.Length #> \"label for Sepal.Length\" \"label for Sepal.Width\" \"label for Petal.Length\" #> Petal.Width Species #> \"label for Petal.Width\" \"label for Species\" if (interactive()) { View(x) # in RStudio data viewer labels are displayed }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Label Attributes of Variables in a data.frame — col_labels","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"Variable labels can stored label attribute variable. functions returns named character vector variable labels (empty sting specified)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"","code":"col_labels(x, fill = FALSE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"function taken 1-1 formatters package, reduce complexity dependency tree.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"x data.frame object fill boolean case label attribute exist TRUE variable names returned, otherwise NA","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"named character vector variable labels, names correspond variable names","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Label Attributes of Variables in a data.frame — col_labels","text":"","code":"x <- iris col_labels(x) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> NA NA NA NA NA col_labels(x) <- paste(\"label for\", names(iris)) col_labels(x) #> Sepal.Length Sepal.Width Petal.Length #> \"label for Sepal.Length\" \"label for Sepal.Width\" \"label for Petal.Length\" #> Petal.Width Species #> \"label for Petal.Width\" \"label for Species\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_relabel.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy and Change Variable Labels of a data.frame — col_relabel","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"Relabel subset variables","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_relabel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"","code":"col_relabel(x, ...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_relabel.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"function taken 1-1 formatters package, reduce complexity dependency tree.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_relabel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"x data.frame object ... name-value pairs, name corresponds variable name x value new variable label","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_relabel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"copy x changed labels according ...","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_relabel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Copy and Change Variable Labels of a data.frame — col_relabel","text":"","code":"x <- col_relabel(iris, Sepal.Length = \"Sepal Length of iris flower\") col_labels(x) #> Sepal.Length Sepal.Width #> \"Sepal Length of iris flower\" NA #> Petal.Length Petal.Width #> NA NA #> Species #> NA"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/csv_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"csv TealDatasetConnector — csv_dataset_connector","text":"","code":"csv_dataset_connector( dataname, file, keys = character(0), label = character(0), code = character(0), script = character(0), metadata = list(type = \"csv\", file = file), ... ) csv_cdisc_dataset_connector( dataname, file, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), metadata = list(type = \"csv\", file = file), ... )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/csv_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"csv TealDatasetConnector — csv_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) path (.csv) (general delimited) file contains data.frame object keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... (optional) additional arguments applied pull function (readr::read_delim) default delim = \",\". parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/csv_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"csv TealDatasetConnector — csv_dataset_connector","text":"Create TealDatasetConnector csv (general delimited file). Create CDISCTealDatasetConnector csv (general delimited) file keys parent name assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/csv_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"csv TealDatasetConnector — csv_dataset_connector","text":"","code":"if (FALSE) { x <- csv_dataset_connector( dataname = \"ADSL\", file = \"path/to/file.csv\", delim = \",\", col_types = quote(readr::cols(AGE = \"i\")) ) x$get_code() }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_connection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor for TealDataConnection class. — data_connection","text":"","code":"data_connection( open_fun = NULL, close_fun = NULL, ping_fun = NULL, if_conn_obj = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_connection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor for TealDataConnection class. — data_connection","text":"open_fun (CallableFunction) function open connection close_fun (CallableFunction) function close connection ping_fun (CallableFunction) function ping connection if_conn_obj optional, (logical) whether store conn object returned opening","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_connection.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The constructor for TealDataConnection class. — data_connection","text":"TealDataConnection object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_connection.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor for TealDataConnection class. — data_connection","text":"","code":"open_fun <- callable_function(data.frame) # define opening function open_fun$set_args(list(x = 1:5)) # define fixed arguments to opening function close_fun <- callable_function(sum) # define closing function close_fun$set_args(list(x = 1:5)) # define fixed arguments to closing function ping_fun <- callable_function(function() TRUE) x <- data_connection( # define connection ping_fun = ping_fun, # define ping function open_fun = open_fun, # define opening function close_fun = close_fun # define closing function ) x$set_open_args(args = list(y = letters[1:5])) # define additional arguments if necessary x$open() # call opening function x$get_open_call() # check reproducible R code #> [1] \"data.frame(x = 1:5, y = c(\\\"a\\\", \\\"b\\\", \\\"c\\\", \\\"d\\\", \\\"e\\\"))\" # get data from connection via TealDataConnector$get_dataset() if (FALSE) { x$open(args = list(x = 1:5, y = letters[1:5])) # able to call opening function with arguments x$close() # call closing function }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label-set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dataset label attribute — data_label<-","text":"","code":"data_label(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label-set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dataset label attribute — data_label<-","text":"x data.frame attribute set value (character) label","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label-set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dataset label attribute — data_label<-","text":"modified x object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label-set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set dataset label attribute — data_label<-","text":"","code":"x <- teal.data::example_cdisc_data(\"ADSL\") data_label(x) <- \"My custom label\" data_label(x) #> [1] \"My custom label\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset label attribute — data_label","text":"","code":"data_label(data)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset label attribute — data_label","text":"data data.frame attribute extracted","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset label attribute — data_label","text":"(character) label NULL missing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/data_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset label attribute — data_label","text":"","code":"data_label(example_cdisc_data(\"ADSL\")) #> [1] \"Subject Level Analysis Dataset\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/datanames.html","id":null,"dir":"Reference","previous_headings":"","what":"Names of Data Sets in teal_data Object — datanames","title":"Names of Data Sets in teal_data Object — datanames","text":"Get set value datanames slot.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/datanames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Names of Data Sets in teal_data Object — datanames","text":"","code":"datanames(x) datanames(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/datanames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Names of Data Sets in teal_data Object — datanames","text":"x (teal_data) object access modify value (character) new value @datanames; elements must names variables existing @env","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/datanames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Names of Data Sets in teal_data Object — datanames","text":"contents @datanames teal_data updated @datanames.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/datanames.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Names of Data Sets in teal_data Object — datanames","text":"@datanames slot teal_data object specifies variables stored environment (@env slot) data sets taken consideration. contents @datanames can specified upon creation default variables @env. Variables created later, may well data sets, automatically considered . Use function update slot.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/datanames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Names of Data Sets in teal_data Object — datanames","text":"","code":"td <- teal_data(iris = iris) td <- within(td, mtcars <- mtcars) datanames(td) #> [1] \"iris\" datanames(td) <- c(\"iris\", \"mtcars\")"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"","code":"# S3 method for MultiAssayExperiment dataset( dataname, x, keys = character(0), label = data_label(x), code = character(0), vars = list(), metadata = NULL ) dataset( dataname, x, keys = character(0), label = data_label(x), code = character(0), vars = list(), metadata = NULL ) # S3 method for data.frame dataset( dataname, x, keys = character(0), label = data_label(x), code = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"dataname (character) given name dataset, contain spaces x (data.frame MultiAssayExperiment) object dataset created keys optional, (character) vector primary keys label (character) label describe dataset code (character) character string defining code needed produce data set x vars (named list) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list NULL) field containing metadata dataset. element list atomic length one.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"TealDataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 method to construct an MAETealDataset object from MultiAssayExperiment — dataset.MultiAssayExperiment","text":"","code":"# Simple example utils::data(miniACC, package = \"MultiAssayExperiment\") mae_d <- dataset( \"MAE\", miniACC, keys = c(\"STUDYID\", \"USUBJID\"), metadata = list(type = \"example\") ) #> Loading required package: MultiAssayExperiment #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #> #> Attaching package: ‘MatrixGenerics’ #> The following objects are masked from ‘package:matrixStats’: #> #> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #> colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #> colWeightedMeans, colWeightedMedians, colWeightedSds, #> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #> rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #> rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #> #> Attaching package: ‘BiocGenerics’ #> The following objects are masked from ‘package:stats’: #> #> IQR, mad, sd, var, xtabs #> The following objects are masked from ‘package:base’: #> #> Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, #> as.data.frame, basename, cbind, colnames, dirname, do.call, #> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, #> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, #> tapply, union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #> #> Attaching package: ‘S4Vectors’ #> The following object is masked from ‘package:utils’: #> #> findMatches #> The following objects are masked from ‘package:base’: #> #> I, expand.grid, unname #> Loading required package: IRanges #> Loading required package: GenomeInfoDb #> #> Attaching package: ‘GenomicRanges’ #> The following object is masked from ‘package:magrittr’: #> #> subtract #> Loading required package: Biobase #> Welcome to Bioconductor #> #> Vignettes contain introductory material; view with #> 'browseVignettes()'. To cite Bioconductor, see #> 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'. #> #> Attaching package: ‘Biobase’ #> The following object is masked from ‘package:MatrixGenerics’: #> #> rowMedians #> The following objects are masked from ‘package:matrixStats’: #> #> anyMissing, rowMedians mae_d$get_dataname() #> [1] \"MAE\" mae_d$get_dataset_label() #> character(0) mae_d$get_metadata() #> $type #> [1] \"example\" #> mae_d$get_code() #> [1] \"\" mae_d$get_raw_data() #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns #> [2] gistict: SummarizedExperiment with 198 rows and 90 columns #> [3] RPPAArray: SummarizedExperiment with 33 rows and 46 columns #> [4] Mutations: matrix with 97 rows and 90 columns #> [5] miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files # Simple example dataset(\"iris\", iris) #> A TealDataset object containing the following data.frame (150 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa #> ... # Example with more arguments if (FALSE) { ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset(dataname = \"ADSL\", x = ADSL) ADSL_dataset$get_dataname() ADSL_dataset <- dataset( dataname = \"ADSL\", x = ADSL, label = \"AdAM subject-level dataset\", code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ADSL_dataset$get_metadata() ADSL_dataset$get_dataset_label() ADSL_dataset$get_code() }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new TealDatasetConnector object — dataset_connector","text":"","code":"dataset_connector( dataname, pull_callable, keys = character(0), label = character(0), code = character(0), script = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new TealDatasetConnector object — dataset_connector","text":"dataname (character) given name dataset may contain spaces pull_callable (CallableFunction) function necessary arguments set fetch data connection. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new TealDatasetConnector object — dataset_connector","text":"new TealDatasetConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a new TealDatasetConnector object — dataset_connector","text":"Create TealDatasetConnector callable_function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a new TealDatasetConnector object — dataset_connector","text":"","code":"library(MultiAssayExperiment) # data.frame example pull_fun2 <- callable_function(data.frame) pull_fun2$set_args(args = list(a = c(1, 2, 3))) dataset_connector(\"test\", pull_fun2) #> A TealDatasetConnector object, named test, containing a TealDataset object that has not been loaded/pulled # MultiAssayExperiment example pull_fun <- callable_function( function() { library(\"MultiAssayExperiment\") data(\"miniACC\") return(miniACC) } ) dataset_connector( \"miniacc\", pull_fun, code = 'library(\"MultiAssayExperiment\"); data(\"miniACC\"); return(miniACC)' ) #> A TealDatasetConnector object, named miniacc, containing a TealDataset object that has not been loaded/pulled"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"","code":"dataset_connector_file(path) cdisc_dataset_connector_file(path)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"path (character) string giving pathname file read .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"TealDatasetConnector object CDISCTealDatasetConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector_file.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"Please note script end call creating desired object. error raised otherwise. Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_connector_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealDatasetConnector object from a file — dataset_connector_file","text":"","code":"# simple example library(magrittr) file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) pull_callable <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \\\"ADSL\\\")) dataset_connector(\\\"ADSL\\\", pull_callable, get_cdisc_keys(\\\"ADSL\\\"))\" ), con = file_example ) x <- dataset_connector_file(file_example) get_code(x) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\" # simple example library(magrittr) file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) pull_callable <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \\\"ADSL\\\")) cdisc_dataset_connector(\\\"ADSL\\\", pull_callable, get_cdisc_keys(\\\"ADSL\\\"))\" ), con = file_example ) x <- cdisc_dataset_connector_file(file_example) get_code(x) #> [1] \"ADSL <- teal.data::example_cdisc_data(dataname = \\\"ADSL\\\")\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Load TealDataset object from a file — dataset_file","title":"Load TealDataset object from a file — dataset_file","text":"Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealDataset object from a file — dataset_file","text":"","code":"dataset_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealDataset object from a file — dataset_file","text":"path (character) string giving pathname file read . code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealDataset object from a file — dataset_file","text":"TealDataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dataset_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealDataset object from a file — dataset_file","text":"","code":"# simple example file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) dataset(dataname = \\\"iris\\\", x = iris, code = \\\"iris\\\")\" ), con = file_example ) x <- dataset_file(file_example, code = character(0)) get_code(x) #> [1] \"iris\" # custom code file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) # code> x <- iris x$a1 <- 1 x$a2 <- 2 # [1] \"x <- iris\\nx$a1 <- 1\\nx$a2 <- 2\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/deep_clone_r6.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to deep copy R6 object — deep_clone_r6","title":"Helper function to deep copy R6 object — deep_clone_r6","text":"cloning R6 object private function deep_clone automatically used. ensure complete clone private function call function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/deep_clone_r6.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to deep copy R6 object — deep_clone_r6","text":"","code":"deep_clone_r6(name, value)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/deep_clone_r6.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to deep copy R6 object — deep_clone_r6","text":"name (character) argument passed deep_clone function. value (R object) argument passed deep_clone function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/default_cdisc_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"List containing the default CDISC join keys — default_cdisc_join_keys","title":"List containing the default CDISC join keys — default_cdisc_join_keys","text":"List containing default CDISC join keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/default_cdisc_join_keys.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List containing the default CDISC join keys — default_cdisc_join_keys","text":"data object created loading time cdisc_datasets/cdisc_datasets.yaml.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/deprecated_join_keys_extract.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extrapolate parents from TealData classes — deprecated_join_keys_extract","text":"","code":"deprecated_join_keys_extract(data_objects, join_keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/deprecated_join_keys_extract.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extrapolate parents from TealData classes — deprecated_join_keys_extract","text":"note: function removed following classes defunct: TealDataConnector, TealDataset, TealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/detect_symbol.html","id":null,"dir":"Reference","previous_headings":"","what":"Detects ","title":"Detects ","text":"Detects \"SYMBOL\" tokens row bounded getParseData() structure","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/detect_symbol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detects ","text":"","code":"detect_symbol(object, calls_pd)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/detect_symbol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detects ","text":"object character containing name object calls_pd list data.frames, result get_children(utils::getParseData(), parent = 0) applied parse(text = code, keep.source = TRUE) code_dependency(code).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/detect_symbol.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detects ","text":"logical vector pointing elements pd SYMBOL token row object text column","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dot-merge_parents.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge parents for 2 join_keys object — .merge_parents","title":"Merge parents for 2 join_keys object — .merge_parents","text":"Merge parents 2 join_keys object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dot-merge_parents.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge parents for 2 join_keys object — .merge_parents","text":"","code":".merge_parents(x, y)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dot-merge_parents.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge parents for 2 join_keys object — .merge_parents","text":"x, y (join_keys) objects merge parents","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/dot-merge_parents.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge parents for 2 join_keys object — .merge_parents","text":"list parents merged 2 join_keys. object .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code enclosed within — enclosed_with","title":"Get code enclosed within — enclosed_with","text":"Extracts lines code enclosed within regexp starts_at stops_at","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get code enclosed within — enclosed_with","text":"","code":"enclosed_with(lines)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get code enclosed within — enclosed_with","text":"lines (character) preprocessing code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get code enclosed within — enclosed_with","text":"(character) subset lines start end preprocessing start stop tags.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with_dataname.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code enclosed within — enclosed_with_dataname","title":"Get code enclosed within — enclosed_with_dataname","text":"Extracts lines code enclosed within regexp starts_at stops_at","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with_dataname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get code enclosed within — enclosed_with_dataname","text":"","code":"enclosed_with_dataname(lines, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with_dataname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get code enclosed within — enclosed_with_dataname","text":"lines (character) preprocessing code. dataname (character) metadata returned lines","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/enclosed_with_dataname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get code enclosed within — enclosed_with_dataname","text":"(list) list lines numbers certain chunks code specific file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/example_cdisc_data.html","id":null,"dir":"Reference","previous_headings":"","what":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"meant retrieve SCDA dataset, dataset maintained .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/example_cdisc_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"","code":"example_cdisc_data(dataname)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/example_cdisc_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"dataname name CDISC dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/example_cdisc_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"cdisc_data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/example_cdisc_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"This function returns a dummy dataset for testing examples and should only be used within teal.data. — example_cdisc_data","text":"function creates copy SCDA data testing purposes. CDISC data includes ADSL, ADAE, ADLB, ADCM, ADEX, ADRS, ADTR ADTTE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/find_source_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Finds lines of code with source call — find_source_code","title":"Finds lines of code with source call — find_source_code","text":"Finds lines preprocessing code source() call located","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/find_source_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finds lines of code with source call — find_source_code","text":"","code":"find_source_code(lines)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/find_source_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finds lines of code with source call — find_source_code","text":"lines (character) preprocessing code.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/fun_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function Dataset Connector — fun_dataset_connector","text":"","code":"fun_dataset_connector( dataname, fun, fun_args = NULL, keys = character(0), label = character(0), code = character(0), script = character(0), func_name = substitute(fun), metadata = NULL, ... ) fun_cdisc_dataset_connector( dataname, fun, fun_args = NULL, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), func_name = substitute(fun), metadata = NULL, ... )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/fun_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function Dataset Connector — fun_dataset_connector","text":"dataname (character) given name dataset may contain spaces fun (function) custom function obtain dataset. fun_args (list) additional arguments (func). keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. func_name (name) internal purposes, please keep default metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... Additional arguments applied pull function. case object code depends raw_data TealDataset, TealDatasetConnector object(s) constant value, /object(s) included. Please note vars included object local vars modified within another dataset. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/fun_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function Dataset Connector — fun_dataset_connector","text":"Create TealDatasetConnector function arguments. Create CDISCTealDatasetConnector function arguments keys parent name assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/fun_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function Dataset Connector — fun_dataset_connector","text":"","code":"my_data <- function(...) { data.frame( ID = paste0(\"ABC_\", seq_len(10)), var1 = rnorm(n = 10), var2 = rnorm(n = 10), var3 = rnorm(n = 10) ) } y <- fun_dataset_connector( dataname = \"XYZ\", fun = my_data ) y$get_code() #> [1] \"my_data <- function(...) {\\n data.frame(ID = paste0(\\\"ABC_\\\", seq_len(10)), var1 = rnorm(n = 10), var2 = rnorm(n = 10), var3 = rnorm(n = 10))\\n}\\nXYZ <- (function(...) {\\n data.frame(ID = paste0(\\\"ABC_\\\", seq_len(10)), var1 = rnorm(n = 10), var2 = rnorm(n = 10), var3 = rnorm(n = 10))\\n})()\" y$pull() get_raw_data(y) #> ID var1 var2 var3 #> 1 ABC_1 -1.67537372 1.0195769 0.73268871 #> 2 ABC_2 -0.70114973 0.4532490 0.20832726 #> 3 ABC_3 0.42969125 0.8243697 -0.61936527 #> 4 ABC_4 -1.25086426 0.6144842 0.09432247 #> 5 ABC_5 -0.33998223 -0.3325400 0.65914064 #> 6 ABC_6 1.65082381 -0.4185447 -0.04291810 #> 7 ABC_7 0.94785568 0.3379617 1.40202883 #> 8 ABC_8 1.33692879 -0.8392215 0.59208309 #> 9 ABC_9 0.92528696 0.4659020 -1.90823250 #> 10 ABC_10 -0.06008311 -1.1272970 -0.69203847"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_attrs.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dataset attributes — get_attrs","title":"Get dataset attributes — get_attrs","text":"Get dataset attributes form named list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_attrs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset attributes — get_attrs","text":"","code":"get_attrs(x) # S3 method for TealDataset get_attrs(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_attrs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset attributes — get_attrs","text":"x object (TealDataset) class","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_attrs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset attributes — get_attrs","text":"named list object attributes","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_attrs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset attributes — get_attrs","text":"","code":"# TealDataset -------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") x1 <- dataset(\"ADSL\", x = ADSL, label = \"custom label\") get_attrs(x1) #> $names #> [1] \"STUDYID\" \"USUBJID\" \"SUBJID\" \"SITEID\" \"AGE\" \"AGEU\" #> [7] \"SEX\" \"RACE\" \"ETHNIC\" \"COUNTRY\" \"DTHFL\" \"INVID\" #> [13] \"INVNAM\" \"ARM\" \"ARMCD\" \"ACTARM\" \"ACTARMCD\" \"TRT01P\" #> [19] \"TRT01A\" \"TRT02P\" \"TRT02A\" \"REGION1\" \"STRATA1\" \"STRATA2\" #> [25] \"BMRKR1\" \"BMRKR2\" \"ITTFL\" \"SAFFL\" \"BMEASIFL\" \"BEP01FL\" #> [31] \"AEWITHFL\" \"RANDDT\" \"TRTSDTM\" \"TRTEDTM\" \"TRT01SDTM\" \"TRT01EDTM\" #> [37] \"TRT02SDTM\" \"TRT02EDTM\" \"AP01SDTM\" \"AP01EDTM\" \"AP02SDTM\" \"AP02EDTM\" #> [43] \"EOSSTT\" \"EOTSTT\" \"EOSDT\" \"EOSDY\" \"DCSREAS\" \"DTHDT\" #> [49] \"DTHCAUS\" \"DTHCAT\" \"LDDTHELD\" \"LDDTHGR1\" \"LSTALVDT\" \"DTHADY\" #> [55] \"ADTHAUT\" #> #> $row.names #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 #> [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 #> [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 #> [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 #> [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 #> [91] 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 #> [109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 #> [127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 #> [145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 #> [163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 #> [181] 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 #> [199] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 #> [217] 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 #> [235] 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 #> [253] 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 #> [271] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 #> [289] 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 #> [307] 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 #> [325] 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 #> [343] 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 #> [361] 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 #> [379] 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 #> [397] 397 398 399 400 #> #> $class #> [1] \"tbl_df\" \"tbl\" \"data.frame\" #> #> $label #> [1] \"Subject Level Analysis Dataset\" #> #> $study_duration_secs #> [1] 63115200 #> #> $`creation date` #> [1] \"2023-03-22\" #> #> $column_labels #> STUDYID #> \"Study Identifier\" #> USUBJID #> \"Unique Subject Identifier\" #> SUBJID #> \"Subject Identifier for the Study\" #> SITEID #> \"Study Site Identifier\" #> AGE #> \"Age\" #> AGEU #> \"Age Units\" #> SEX #> \"Sex\" #> RACE #> \"Race\" #> ETHNIC #> \"Ethnicity\" #> COUNTRY #> \"Country\" #> DTHFL #> \"Subject Death Flag\" #> INVID #> \"Investigator Identifier\" #> INVNAM #> \"Investigator Name\" #> ARM #> \"Description of Planned Arm\" #> ARMCD #> \"Planned Arm Code\" #> ACTARM #> \"Description of Actual Arm\" #> ACTARMCD #> \"Actual Arm Code\" #> TRT01P #> \"Planned Treatment for Period 01\" #> TRT01A #> \"Actual Treatment for Period 01\" #> TRT02P #> \"Planned Treatment for Period 02\" #> TRT02A #> \"Actual Treatment for Period 02\" #> REGION1 #> \"Geographic Region 1\" #> STRATA1 #> \"Stratification Factor 1\" #> STRATA2 #> \"Stratification Factor 2\" #> BMRKR1 #> \"Continuous Level Biomarker 1\" #> BMRKR2 #> \"Categorical Level Biomarker 2\" #> ITTFL #> \"Intent-To-Treat Population Flag\" #> SAFFL #> \"Safety Population Flag\" #> BMEASIFL #> \"Response Evaluable Population Flag\" #> BEP01FL #> \"Biomarker Evaluable Population Flag\" #> AEWITHFL #> \"AE Leading to Drug Withdrawal Flag\" #> RANDDT #> \"Date of Randomization\" #> TRTSDTM #> \"Datetime of First Exposure to Treatment\" #> TRTEDTM #> \"Datetime of Last Exposure to Treatment\" #> TRT01SDTM #> \"Datetime of First Exposure to Treatment in Period 01\" #> TRT01EDTM #> \"Datetime of Last Exposure in Period 01\" #> TRT02SDTM #> \"Datetime of First Exposure to Treatment in Period 02\" #> TRT02EDTM #> \"Datetime of Last Exposure to Treatment in Period 02\" #> AP01SDTM #> \"Period 01 Start Datetime\" #> AP01EDTM #> \"Period 01 End Datetime\" #> AP02SDTM #> \"Period 02 Start Datetime\" #> AP02EDTM #> \"Period 02 End Datetime\" #> EOSSTT #> \"End of Study Status\" #> EOTSTT #> \"End of Treatment Status\" #> EOSDT #> \"End of Study Date\" #> EOSDY #> \"End of Study Relative Day\" #> DCSREAS #> \"Reason for Discontinuation from Study\" #> DTHDT #> \"Date of Death\" #> DTHCAUS #> \"Cause of Death\" #> DTHCAT #> \"Cause of Death Category\" #> LDDTHELD #> \"Elapsed Days from Last Dose to Death\" #> LDDTHGR1 #> \"Last Dose to Death - Days Elapsed Grp 1\" #> LSTALVDT #> \"Date Last Known Alive\" #> DTHADY #> \"Relative Day of Death\" #> ADTHAUT #> \"Autopsy Performed\" #> #> $row_labels #> NULL #> #> $dataname #> [1] \"ADSL\" #> #> $dataset_label #> [1] \"custom label\" #> #> $keys #> character(0) #> x2 <- dataset( \"ADSL\", x = ADSL, keys = get_cdisc_keys(\"ADSL\"), label = \"custom label\" ) get_attrs(x2) #> $names #> [1] \"STUDYID\" \"USUBJID\" \"SUBJID\" \"SITEID\" \"AGE\" \"AGEU\" #> [7] \"SEX\" \"RACE\" \"ETHNIC\" \"COUNTRY\" \"DTHFL\" \"INVID\" #> [13] \"INVNAM\" \"ARM\" \"ARMCD\" \"ACTARM\" \"ACTARMCD\" \"TRT01P\" #> [19] \"TRT01A\" \"TRT02P\" \"TRT02A\" \"REGION1\" \"STRATA1\" \"STRATA2\" #> [25] \"BMRKR1\" \"BMRKR2\" \"ITTFL\" \"SAFFL\" \"BMEASIFL\" \"BEP01FL\" #> [31] \"AEWITHFL\" \"RANDDT\" \"TRTSDTM\" \"TRTEDTM\" \"TRT01SDTM\" \"TRT01EDTM\" #> [37] \"TRT02SDTM\" \"TRT02EDTM\" \"AP01SDTM\" \"AP01EDTM\" \"AP02SDTM\" \"AP02EDTM\" #> [43] \"EOSSTT\" \"EOTSTT\" \"EOSDT\" \"EOSDY\" \"DCSREAS\" \"DTHDT\" #> [49] \"DTHCAUS\" \"DTHCAT\" \"LDDTHELD\" \"LDDTHGR1\" \"LSTALVDT\" \"DTHADY\" #> [55] \"ADTHAUT\" #> #> $row.names #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 #> [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 #> [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 #> [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 #> [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 #> [91] 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 #> [109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 #> [127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 #> [145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 #> [163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 #> [181] 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 #> [199] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 #> [217] 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 #> [235] 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 #> [253] 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 #> [271] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 #> [289] 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 #> [307] 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 #> [325] 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 #> [343] 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 #> [361] 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 #> [379] 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 #> [397] 397 398 399 400 #> #> $class #> [1] \"tbl_df\" \"tbl\" \"data.frame\" #> #> $label #> [1] \"Subject Level Analysis Dataset\" #> #> $study_duration_secs #> [1] 63115200 #> #> $`creation date` #> [1] \"2023-03-22\" #> #> $column_labels #> STUDYID #> \"Study Identifier\" #> USUBJID #> \"Unique Subject Identifier\" #> SUBJID #> \"Subject Identifier for the Study\" #> SITEID #> \"Study Site Identifier\" #> AGE #> \"Age\" #> AGEU #> \"Age Units\" #> SEX #> \"Sex\" #> RACE #> \"Race\" #> ETHNIC #> \"Ethnicity\" #> COUNTRY #> \"Country\" #> DTHFL #> \"Subject Death Flag\" #> INVID #> \"Investigator Identifier\" #> INVNAM #> \"Investigator Name\" #> ARM #> \"Description of Planned Arm\" #> ARMCD #> \"Planned Arm Code\" #> ACTARM #> \"Description of Actual Arm\" #> ACTARMCD #> \"Actual Arm Code\" #> TRT01P #> \"Planned Treatment for Period 01\" #> TRT01A #> \"Actual Treatment for Period 01\" #> TRT02P #> \"Planned Treatment for Period 02\" #> TRT02A #> \"Actual Treatment for Period 02\" #> REGION1 #> \"Geographic Region 1\" #> STRATA1 #> \"Stratification Factor 1\" #> STRATA2 #> \"Stratification Factor 2\" #> BMRKR1 #> \"Continuous Level Biomarker 1\" #> BMRKR2 #> \"Categorical Level Biomarker 2\" #> ITTFL #> \"Intent-To-Treat Population Flag\" #> SAFFL #> \"Safety Population Flag\" #> BMEASIFL #> \"Response Evaluable Population Flag\" #> BEP01FL #> \"Biomarker Evaluable Population Flag\" #> AEWITHFL #> \"AE Leading to Drug Withdrawal Flag\" #> RANDDT #> \"Date of Randomization\" #> TRTSDTM #> \"Datetime of First Exposure to Treatment\" #> TRTEDTM #> \"Datetime of Last Exposure to Treatment\" #> TRT01SDTM #> \"Datetime of First Exposure to Treatment in Period 01\" #> TRT01EDTM #> \"Datetime of Last Exposure in Period 01\" #> TRT02SDTM #> \"Datetime of First Exposure to Treatment in Period 02\" #> TRT02EDTM #> \"Datetime of Last Exposure to Treatment in Period 02\" #> AP01SDTM #> \"Period 01 Start Datetime\" #> AP01EDTM #> \"Period 01 End Datetime\" #> AP02SDTM #> \"Period 02 Start Datetime\" #> AP02EDTM #> \"Period 02 End Datetime\" #> EOSSTT #> \"End of Study Status\" #> EOTSTT #> \"End of Treatment Status\" #> EOSDT #> \"End of Study Date\" #> EOSDY #> \"End of Study Relative Day\" #> DCSREAS #> \"Reason for Discontinuation from Study\" #> DTHDT #> \"Date of Death\" #> DTHCAUS #> \"Cause of Death\" #> DTHCAT #> \"Cause of Death Category\" #> LDDTHELD #> \"Elapsed Days from Last Dose to Death\" #> LDDTHGR1 #> \"Last Dose to Death - Days Elapsed Grp 1\" #> LSTALVDT #> \"Date Last Known Alive\" #> DTHADY #> \"Relative Day of Death\" #> ADTHAUT #> \"Autopsy Performed\" #> #> $row_labels #> NULL #> #> $dataname #> [1] \"ADSL\" #> #> $dataset_label #> [1] \"custom label\" #> #> $keys #> [1] \"STUDYID\" \"USUBJID\" #> # CDISCTealDataset -------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") x3 <- cdisc_dataset( \"ADSL\", x = ADSL, keys = get_cdisc_keys(\"ADSL\"), label = \"custom label\" ) get_attrs(x3) #> $names #> [1] \"STUDYID\" \"USUBJID\" \"SUBJID\" \"SITEID\" \"AGE\" \"AGEU\" #> [7] \"SEX\" \"RACE\" \"ETHNIC\" \"COUNTRY\" \"DTHFL\" \"INVID\" #> [13] \"INVNAM\" \"ARM\" \"ARMCD\" \"ACTARM\" \"ACTARMCD\" \"TRT01P\" #> [19] \"TRT01A\" \"TRT02P\" \"TRT02A\" \"REGION1\" \"STRATA1\" \"STRATA2\" #> [25] \"BMRKR1\" \"BMRKR2\" \"ITTFL\" \"SAFFL\" \"BMEASIFL\" \"BEP01FL\" #> [31] \"AEWITHFL\" \"RANDDT\" \"TRTSDTM\" \"TRTEDTM\" \"TRT01SDTM\" \"TRT01EDTM\" #> [37] \"TRT02SDTM\" \"TRT02EDTM\" \"AP01SDTM\" \"AP01EDTM\" \"AP02SDTM\" \"AP02EDTM\" #> [43] \"EOSSTT\" \"EOTSTT\" \"EOSDT\" \"EOSDY\" \"DCSREAS\" \"DTHDT\" #> [49] \"DTHCAUS\" \"DTHCAT\" \"LDDTHELD\" \"LDDTHGR1\" \"LSTALVDT\" \"DTHADY\" #> [55] \"ADTHAUT\" #> #> $row.names #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 #> [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 #> [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 #> [55] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 #> [73] 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 #> [91] 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 #> [109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 #> [127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 #> [145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 #> [163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 #> [181] 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 #> [199] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 #> [217] 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 #> [235] 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 #> [253] 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 #> [271] 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 #> [289] 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 #> [307] 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 #> [325] 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 #> [343] 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 #> [361] 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 #> [379] 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 #> [397] 397 398 399 400 #> #> $class #> [1] \"tbl_df\" \"tbl\" \"data.frame\" #> #> $label #> [1] \"Subject Level Analysis Dataset\" #> #> $study_duration_secs #> [1] 63115200 #> #> $`creation date` #> [1] \"2023-03-22\" #> #> $column_labels #> STUDYID #> \"Study Identifier\" #> USUBJID #> \"Unique Subject Identifier\" #> SUBJID #> \"Subject Identifier for the Study\" #> SITEID #> \"Study Site Identifier\" #> AGE #> \"Age\" #> AGEU #> \"Age Units\" #> SEX #> \"Sex\" #> RACE #> \"Race\" #> ETHNIC #> \"Ethnicity\" #> COUNTRY #> \"Country\" #> DTHFL #> \"Subject Death Flag\" #> INVID #> \"Investigator Identifier\" #> INVNAM #> \"Investigator Name\" #> ARM #> \"Description of Planned Arm\" #> ARMCD #> \"Planned Arm Code\" #> ACTARM #> \"Description of Actual Arm\" #> ACTARMCD #> \"Actual Arm Code\" #> TRT01P #> \"Planned Treatment for Period 01\" #> TRT01A #> \"Actual Treatment for Period 01\" #> TRT02P #> \"Planned Treatment for Period 02\" #> TRT02A #> \"Actual Treatment for Period 02\" #> REGION1 #> \"Geographic Region 1\" #> STRATA1 #> \"Stratification Factor 1\" #> STRATA2 #> \"Stratification Factor 2\" #> BMRKR1 #> \"Continuous Level Biomarker 1\" #> BMRKR2 #> \"Categorical Level Biomarker 2\" #> ITTFL #> \"Intent-To-Treat Population Flag\" #> SAFFL #> \"Safety Population Flag\" #> BMEASIFL #> \"Response Evaluable Population Flag\" #> BEP01FL #> \"Biomarker Evaluable Population Flag\" #> AEWITHFL #> \"AE Leading to Drug Withdrawal Flag\" #> RANDDT #> \"Date of Randomization\" #> TRTSDTM #> \"Datetime of First Exposure to Treatment\" #> TRTEDTM #> \"Datetime of Last Exposure to Treatment\" #> TRT01SDTM #> \"Datetime of First Exposure to Treatment in Period 01\" #> TRT01EDTM #> \"Datetime of Last Exposure in Period 01\" #> TRT02SDTM #> \"Datetime of First Exposure to Treatment in Period 02\" #> TRT02EDTM #> \"Datetime of Last Exposure to Treatment in Period 02\" #> AP01SDTM #> \"Period 01 Start Datetime\" #> AP01EDTM #> \"Period 01 End Datetime\" #> AP02SDTM #> \"Period 02 Start Datetime\" #> AP02EDTM #> \"Period 02 End Datetime\" #> EOSSTT #> \"End of Study Status\" #> EOTSTT #> \"End of Treatment Status\" #> EOSDT #> \"End of Study Date\" #> EOSDY #> \"End of Study Relative Day\" #> DCSREAS #> \"Reason for Discontinuation from Study\" #> DTHDT #> \"Date of Death\" #> DTHCAUS #> \"Cause of Death\" #> DTHCAT #> \"Cause of Death Category\" #> LDDTHELD #> \"Elapsed Days from Last Dose to Death\" #> LDDTHGR1 #> \"Last Dose to Death - Days Elapsed Grp 1\" #> LSTALVDT #> \"Date Last Known Alive\" #> DTHADY #> \"Relative Day of Death\" #> ADTHAUT #> \"Autopsy Performed\" #> #> $row_labels #> NULL #> #> $dataname #> [1] \"ADSL\" #> #> $dataset_label #> [1] \"custom label\" #> #> $keys #> [1] \"STUDYID\" \"USUBJID\" #> #> $parent #> character(0) #>"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_binding_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets the name of the binding — get_binding_name","title":"Gets the name of the binding — get_binding_name","text":"Gets name object finding origin. Depending type object function uses different methods obtain original location. env specified object tracked substitute along sys.frames. env specified search limited specified environment.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_binding_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets the name of the binding — get_binding_name","text":"","code":"get_binding_name(object, envir)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_binding_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets the name of the binding — get_binding_name","text":"object (R object) R object envir (environment) origin object known provided precise search","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_binding_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets the name of the binding — get_binding_name","text":"character","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_binding_name.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Gets the name of the binding — get_binding_name","text":"Raises error object found environment.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_cdisc_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"","code":"get_cdisc_keys(dataname)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_cdisc_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"dataname name CDISC dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_cdisc_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"keys object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_cdisc_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function that returns the default keys for a CDISC dataset by name — get_cdisc_keys","text":"","code":"get_cdisc_keys(\"ADSL\") #> [1] \"STUDYID\" \"USUBJID\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_children.html","id":null,"dir":"Reference","previous_headings":"","what":"Get child calls within getParseData() object — get_children","title":"Get child calls within getParseData() object — get_children","text":"Get child calls within getParseData() object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_children.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get child calls within getParseData() object — get_children","text":"","code":"get_children(pd, parent)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_children.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get child calls within getParseData() object — get_children","text":"pd (data.frame) result utils::getParseData(). parent Object parent id utils::getParseData().","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_children.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get child calls within getParseData() object — get_children","text":"Row bounded utils::getParseData() elements call pointing parent id.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code — get_code","title":"Get code — get_code","text":"Reads code specified files R6 object. reading R6: get R code stored inside object. reading files: Includes code source reading files. Method reads code without library() require() calls. Function created teal app, can used file. Get code certain files specific datasets Reads code specified files specific code chunks. Code chunks described : open chunk #code> #code ADSL> #code ADSL ADTTE> close chunk # # [1] \"XY <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\\nXYZ <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\" get_code(rd, \"XY\") #> [1] \"XY <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\" get_code(rd, \"XYZ\") #> [1] \"XYZ <- data.frame(x = c(1, 2), y = c(\\\"aa\\\", \\\"bb\\\"), stringsAsFactors = FALSE)\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"Return lines code (side-effects) needed reproduce object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"","code":"get_code_dependency(code, names)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"code expression srcref attribute character code. names character(n) object names.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the lines of code (with side-effects) needed to reproduce the object — get_code_dependency","text":"character vector elements code calls required build side-effects influencing objects impact object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Get code — get_code_single","title":"Get code — get_code_single","text":"Get code specified file.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get code — get_code_single","text":"","code":"get_code_single(file_path, read_sources, if_url = grepl(\"^http[s]\", file_path))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_single.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get code — get_code_single","text":"file_path (character) path URL address file parsed read_sources (logical) whether replace source(\"path\") code lines sourced file. read_sources = TRUE changing working directory inside preprocessing allowed. if_url (logical) (optional) TRUE URL address provided","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get code — get_code_single","text":"lines (character) preprocessing code","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 method for getting a dataname(s) of\n(TealDataAbstract, (TealDatasetConnector or\nTealDataset) R6 object — get_dataname","text":"","code":"get_dataname(x) # S3 method for TealDataAbstract get_dataname(x) # S3 method for TealDatasetConnector get_dataname(x) # S3 method for TealDataset get_dataname(x) # S3 method for teal_data get_dataname(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 method for getting a dataname(s) of\n(TealDataAbstract, (TealDatasetConnector or\nTealDataset) R6 object — get_dataname","text":"x (TealDataAbstract, TealDatasetConnector TealDataset) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 method for getting a dataname(s) of\n(TealDataAbstract, (TealDatasetConnector or\nTealDataset) R6 object — get_dataname","text":"dataname (character) given name dataset(s) may contain spaces","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dataset from TealDatasetConnector — get_dataset","title":"Get dataset from TealDatasetConnector — get_dataset","text":"Get dataset TealDatasetConnector","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset from TealDatasetConnector — get_dataset","text":"","code":"get_dataset(x, dataname) # S3 method for TealDatasetConnector get_dataset(x, dataname = NULL) # S3 method for TealDataset get_dataset(x, dataname = NULL) # S3 method for TealDataAbstract get_dataset(x, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset from TealDatasetConnector — get_dataset","text":"x (TealDatasetConnector TealDatasetConnector TealDataAbstract) dataname (character) name dataset retrieved","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset from TealDatasetConnector — get_dataset","text":"(TealDataset)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get dataset from TealDatasetConnector — get_dataset","text":"See help(TealDataConnector) help(TealData) complex examples.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset from TealDatasetConnector — get_dataset","text":"","code":"# TealDatasetConnector -------- library(magrittr) pull_fun_adae <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) ADSL <- teal.data::example_cdisc_data(\"ADSL\") dc <- dataset_connector( dataname = \"ADAE\", pull_callable = pull_fun_adae, keys = get_cdisc_keys(\"ADSL\") ) if (FALSE) { load_dataset(dc) get_dataset(dc) } # TealDataset -------- ADSL <- example_cdisc_data(\"ADSL\") x <- dataset(\"ADSL\", ADSL) get_dataset(x) #> A TealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... # TealData (not containing connectors) -------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- example_cdisc_data(\\\"ADSL\\\")\" ) adae <- cdisc_dataset( dataname = \"ADAE\", x = example_cdisc_data(\"ADAE\"), code = \"library(teal.data)\\nADAE <- example_cdisc_data(\\\"ADAE\\\")\" ) rd <- teal.data:::TealData$new(adsl, adae) get_dataset(rd, \"ADSL\") #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ..."},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"","code":"get_dataset_label(x) # S3 method for TealDatasetConnector get_dataset_label(x) # S3 method for TealDataset get_dataset_label(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"x (TealDatasetConnector TealDataset) R6 object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"label (character) Label describe dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_dataset_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 method for getting a label of\n(TealDatasetConnector or TealDataset) R6 object — get_dataset_label","text":"","code":"fun <- callable_function(data.frame) fun$set_args(list(c1 = seq_len(10))) x <- dataset_connector( pull_callable = fun, dataname = \"ADSL\", label = \"My custom label\" ) get_dataset_label(x) #> [1] \"My custom label\" ADSL <- example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset(dataname = \"ADSL\", x = ADSL, label = \"My custom label\") get_dataset_label(ADSL_dataset) #> [1] \"My custom label\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a TealDataset objects. — get_datasets","text":"","code":"get_datasets(x) # S3 method for TealDataAbstract get_datasets(x) # S3 method for TealDatasetConnector get_datasets(x) # S3 method for TealDataset get_datasets(x) # S3 method for teal_data get_datasets(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a TealDataset objects. — get_datasets","text":"x (TealData) object containing datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a TealDataset objects. — get_datasets","text":"list TealDataset objects","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a TealDataset objects. — get_datasets","text":"","code":"library(magrittr) # TealData -------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), , code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) adae <- cdisc_dataset( dataname = \"ADAE\", x = teal.data::example_cdisc_data(\"ADAE\"), code = \"library(teal.data)\\nADAE <- teal.data::example_cdisc_data(\\\"ADAE\\\")\" ) rd <- cdisc_data(adsl, adae) get_datasets(rd) #> $ADSL #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... #> #> $ADAE #> A CDISCTealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ... #> # TealDataConnector -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) adlb_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADLB\")) adlb <- cdisc_dataset_connector( dataname = \"ADLB\", pull_callable = adlb_cf, keys = get_cdisc_keys(\"ADLB\") ) rdc <- relational_data_connector( connection = data_connection(), connectors = list(adsl, adlb) ) rdc$set_ui(function(id, connection, connectors) p(\"Example UI\")) rdc$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # Note this is simplified as we are not opening a real connection here for (connector in connectors) { set_args(connector, args = list(name = input$name)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } ) } ) if (FALSE) { load_datasets(rdc) get_datasets(rdc) } # TealData -------- if (FALSE) { drc <- cdisc_data(rdc, adae) get_datasets(drc) } # TealDatasetConnector -------- adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) rdc <- cdisc_dataset_connector(\"ADSL\", adsl_cf, keys = get_cdisc_keys(\"ADSL\")) if (FALSE) { load_datasets(rdc) get_datasets(rdc) } # TealDataset -------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- example_cdisc_data(\\\"ADSL\\\")\" ) get_datasets(adsl) #> A CDISCTealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ..."},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to get join keys from a `` object — get_join_keys","title":"Function to get join keys from a `` object — get_join_keys","text":"Function get join keys `` object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to get join keys from a `` object — get_join_keys","text":"","code":"get_join_keys(data) get_join_keys(data, dataset_1, dataset_2 = NULL) <- value"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to get join keys from a `` object — get_join_keys","text":"data `` - object extract join keys dataset_1, dataset_2 (character(1)) dataset names. dataset_2 omitted, primary key dataset_1 created. value value assign","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_join_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to get join keys from a `` object — get_join_keys","text":"Either join_keys object NULL join keys","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"","code":"get_key_duplicates(dataset, keys = NULL) # S3 method for TealDataset get_key_duplicates(dataset, keys = NULL) # S3 method for data.frame get_key_duplicates(dataset, keys = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"dataset TealDataset data.frame dataset, tested keys character vector variable names dataset consisting key keys object, primary element vector variable names dataset consisting key. Optional, default: NULL","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"tibble variables consisting key row_no duplicates_count columns","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"information summary provides row numbers number duplicates duplicated key value.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"Raises exception function determine primary key columns tested object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 generic for creating an information summary about the duplicate key values in a dataset — get_key_duplicates","text":"","code":"adsl <- teal.data::example_cdisc_data(\"ADSL\") # create a TealDataset with default keys rel_adsl <- cdisc_dataset(\"ADSL\", adsl) get_key_duplicates(rel_adsl) #> # A tibble: 0 × 4 #> # ℹ 4 variables: STUDYID , USUBJID , rows , n df <- as.data.frame( list(a = c(\"a\", \"a\", \"b\", \"b\", \"c\"), b = c(1, 2, 3, 3, 4), c = c(1, 2, 3, 4, 5)) ) res <- get_key_duplicates(df, keys = c(\"a\", \"b\")) # duplicated keys are in rows 3 and 4 print(res) # prints a tibble #> a b rows n #> 1 b 3 3,4 2 if (FALSE) { get_key_duplicates(df) # raises an exception, because keys are missing with no default }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates_util.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates a duplicate keys information summary. — get_key_duplicates_util","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"Creates duplicate keys information summary.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates_util.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"","code":"get_key_duplicates_util(dataframe, keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates_util.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"dataframe dataframe keys character vector variable names consisting key data.frame","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates_util.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"data.frame duplicate keys information summary","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates_util.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"Accepts list variable names - keys, treated key data.frame argument. instance duplicated key defined two rows, values columns defined keys. Per key value duplicates returns row tibble. return table columns corresponding variable names passed keys two additional columns: rows n, provide information row numbers original dataframe, contain duplicated keys total duplicates counts.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_key_duplicates_util.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates a duplicate keys information summary. — get_key_duplicates_util","text":"","code":"df <- data.frame( a = c(\"a\", \"a\", \"b\", \"b\", \"c\"), b = c(1, 2, 3, 3, 4), c = c(1, 2, 3, 4, 5) ) res <- teal.data:::get_key_duplicates_util(df, keys = c(\"a\", \"b\")) print(res) # duplicated keys are in rows 3 and 4 #> a b rows n #> 1 b 3 3,4 2"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dataset primary keys — get_keys","title":"Get dataset primary keys — get_keys","text":"Get dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dataset primary keys — get_keys","text":"","code":"get_keys(x, ...) # S3 method for TealDataset get_keys(x, ...) # S3 method for TealDatasetConnector get_keys(x, ...) # S3 method for TealDataAbstract get_keys(x, dataname, ...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dataset primary keys — get_keys","text":"x object TealDataset TealDatasetConnector class ... used, support S3 dataname (character) name dataset return keys ","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dataset primary keys — get_keys","text":"(character) vector column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dataset primary keys — get_keys","text":"","code":"# TealDataset -------- get_keys( dataset( \"ADSL\", teal.data::example_cdisc_data(\"ADSL\"), keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ) #> [1] \"STUDYID\" \"USUBJID\" # TealDatasetConnector -------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADAE\")) get_keys( dataset_connector( \"ADSL\", pull_fun_adsl, keys = get_cdisc_keys(\"ADSL\"), ) ) #> [1] \"STUDYID\" \"USUBJID\" # TealData -------- get_keys( teal_data( dataset(\"x\", data.frame(x1 = 1:10, y1 = 11:20), keys = \"x1\"), dataset(\"y\", data.frame(x2 = 1:10, y2 = 11:20), keys = \"x2\") ), \"x\" ) #> [1] \"x1\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"","code":"get_labels(data, fill = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"data (data.frame) table extract labels fill (logical(1)) TRUE, function return variable names columns non-existent labels; otherwise return NA ","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"list two keys: dataset_labels column_labels","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extracts dataset and variable labels from a dataset. — get_labels","text":"","code":"iris_with_labels <- iris attr(iris_with_labels, \"label\") <- \"Custom iris dataset with labels\" attr(iris_with_labels[\"Sepal.Length\"], \"label\") <- c(`Sepal.Length` = \"Sepal Length\") get_labels(iris_with_labels, fill = TRUE) #> $dataset_label #> [1] \"Custom iris dataset with labels\" #> #> $column_labels #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> \"Sepal.Length\" \"Sepal.Width\" \"Petal.Length\" \"Petal.Width\" \"Species\" #> get_labels(iris_with_labels, fill = FALSE) #> $dataset_label #> [1] \"Custom iris dataset with labels\" #> #> $column_labels #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> NA NA NA NA NA #>"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_package_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to get a file out of a package — get_package_file","title":"Function to get a file out of a package — get_package_file","text":"Function get file package","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_package_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to get a file out of a package — get_package_file","text":"","code":"get_package_file(pkg = NULL, file_name = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_package_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to get a file out of a package — get_package_file","text":"pkg (character) name package file received . file_name (character) name file received path starting base package path.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_package_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to get a file out of a package — get_package_file","text":"path file","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_package_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to get a file out of a package — get_package_file","text":"","code":"teal.data:::get_package_file(\"teal.data\", \"WORDLIST\") #> [1] \"/__w/teal.data/teal.data/teal.data/inst/WORDLIST\" teal.data:::get_package_file(\"teal.data\", \"cdisc_datasets/cdisc_datasets.yaml\") #> [1] \"/__w/teal.data/teal.data/teal.data/inst/cdisc_datasets/cdisc_datasets.yaml\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_raw_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve raw data — get_raw_data","text":"","code":"get_raw_data(x, dataname = NULL) # S3 method for TealDataset get_raw_data(x, dataname = NULL) # S3 method for TealDatasetConnector get_raw_data(x, dataname = NULL) # S3 method for TealDataAbstract get_raw_data(x, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_raw_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve raw data — get_raw_data","text":"x (TealDataset, TealDatasetConnector, TealDataAbstract) object dataname (character) Name dataset return raw data .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_raw_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve raw data — get_raw_data","text":"data.frame raw data inserted R6 objects. case TealDataAbstract, list data.frame can returned user specify dataname - (get_raw_data datasets).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_raw_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve raw data — get_raw_data","text":"","code":"# TealDataset --------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") x <- dataset(dataname = \"ADSL\", x = ADSL) get_raw_data(x) #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … # TealDatasetConnector --------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) dc <- dataset_connector(\"ADSL\", pull_fun_adsl) load_dataset(dc) get_raw_data(dc) #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … # TealData ---------------- adsl <- cdisc_dataset( dataname = \"ADSL\", x = teal.data::example_cdisc_data(\"ADSL\"), code = \"library(teal.data)\\nADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) adtte <- cdisc_dataset( dataname = \"ADTTE\", x = teal.data::example_cdisc_data(\"ADTTE\"), code = \"library(teal.data)\\nADTTE <- teal.data::example_cdisc_data(\\\"ADTTE\\\")\" ) rd <- teal.data:::TealData$new(adsl, adtte) get_raw_data(rd) #> $ADSL #> # A tibble: 400 × 55 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y #> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N #> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N #> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N #> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N #> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y #> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N #> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N #> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N #> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y #> # ℹ 390 more rows #> # ℹ 44 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … #> #> $ADTTE #> # A tibble: 2,000 × 67 #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL #> #> 1 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 2 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 3 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 4 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 5 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N #> 6 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 7 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 8 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 9 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> 10 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y #> # ℹ 1,990 more rows #> # ℹ 56 more variables: INVID , INVNAM , ARM , ARMCD , #> # ACTARM , ACTARMCD , TRT01P , TRT01A , TRT02P , #> # TRT02A , REGION1 , STRATA1 , STRATA2 , BMRKR1 , #> # BMRKR2 , ITTFL , SAFFL , BMEASIFL , BEP01FL , #> # AEWITHFL , RANDDT , TRTSDTM , TRTEDTM , #> # TRT01SDTM , TRT01EDTM , TRT02SDTM , TRT02EDTM , … #> # TealDataConnector -------- library(magrittr) slice_cdisc_data <- function(dataname, n) { head(example_cdisc_data(dataname), n) } random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = slice_cdisc_data, fun_args = list(dataname = dataname), ) } open_fun <- callable_function(library) open_fun$set_args(list(package = \"teal.data\")) con <- data_connection(open_fun = open_fun) con$set_open_server( function(id, connection) { moduleServer( id = id, module = function(input, output, session) { connection$open(try = TRUE) return(invisible(connection)) } ) } ) rdc <- relational_data_connector( connection = con, connectors = list(random_data_connector(\"ADSL\"), random_data_connector(\"ADLB\")) ) rdc$set_ui( function(id, connection, connectors) { ns <- NS(id) tagList( connection$get_open_ui(ns(\"open_connection\")), numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) rdc$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection connection$get_open_server()(id = \"open_connection\", connection = connection) if (connection$is_opened()) { for (connector in connectors) { set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } } ) } ) if (FALSE) { load_datasets(rdc) get_raw_data(rdc) } # TealData (with connectors) -------- drc <- cdisc_data(rdc) if (FALSE) { get_raw_data(drc) }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_teal_bs_theme.html","id":null,"dir":"Reference","previous_headings":"","what":"Resolve the expected bootstrap theme — get_teal_bs_theme","title":"Resolve the expected bootstrap theme — get_teal_bs_theme","text":"Resolve expected bootstrap theme","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_teal_bs_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Resolve the expected bootstrap theme — get_teal_bs_theme","text":"","code":"get_teal_bs_theme()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_js_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include JS files from /inst/js/ package directory to application header — include_js_files","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_js_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"","code":"include_js_files(pattern = NULL, except = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_js_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"pattern (character) pattern files included, passed system.file except (character) vector basename filenames excluded","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_js_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"HTML code includes JS files","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_source_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Includes source in preprocessing code lines — include_source_code","title":"Includes source in preprocessing code lines — include_source_code","text":"Includes source preprocessing code lines","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_source_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Includes source in preprocessing code lines — include_source_code","text":"","code":"include_source_code(lines, dir = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_source_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Includes source in preprocessing code lines — include_source_code","text":"lines (character) preprocessing code. dir file source called .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/include_source_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Includes source in preprocessing code lines — include_source_code","text":"lines code source text included","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_dag.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"Checks whether graph Directed Acyclic Graph (DAG)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_dag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"","code":"is_dag(graph)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_dag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"graph (named list) list node vector elements","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_dag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks whether a graph is a Directed Acyclic Graph (DAG) — is_dag","text":"logical(1) TRUE graph DAG; FALSE otherwise","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_pulled.html","id":null,"dir":"Reference","previous_headings":"","what":"Is pulled — is_pulled","title":"Is pulled — is_pulled","text":"S3 method determine dataset pulled (loaded).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_pulled.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Is pulled — is_pulled","text":"","code":"is_pulled(x) # S3 method for TealDatasetConnector is_pulled(x) # S3 method for TealDataset is_pulled(x) # S3 method for TealDataAbstract is_pulled(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_pulled.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Is pulled — is_pulled","text":"x (TealDatasetConnector, TealDataset TealDataAbstract)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_pulled.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Is pulled — is_pulled","text":"(logical) TRUE connector already pulled, else FALSE.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/is_pulled.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Is pulled — is_pulled","text":"","code":"# TealDatasetConnector -------- library(magrittr) pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) x <- dataset_connector(\"ADSL\", pull_fun_adsl) is_pulled(x) #> [1] FALSE load_dataset(x) is_pulled(x) #> [1] TRUE # TealDataset -------- x <- dataset( dataname = \"XY\", x = data.frame(x = c(1, 2), y = c(\"a\", \"b\"), stringsAsFactors = FALSE), keys = \"y\", code = \"XY <- data.frame(x = c(1, 2), y = c('aa', 'bb'), stringsAsFactors = FALSE)\" ) is_pulled(x) #> [1] TRUE library(magrittr) # TealData -------- x1 <- dataset( x = teal.data::example_cdisc_data(\"ADSL\"), dataname = \"ADSL\", keys = get_cdisc_keys(\"ADSL\"), code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\", label = \"ADTTE dataset\" ) x2 <- dataset( x = teal.data::example_cdisc_data(\"ADTTE\"), dataname = \"ADTTE\", keys = get_cdisc_keys(\"ADTTE\"), code = \"ADTTE <- teal.data::example_cdisc_data(\\\"ADTTE\\\")\", label = \"ADTTE dataset\" ) rd <- teal_data(x1, x2) is_pulled(rd) #> [1] TRUE # TealDataConnector -------- adsl_cf <- callable_function(teal.data::example_cdisc_data) %>% set_args(list(dataname = \"ADSL\")) adsl <- cdisc_dataset_connector( dataname = \"ADSL\", pull_callable = adsl_cf, keys = get_cdisc_keys(\"ADSL\") ) new_cf <- callable_function(function(x) { x$NEW <- 1:nrow(x) x }) new_cf$set_args(list(x = as.name(\"x\"))) new <- cdisc_dataset_connector( dataname = \"NEW\", pull_callable = new_cf, keys = get_cdisc_keys(\"ADSL\"), vars = list(x = adsl) ) rdc <- cdisc_data(adsl, new) is_pulled(rdc) #> [1] FALSE if (FALSE) { load_datasets(rdc) is_pulled(rdc) }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a relationship between a pair of datasets — join_key","text":"","code":"join_key(dataset_1, dataset_2 = dataset_1, keys)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a relationship between a pair of datasets — join_key","text":"dataset_1, dataset_2 (character(1)) dataset names. dataset_2 omitted, primary key dataset_1 created. keys (optionally named character) names(keys) columns dataset_1 corresponding columns dataset_2 given elements keys. unnamed, column names used datasets. element keys vector empty non-empty name, name used datasets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a relationship between a pair of datasets — join_key","text":"object class join_key_set passed join_keys function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_key.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a relationship between a pair of datasets — join_key","text":"join_key() create relationship variables pair datasets.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_key.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a relationship between a pair of datasets — join_key","text":"","code":"join_key(\"d1\", \"d2\", c(\"A\")) #> $d1 #> $d1$d2 #> A #> \"A\" #> #> #> attr(,\"class\") #> [1] \"join_key_set\" join_key(\"d1\", \"d2\", c(\"A\" = \"B\")) #> $d1 #> $d1$d2 #> A #> \"B\" #> #> #> attr(,\"class\") #> [1] \"join_key_set\" join_key(\"d1\", \"d2\", c(\"A\" = \"B\", \"C\")) #> $d1 #> $d1$d2 #> A C #> \"B\" \"C\" #> #> #> attr(,\"class\") #> [1] \"join_key_set\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Manage relationships between datasets using join_keys — join_keys","title":"Manage relationships between datasets using join_keys — join_keys","text":"join_keys() facilitates creation retrieval relationships datasets. join_keys class extends list contains keys connecting pairs datasets. element list contains keys specific dataset. dataset can relationship (primary key) datasets. Note join_keys list symmetrical, , keys set dat1 dat2 automatically mirrored dat2 dat1.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Manage relationships between datasets using join_keys — join_keys","text":"","code":"## Constructor, getter and setter join_keys(...) # S3 method for default join_keys(...) # S3 method for join_keys join_keys(...) # S3 method for teal_data join_keys(...) # S3 method for TealData join_keys(...) # S3 method for join_keys [(x, i, j) # S3 method for join_keys [(x, i, j) <- value # S3 method for join_keys c(...) # S3 method for join_key_set c(...) join_keys(x) <- value # S3 method for join_keys join_keys(x) <- value # S3 method for teal_data join_keys(x) <- value # S3 method for join_keys format(x, ...) # S3 method for join_keys print(x, ...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Manage relationships between datasets using join_keys — join_keys","text":"... (optional) either teal_data join_keys extract join_keys, number join_key_set objects create join_keys, nothing create empty join_keys x (join_keys) empty object set new relationship pairs. x typically object join_keys class. called join_keys(x) join_keys(x) <- value can also take supported class (teal_data, join_keys) , j indices specifying elements extract replace. Index character vector, can also take numeric, logical, NULL missing. value (join_key_set list join_key_set) relationship pairs add join_keys list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Manage relationships between datasets using join_keys — join_keys","text":"join_keys object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_keys.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Manage relationships between datasets using join_keys — join_keys","text":"join_keys(): Returns empty join_keys object called without arguments. join_keys(join_keys): Returns . join_keys(teal_data): Returns join_keys object contained teal_data. join_keys(...): Creates new object one join_key_set parameters.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_keys.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Manage relationships between datasets using join_keys — join_keys","text":"x[datanames]: Returns subset join_keys object given datanames, including parent datanames symmetric mirror keys datanames result. x[, j]: Returns join keys datasets j, including implicit keys inferred relationship parent. x[, j] <- value: Assignment key pair (, j). x[] <- value: (without j parameter) supported operation join_keys. join_keys(x)[, j] <- value: Assignment join_keys object stored x, teal_data join_keys . join_keys(x) <- value: Assignment join_keys object value. value needs object class join_keys join_key_set.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/join_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Manage relationships between datasets using join_keys — join_keys","text":"","code":"# Creating a new join keys ---- jk <- join_keys( join_key(\"ds1\", \"ds1\", \"pk1\"), join_key(\"ds2\", \"ds2\", \"pk2\"), join_key(\"ds3\", \"ds3\", \"pk3\"), join_key(\"ds2\", \"ds1\", c(pk2 = \"pk1\")), join_key(\"ds3\", \"ds1\", c(pk3 = \"pk1\")) ) jk #> A join_keys object containing foreign keys between 3 datasets: #> ds1: [pk1] #> <-> ds2: [pk2] #> <-> ds3: [pk3] #> ds2: [pk2] #> <-> ds1: [pk1] #> ds3: [pk3] #> <-> ds1: [pk1] # Getter for join_keys --- jk[\"ds1\", \"ds2\"] #> pk1 #> \"pk2\" # Subsetting join_keys ---- jk[\"ds1\"] #> A join_keys object containing foreign keys between 1 datasets: #> ds1: [pk1] jk[1:2] #> A join_keys object containing foreign keys between 2 datasets: #> ds1: [pk1] #> <-> ds2: [pk2] #> ds2: [pk2] #> <-> ds1: [pk1] jk[c(\"ds1\", \"ds2\")] #> A join_keys object containing foreign keys between 2 datasets: #> ds1: [pk1] #> <-> ds2: [pk2] #> ds2: [pk2] #> <-> ds1: [pk1] # Setting a new primary key --- jk[\"ds4\", \"ds4\"] <- \"pk4\" jk[\"ds5\", \"ds5\"] <- \"pk5\" # Setting a single relationship pair --- jk[\"ds4\", \"ds1\"] <- c(\"pk4\" = \"pk1\") # Removing a key --- jk[\"ds5\", \"ds5\"] <- NULL # Merging multiple `join_keys` --- jk_merged <- c( jk, join_keys( join_key(\"ds4\", keys = c(\"pk4\", \"pk4_2\")), join_key(\"ds4\", \"ds3\", c(pk4_2 = \"pk3\")) ) ) # note: merge can be performed with both join_keys and join_key_set jk_merged <- c( jk_merged, join_key(\"ds5\", keys = \"pk5\"), join_key(\"ds5\", \"ds1\", c(pk5 = \"pk1\")) ) # Assigning keys via join_keys(x)[i, j] <- value ---- obj <- join_keys() # or obj <- teal_data() join_keys(obj)[\"ds1\", \"ds1\"] <- \"pk1\" join_keys(obj)[\"ds2\", \"ds2\"] <- \"pk2\" join_keys(obj)[\"ds3\", \"ds3\"] <- \"pk3\" join_keys(obj)[\"ds2\", \"ds1\"] <- c(pk2 = \"pk1\") join_keys(obj)[\"ds3\", \"ds1\"] <- c(pk3 = \"pk1\") identical(jk, join_keys(obj)) #> [1] FALSE # Setter for join_keys within teal_data ---- td <- teal_data() join_keys(td) <- jk join_keys(td)[\"ds1\", \"ds2\"] <- \"new_key\" join_keys(td) <- c(join_keys(td), join_keys(join_key(\"ds3\", \"ds2\", \"key3\"))) join_keys(td) #> A join_keys object containing foreign keys between 4 datasets: #> ds1: [pk1] #> <-> ds2: [new_key] #> <-> ds3: [pk3] #> <-> ds4: [pk4] #> ds2: [pk2] #> <-> ds1: [new_key] #> <-> ds3: [key3] #> ds3: [pk3] #> <-> ds1: [pk1] #> <-> ds2: [key3] #> ds4: [pk4] #> <-> ds1: [pk1]"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_dataset.html","id":null,"dir":"Reference","previous_headings":"","what":"Load data from connection — load_dataset","title":"Load data from connection — load_dataset","text":"Load data connection. Function used TealDatasetConnector TealDataset obtain data connection.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load data from connection — load_dataset","text":"","code":"load_dataset(x, ...) # S3 method for TealDataset load_dataset(x, ...) # S3 method for TealDatasetConnector load_dataset(x, args = NULL, try = FALSE, conn = NULL, ...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load data from connection — load_dataset","text":"x (TealDatasetConnector TealDataset) ... used, support S3 args (NULL named list) additional dynamic arguments passed function loads data. try (logical) whether perform function evaluation inside try clause conn Optional (TealDataConnection) object required pull data.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load data from connection — load_dataset","text":"x loaded dataset object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load data from connection — load_dataset","text":"","code":"# TealDataset -------- ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset(\"ADSL\", x = ADSL) load_dataset(ADSL_dataset) # TealDatasetConnector -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") load_dataset(adsl) get_dataset(adsl) #> A TealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... adae <- random_data_connector(dataname = \"ADAE\") load_dataset(adae) get_dataset(adae) #> A TealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ..."},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load datasets — load_datasets","text":"","code":"load_datasets(x, ...) # S3 method for TealDataset load_datasets(x, ...) # S3 method for TealDatasetConnector load_datasets(x, args = NULL, try = FALSE, ...) # S3 method for TealDataConnector load_datasets(x, ...) # S3 method for TealData load_datasets(x, ...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load datasets — load_datasets","text":"x (TealData, TealDataset TealDatasetConnector) ... (used) support S3 args (NULL named list) additional dynamic arguments passed function loads data. Applicable TealDatasetConnector) try (logical) whether perform function evaluation inside try clause. Applicable TealDatasetConnector)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load datasets — load_datasets","text":"executed interactive session shiny app opened load data. executed shiny application - returns shiny server module.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/load_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load datasets — load_datasets","text":"","code":"# TealDataset ------ ADSL <- teal.data::example_cdisc_data(\"ADSL\") x <- dataset(\"ADSL\", x = ADSL) load_datasets(x) # TealDatasetConnector ------ random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") load_datasets(adsl) get_dataset(adsl) #> A TealDataset object containing the following data.frame (400 rows and 55 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX #> 1 AB12345 AB12345-CHN-3-id-128 id-128 CHN-3 32 YEARS M #> 2 AB12345 AB12345-CHN-15-id-262 id-262 CHN-15 35 YEARS M #> 3 AB12345 AB12345-RUS-3-id-378 id-378 RUS-3 30 YEARS F #> 4 AB12345 AB12345-CHN-11-id-220 id-220 CHN-11 26 YEARS F #> 5 AB12345 AB12345-CHN-7-id-267 id-267 CHN-7 40 YEARS M #> 6 AB12345 AB12345-CHN-15-id-201 id-201 CHN-15 49 YEARS M #> RACE ETHNIC COUNTRY DTHFL INVID #> 1 ASIAN HISPANIC OR LATINO CHN Y INV ID CHN-3 #> 2 BLACK OR AFRICAN AMERICAN NOT HISPANIC OR LATINO CHN N INV ID CHN-15 #> 3 ASIAN NOT HISPANIC OR LATINO RUS N INV ID RUS-3 #> 4 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-11 #> 5 ASIAN NOT HISPANIC OR LATINO CHN N INV ID CHN-7 #> 6 ASIAN NOT HISPANIC OR LATINO CHN Y INV ID CHN-15 #> INVNAM ARM ARMCD ACTARM ACTARMCD TRT01P #> 1 Dr. CHN-3 Doe A: Drug X ARM A A: Drug X ARM A A: Drug X #> 2 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 3 Dr. RUS-3 Doe C: Combination ARM C C: Combination ARM C C: Combination #> 4 Dr. CHN-11 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 5 Dr. CHN-7 Doe B: Placebo ARM B B: Placebo ARM B B: Placebo #> 6 Dr. CHN-15 Doe C: Combination ARM C C: Combination ARM C C: Combination #> TRT01A TRT02P TRT02A REGION1 STRATA1 STRATA2 #> 1 A: Drug X B: Placebo A: Drug X Asia C S2 #> 2 C: Combination B: Placebo C: Combination Asia C S1 #> 3 C: Combination A: Drug X B: Placebo Eurasia A S1 #> 4 B: Placebo B: Placebo B: Placebo Asia B S2 #> 5 B: Placebo C: Combination A: Drug X Asia C S1 #> 6 C: Combination B: Placebo C: Combination Asia C S2 #> BMRKR1 BMRKR2 ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT #> 1 14.424934 MEDIUM Y Y Y Y N 2019-02-22 #> 2 4.055463 LOW Y Y N N Y 2019-02-26 #> 3 2.803240 HIGH Y Y Y N N 2019-02-24 #> 4 10.262734 MEDIUM Y Y Y Y N 2019-02-27 #> 5 6.206763 LOW Y Y N N N 2019-03-01 #> 6 6.906799 MEDIUM Y Y Y N N 2019-03-05 #> TRTSDTM TRTEDTM TRT01SDTM #> 1 2019-02-24 11:09:25 2022-02-12 04:28:08 2019-02-24 11:09:25 #> 2 2019-02-26 09:05:10 2022-02-26 03:05:10 2019-02-26 09:05:10 #> 3 2019-02-28 03:19:22 2022-02-27 21:19:22 2019-02-28 03:19:22 #> 4 2019-03-01 13:33:19 2022-03-01 07:33:19 2019-03-01 13:33:19 #> 5 2019-03-02 00:09:33 2022-03-01 18:09:33 2019-03-02 00:09:33 #> 6 2019-03-05 15:24:07 2022-02-19 04:06:48 2019-03-05 15:24:07 #> TRT01EDTM TRT02SDTM TRT02EDTM #> 1 2021-02-11 22:28:08 2021-02-11 22:28:08 2022-02-12 04:28:08 #> 2 2021-02-25 21:05:10 2021-02-25 21:05:10 2022-02-26 03:05:10 #> 3 2021-02-27 15:19:22 2021-02-27 15:19:22 2022-02-27 21:19:22 #> 4 2021-03-01 01:33:19 2021-03-01 01:33:19 2022-03-01 07:33:19 #> 5 2021-03-01 12:09:33 2021-03-01 12:09:33 2022-03-01 18:09:33 #> 6 2021-02-18 22:06:48 2021-02-18 22:06:48 2022-02-19 04:06:48 #> AP01SDTM AP01EDTM AP02SDTM #> 1 2019-02-24 11:09:25 2021-02-11 22:28:08 2021-02-11 22:28:08 #> 2 2019-02-26 09:05:10 2021-02-25 21:05:10 2021-02-25 21:05:10 #> 3 2019-02-28 03:19:22 2021-02-27 15:19:22 2021-02-27 15:19:22 #> 4 2019-03-01 13:33:19 2021-03-01 01:33:19 2021-03-01 01:33:19 #> 5 2019-03-02 00:09:33 2021-03-01 12:09:33 2021-03-01 12:09:33 #> 6 2019-03-05 15:24:07 2021-02-18 22:06:48 2021-02-18 22:06:48 #> AP02EDTM EOSSTT EOTSTT EOSDT EOSDY DCSREAS #> 1 2022-02-12 04:28:08 DISCONTINUED DISCONTINUED 2022-02-12 1084 DEATH #> 2 2022-02-26 03:05:10 COMPLETED COMPLETED 2022-02-26 1096 #> 3 2022-02-27 21:19:22 COMPLETED COMPLETED 2022-02-27 1096 #> 4 2022-03-01 07:33:19 COMPLETED COMPLETED 2022-03-01 1096 #> 5 2022-03-01 18:09:33 COMPLETED COMPLETED 2022-03-01 1096 #> 6 2022-02-19 04:06:48 DISCONTINUED DISCONTINUED 2022-02-19 1082 DEATH #> DTHDT DTHCAUS DTHCAT LDDTHELD LDDTHGR1 LSTALVDT DTHADY #> 1 2022-03-06 ADVERSE EVENT ADVERSE EVENT 22 <=30 2022-03-06 1105 #> 2 NA 2022-03-17 NA #> 3 NA 2022-03-11 NA #> 4 NA 2022-03-26 NA #> 5 NA 2022-03-15 NA #> 6 2022-02-22 ADVERSE EVENT ADVERSE EVENT 3 <=30 2022-02-22 1084 #> ADTHAUT #> 1 Yes #> 2 #> 3 #> 4 #> 5 #> 6 Yes #> ... adae <- random_data_connector(dataname = \"ADAE\") load_datasets(adae) get_dataset(adae) #> A TealDataset object containing the following data.frame (1934 rows and 92 columns): #> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE #> 1 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 2 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 3 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 4 AB12345 AB12345-BRA-1-id-134 id-134 BRA-1 47 YEARS M WHITE #> 5 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> 6 AB12345 AB12345-BRA-1-id-141 id-141 BRA-1 35 YEARS F WHITE #> ETHNIC COUNTRY DTHFL INVID INVNAM #> 1 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 2 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 3 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 4 NOT HISPANIC OR LATINO BRA Y INV ID BRA-1 Dr. BRA-1 Doe #> 5 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> 6 NOT HISPANIC OR LATINO BRA N INV ID BRA-1 Dr. BRA-1 Doe #> ARM ARMCD ACTARM ACTARMCD TRT01P TRT01A #> 1 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 2 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 3 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 4 A: Drug X ARM A A: Drug X ARM A A: Drug X A: Drug X #> 5 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> 6 C: Combination ARM C C: Combination ARM C C: Combination C: Combination #> TRT02P TRT02A REGION1 STRATA1 STRATA2 BMRKR1 BMRKR2 #> 1 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 2 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 3 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 4 B: Placebo A: Drug X South America B S2 6.462991 LOW #> 5 C: Combination C: Combination South America B S1 7.516076 HIGH #> 6 C: Combination C: Combination South America B S1 7.516076 HIGH #> ITTFL SAFFL BMEASIFL BEP01FL AEWITHFL RANDDT TRTSDTM #> 1 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 2 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 3 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 4 Y Y Y N N 2020-11-03 2020-11-04 04:08:58 #> 5 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> 6 Y Y Y Y N 2020-07-22 2020-07-25 14:26:21 #> TRTEDTM TRT01SDTM TRT01EDTM #> 1 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 2 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 3 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 4 2022-02-20 03:33:55 2020-11-04 04:08:58 2021-02-19 21:33:55 #> 5 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> 6 2023-07-26 08:26:21 2020-07-25 14:26:21 2022-07-26 02:26:21 #> TRT02SDTM TRT02EDTM AP01SDTM #> 1 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 2 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 3 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 4 2021-02-19 21:33:55 2022-02-20 03:33:55 2020-11-04 04:08:58 #> 5 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> 6 2022-07-26 02:26:21 2023-07-26 08:26:21 2020-07-25 14:26:21 #> AP01EDTM AP02SDTM AP02EDTM EOSSTT #> 1 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 2 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 3 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 4 2021-02-19 21:33:55 2021-02-19 21:33:55 2022-02-20 03:33:55 DISCONTINUED #> 5 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> 6 2022-07-26 02:26:21 2022-07-26 02:26:21 2023-07-26 08:26:21 COMPLETED #> EOTSTT EOSDT EOSDY DCSREAS DTHDT DTHCAUS DTHCAT #> 1 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 2 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 3 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 4 DISCONTINUED 2022-02-20 473 DEATH 2022-03-16 ADVERSE EVENT ADVERSE EVENT #> 5 COMPLETED 2023-07-26 1096 #> 6 COMPLETED 2023-07-26 1096 #> LDDTHELD LDDTHGR1 LSTALVDT DTHADY ADTHAUT ASEQ AESEQ AETERM #> 1 24 <=30 2022-03-16 496 Yes 1 1 trm B.2.1.2.1 #> 2 24 <=30 2022-03-16 496 Yes 2 2 trm D.1.1.4.2 #> 3 24 <=30 2022-03-16 496 Yes 3 3 trm A.1.1.1.2 #> 4 24 <=30 2022-03-16 496 Yes 4 4 trm A.1.1.1.2 #> 5 NA 2023-08-08 NA 1 1 trm B.2.1.2.1 #> 6 NA 2023-08-08 NA 2 2 trm D.2.1.5.3 #> AELLT AEDECOD AEHLT AEHLGT AEBODSYS AESOC AESEV #> 1 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 2 llt D.1.1.4.2 dcd D.1.1.4.2 hlt D.1.1.4 hlgt D.1.1 cl D.1 cl D MODERATE #> 3 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 4 llt A.1.1.1.2 dcd A.1.1.1.2 hlt A.1.1.1 hlgt A.1.1 cl A.1 cl A MODERATE #> 5 llt B.2.1.2.1 dcd B.2.1.2.1 hlt B.2.1.2 hlgt B.2.1 cl B.2 cl B MODERATE #> 6 llt D.2.1.5.3 dcd D.2.1.5.3 hlt D.2.1.5 hlgt D.2.1 cl D.2 cl D MILD #> AESER AEACN AEREL AEOUT AESDTH AESCONG AESDISAB #> 1 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 2 N DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 3 Y DOSE NOT CHANGED N RECOVERING/RESOLVING N N Y #> 4 Y DRUG WITHDRAWN N RECOVERING/RESOLVING N Y N #> 5 N DOSE INCREASED N RECOVERED/RESOLVED N N N #> 6 N DOSE INCREASED Y RECOVERED/RESOLVED N N Y #> AESHOSP AESLIFE AESMIE TRTEMFL AECONTRT ASTDTM #> 1 N N N Y Y 2021-04-15 04:08:58 #> 2 N N N Y N 2021-05-19 04:08:58 #> 3 N N N Y Y 2021-09-21 04:08:58 #> 4 N N N Y N 2021-12-02 04:08:58 #> 5 Y N N Y Y 2021-08-16 14:26:21 #> 6 N N N Y N 2021-10-23 14:26:21 #> AENDTM ASTDY AENDY LDOSEDTM LDRELTM AETOXGR #> 1 2021-10-04 04:08:58 162 334 2020-11-07 09:05:04 228663.896 3 #> 2 2021-10-31 04:08:58 196 361 2021-05-17 07:21:09 2687.814 3 #> 3 2022-02-16 04:08:58 321 469 2021-05-23 15:14:37 173574.345 2 #> 4 2022-01-13 04:08:58 393 435 2021-03-19 08:52:05 371236.878 2 #> 5 2021-08-26 14:26:21 387 397 2021-07-22 06:04:04 36502.291 3 #> 6 2023-07-12 14:26:21 455 1082 2021-07-16 21:30:39 142135.710 1 #> SMQ01NAM SMQ02NAM SMQ01SC SMQ02SC CQ01NAM ANL01FL #> 1 Y #> 2 Y #> 3 Y #> 4 Y #> 5 Y #> 6 D.2.1.5.3/A.1.1.1.1 AESI Y #> AERELNST AEACNOTH #> 1 NONE PROCEDURE/SURGERY #> 2 CONCURRENT ILLNESS MEDICATION #> 3 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 4 CONCURRENT ILLNESS SUBJECT DISCONTINUED FROM STUDY #> 5 CONCURRENT ILLNESS PROCEDURE/SURGERY #> 6 CONCURRENT ILLNESS MEDICATION #> ... # TealDataConnector -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") adrs <- random_data_connector(dataname = \"ADRS\") rdc <- cdisc_data(adsl, adrs) if (FALSE) { load_datasets(rdc) } # TealData -------- random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } adsl <- random_data_connector(dataname = \"ADSL\") adlb <- random_data_connector(dataname = \"ADLB\") adrs <- random_data_connector(dataname = \"ADRS\") tc <- cdisc_data(adsl, adlb, adrs) if (FALSE) { load_datasets(tc) }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/local_cdisc_data_mixed_call.html","id":null,"dir":"Reference","previous_headings":"","what":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"(test helper) Create test data CDISC data","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/local_cdisc_data_mixed_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"","code":"local_cdisc_data_mixed_call(check = TRUE, join_keys1 = join_keys())"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/local_cdisc_data_mixed_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"check (logical) reproducibility check - whether perform check pre-processing code included object definitions actually produces objects. check true preprocessing code empty error thrown.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/local_cdisc_data_mixed_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(test helper) Create test data for CDISC data — local_cdisc_data_mixed_call","text":"CDISC data set following tables: ADSL, ADTTE ADAE","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mae_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor of MAETealDataset — mae_dataset","text":"","code":"mae_dataset( dataname, x, label = data_label(x), code = character(0), vars = list() )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mae_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor of MAETealDataset — mae_dataset","text":"dataname (character) given name dataset, contain spaces x (MultiAssayExperiment) label (character) label describe dataset code (character) character string defining code needed produce data set x vars (named list) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mae_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor of MAETealDataset — mae_dataset","text":"","code":"# Simple example utils::data(miniACC, package = \"MultiAssayExperiment\") mae_d <- dataset(\"MAE\", miniACC) mae_d$get_dataname() #> [1] \"MAE\" mae_d$get_dataset_label() #> character(0) mae_d$get_code() #> [1] \"\" mae_d$get_raw_data() #> A MultiAssayExperiment object of 5 listed #> experiments with user-defined names and respective classes. #> Containing an ExperimentList class object of length 5: #> [1] RNASeq2GeneNorm: SummarizedExperiment with 198 rows and 79 columns #> [2] gistict: SummarizedExperiment with 198 rows and 90 columns #> [3] RPPAArray: SummarizedExperiment with 33 rows and 46 columns #> [4] Mutations: matrix with 97 rows and 90 columns #> [5] miRNASeqGene: SummarizedExperiment with 471 rows and 80 columns #> Functionality: #> experiments() - obtain the ExperimentList instance #> colData() - the primary/phenotype DataFrame #> sampleMap() - the sample coordination DataFrame #> `$`, `[`, `[[` - extract colData columns, subset, or experiment #> *Format() - convert into a long or wide DataFrame #> assays() - convert ExperimentList to a SimpleList of matrices #> exportClass() - save data to flat files"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Mutate data by code — mutate_data","title":"Mutate data by code — mutate_data","text":"Code used mutation linked particular refers datasets. Consequence using get_code() part code returned dataset specified. method used particular call involve changing multiple datasets. Otherwise please use mutate_dataset. Execution code delayed datasets pulled (isTRUE(is_pulled)).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mutate data by code — mutate_data","text":"","code":"mutate_data(x, code = character(0), script = character(0), vars = list()) # S3 method for TealDataAbstract mutate_data(x, code = character(0), script = character(0), vars = list())"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mutate data by code — mutate_data","text":"x (TealDataAbstract) object. code (character) Code mutate dataset. Must contain dataset$dataname. can also object class PythonCodeClass returned python_code. script (character) file contains R Code can read using read_script. Preferred code argument. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mutate data by code — mutate_data","text":"modified x object","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_dataset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mutate dataset by code — mutate_dataset","text":"","code":"mutate_dataset(x, ...) # S3 method for TealDataset mutate_dataset( x, code = character(0), script = character(0), vars = list(), ... ) # S3 method for TealDatasetConnector mutate_dataset( x, code = character(0), script = character(0), vars = list(), ... ) # S3 method for TealDataAbstract mutate_dataset( x, dataname, code = character(0), script = character(0), vars = list(), ... )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_dataset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mutate dataset by code — mutate_dataset","text":"x (TealDataset) object. ... used, support S3 code (character) Code mutate dataset. Must contain dataset$dataname. can also object class PythonCodeClass returned python_code. script (character) file contains R Code can read using read_script. Preferred code argument. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. dataname (character)Dataname mutated.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_dataset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mutate dataset by code — mutate_dataset","text":"modified x object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/mutate_dataset.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mutate dataset by code — mutate_dataset","text":"","code":"library(magrittr) ADSL <- teal.data::example_cdisc_data(\"ADSL\") ADSL_dataset <- dataset( dataname = \"ADSL\", x = ADSL, label = \"AdAM subject-level dataset\", code = \"ADSL <- teal.data::example_cdisc_data(\\\"ADSL\\\")\" ) ADSL_mutated <- ADSL_dataset %>% mutate_dataset(code = \"ADSL$new_variable <- 1\") ADSL_mutated$get_raw_data()$new_variable[1] #> [1] 1 # Use an R script to mutate the data file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"ADSL <- ADSL %>% dplyr::mutate(new_variable = new_variable * 2)\" ), con = file_example ) ADSL_mutated <- ADSL_mutated %>% mutate_dataset(script = file_example) ADSL_mutated$get_raw_data()$new_variable[1] #> [1] 2 ADSL_mutated <- ADSL_mutated %>% mutate_dataset(code = read_script(file_example)) ADSL_mutated$get_raw_data()$new_variable[1] #> [1] 4"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/names-set-.join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"The Names of an join_keys Object — names<-.join_keys","title":"The Names of an join_keys Object — names<-.join_keys","text":"Names join_keys Object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/names-set-.join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The Names of an join_keys Object — names<-.join_keys","text":"","code":"# S3 method for join_keys names(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/names-set-.join_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The Names of an join_keys Object — names<-.join_keys","text":"x R object. value character vector length x, NULL.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/new_join_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal constructor — new_join_keys","title":"Internal constructor — new_join_keys","text":"Internal constructor","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/new_join_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal constructor — new_join_keys","text":"","code":"new_join_keys()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/new_join_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Internal constructor — new_join_keys","text":"empty join_keys list","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/new_teal_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize teal_data object — new_teal_data","title":"Initialize teal_data object — new_teal_data","text":"Initialize teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/new_teal_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize teal_data object — new_teal_data","text":"","code":"new_teal_data( data, code = character(0), join_keys = join_keys(), datanames = union(names(data), names(join_keys)) )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/new_teal_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize teal_data object — new_teal_data","text":"data (named list) List data. code (character language) code reproduce data. Accepts stores comments also. join_keys (join_keys) object datanames (character) names datasets passed data. Needed non-dataset objects needed env slot.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/parents.html","id":null,"dir":"Reference","previous_headings":"","what":"Getter and setter functions for parents attribute of join_keys — parents","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"parents() facilitates creation dependencies datasets assigning parent-child relationship. element defined list element, list(\"child\" = \"parent\").","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/parents.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"","code":"parents(x) # S3 method for join_keys parents(x) # S3 method for teal_data parents(x) parents(x) <- value # S3 method for join_keys parents(x) <- value # S3 method for teal_data parents(x) <- value parent(x, dataset_name)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/parents.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"x (join_keys teal_data) object contains \"parents\" information retrieve manipulate. value (named list) character vectors. dataset_name (character(1)) Name dataset query parent.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/parents.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"list character representing parents. parent(x, dataset_name) returns NULL parent exist.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/parents.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"parents(join_keys): Retrieves parents join_keys object. parents(teal_data): Retrieves parents join_keys inside teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/parents.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"parents(x) <- value: Assignment parents join_keys object. parents(join_keys) <- value: Assignment parents join_keys object. parents(teal_data) <- value: Assignment parents join_keys inside teal_data object. parent(): Getter individual parent","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/parents.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Getter and setter functions for parents attribute of join_keys — parents","text":"","code":"# Get parents of join_keys --- jk <- default_cdisc_join_keys[\"ADEX\"] parents(jk) #> $ADEX #> [1] \"ADSL\" #> # Get parents of join_keys inside teal_data object --- td <- teal_data( ADSL = teal.data::rADSL, ADTTE = teal.data::rADTTE, ADRS = teal.data::rADRS, join_keys = default_cdisc_join_keys[c(\"ADSL\", \"ADTTE\", \"ADRS\")] ) parents(td) #> $ADTTE #> [1] \"ADSL\" #> #> $ADRS #> [1] \"ADSL\" #> # Assigment of parents --- jk <- join_keys( join_key(\"ds1\", \"ds2\", \"id\"), join_key(\"ds5\", \"ds6\", \"id\"), join_key(\"ds7\", \"ds6\", \"id\") ) parents(jk) <- list(ds2 = \"ds1\") # Setting individual parent-child relationship parents(jk)[\"ds6\"] <- \"ds5\" parents(jk)[\"ds7\"] <- \"ds6\" # Assigment of parents of join_keys inside teal_data object --- parents(td) <- list(\"ADTTE\" = \"ADSL\") # replace existing parents(td)[\"ADRS\"] <- \"ADSL\" # add new parent # Get individual parent --- parent(jk, \"ds2\") #> [1] \"ds1\" parent(td, \"ADTTE\") #> [1] \"ADSL\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/pretty_code_string.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a vector of code into a string — pretty_code_string","title":"Format a vector of code into a string — pretty_code_string","text":"Format vector code string","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/pretty_code_string.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a vector of code into a string — pretty_code_string","text":"","code":"pretty_code_string(code_vector)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/pretty_code_string.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a vector of code into a string — pretty_code_string","text":"code_vector (character) vector containing lines code format string.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/pretty_code_string.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a vector of code into a string — pretty_code_string","text":"(character) string containing formatted code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Python Code — python_code","title":"Python Code — python_code","text":"Create python code object directly python code script containing python code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Python Code — python_code","text":"","code":"python_code(code = character(0), script = character(0))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Python Code — python_code","text":"code (character) Code mutate dataset. Must contain dataset$dataname. script (character) file contains python Code can read using reticulate::py_run_script.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Python Code — python_code","text":"(PythonCodeClass) object containing python code","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_code.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Python Code — python_code","text":"Used mutate dataset connector objects python code. See mutate_dataset mutate_data details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_code.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Python Code — python_code","text":"","code":"if (FALSE) { library(reticulate) library(magrittr) # mutate dataset object random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } x <- random_data_connector(dataname = \"ADSL\") x %>% mutate_dataset(python_code(\"import pandas as pd r.ADSL = pd.DataFrame({'x': [1]})\")) x$get_code() x$pull() x$get_raw_data() # mutate data object y <- 8 tc <- cdisc_data( random_data_connector(dataname = \"ADSL\"), random_data_connector(dataname = \"ADLB\") ) tc %>% mutate_data(python_code(\"import pandas as pd r.ADSL = pd.DataFrame({'STUDYID': [r.y], 'USUBJID': [r.y]})\"), vars = list(y = y)) load_datasets(tc) # submit all ds <- tc$get_dataset(\"ADSL\") ds$get_raw_data() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_dataset_connector.html","id":null,"dir":"Reference","previous_headings":"","what":"Python TealDatasetConnector — python_dataset_connector","title":"Python TealDatasetConnector — python_dataset_connector","text":"Create TealDatasetConnector .py file python code supplied directly. Create CDISCTealDatasetConnector .py file python code supplied directly.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Python TealDatasetConnector — python_dataset_connector","text":"","code":"python_dataset_connector( dataname, file, code, object = dataname, keys = character(0), label = character(0), mutate_code = character(0), mutate_script = character(0), vars = list(), metadata = NULL ) python_cdisc_dataset_connector( dataname, file, code, object = dataname, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", mutate_code = character(0), mutate_script = character(0), label = character(0), vars = list(), metadata = NULL )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Python TealDatasetConnector — python_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) Path file location containing python script used generate object. code (character) string containing python code run using reticulate. Carefully consider indentation follow proper python syntax. object (character) name object python script assigned dataset used. keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. mutate_code (character) String containing code used mutate object produced. mutate_script (character) Alternatively mutate_code - location file containing modification code. used simultaneously mutate_script. vars (named list)) case object code depends TealDataset object(s) constant value, /object(s) included named element(s) list. example object code needs ADSL object specify vars = list(ADSL = ). recommended include TealDataset TealDatasetConnector objects vars list preserve reproducibility. Please note vars included object local vars modified within another dataset. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Python TealDatasetConnector — python_dataset_connector","text":"Note addition reticulate package, support python requires existing python installation. default, reticulate attempt use location Sys.(\"python\"), however path python installation can supplied directly via reticulate::use_python. teal API delayed data requires python code script return data.frame object. , pandas package required. can installed using reticulate::py_install(\"pandas\"). Please see package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_dataset_connector.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Python TealDatasetConnector — python_dataset_connector","text":"Raises error passed code file passed time. using code, keep mind using reticulate delayed data, python functions access objects code must self contained. following example, function makedata() access variable x: using custom functions, function environment must entirely self contained: Additional reticulate considerations: Note using pull vars, R objects referenced python code script prefixed r.. reticulate able convert POSIXct objects. Please take extra care working datetime variables. Please read official documentation reticulate package additional features current limitations.","code":"import pandas as pd x = 1 def makedata(): return pd.DataFrame({'x': [x, 2], 'y': [3, 4]}) data = makedata() def makedata(): import pandas as pd x = 1 return pd.DataFrame({'x': [x, 2], 'y': [3, 4]}) data = makedata()"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/python_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Python TealDatasetConnector — python_dataset_connector","text":"","code":"if (FALSE) { library(reticulate) # supply python code directly in R x <- python_dataset_connector( \"ADSL\", code = \"import pandas as pd data = pd.DataFrame({'STUDYID': [1, 2], 'USUBJID': [3, 4]})\", object = \"data\" ) x$pull() x$get_raw_data() # supply an external python script python_file <- tempfile(fileext = \".py\") writeLines( text = \"import pandas as pd data = pd.DataFrame({'STUDYID': [1, 2], 'USUBJID': [3, 4]})\", con = python_file ) x <- python_dataset_connector( \"ADSL\", file = python_file, object = \"data\", ) x$pull() x$get_raw_data() # supply pull `vars` from R y <- 8 x <- python_dataset_connector( \"ADSL\", code = \"import pandas as pd data = pd.DataFrame({'STUDYID': [r.y], 'USUBJID': [r.y]})\", object = \"data\", vars = list(y = y) ) x$pull() x$get_raw_data() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADAE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random adverse events — rADAE","title":"Random adverse events — rADAE","text":"Random adverse events","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADAE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random adverse events — rADAE","text":"","code":"rADAE"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADAE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random adverse events — rADAE","text":"object class tbl_df (inherits tbl, data.frame) 1934 rows 92 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADAE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random adverse events — rADAE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADCM.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Concomitant Medications — rADCM","title":"Random Concomitant Medications — rADCM","text":"Random Concomitant Medications","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADCM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Concomitant Medications — rADCM","text":"","code":"rADCM"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADCM.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Concomitant Medications — rADCM","text":"object class tbl_df (inherits tbl, data.frame) 3685 rows 83 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADCM.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Concomitant Medications — rADCM","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADEX.html","id":null,"dir":"Reference","previous_headings":"","what":"Random response — rADEX","title":"Random response — rADEX","text":"Random Exposure","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADEX.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random response — rADEX","text":"","code":"rADEX"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADEX.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random response — rADEX","text":"object class tbl_df (inherits tbl, data.frame) 6400 rows 79 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADEX.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random response — rADEX","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADLB.html","id":null,"dir":"Reference","previous_headings":"","what":"Random lab analysis — rADLB","title":"Random lab analysis — rADLB","text":"Random lab analysis","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADLB.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random lab analysis — rADLB","text":"","code":"rADLB"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADLB.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random lab analysis — rADLB","text":"object class tbl_df (inherits tbl, data.frame) 8400 rows 102 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADLB.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random lab analysis — rADLB","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADRS.html","id":null,"dir":"Reference","previous_headings":"","what":"Random response — rADRS","title":"Random response — rADRS","text":"Random response","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADRS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random response — rADRS","text":"","code":"rADRS"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADRS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random response — rADRS","text":"object class tbl_df (inherits tbl, data.frame) 3200 rows 65 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADRS.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random response — rADRS","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADSL.html","id":null,"dir":"Reference","previous_headings":"","what":"Random patient listing — rADSL","title":"Random patient listing — rADSL","text":"Random patient listing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADSL.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random patient listing — rADSL","text":"","code":"rADSL"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADSL.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random patient listing — rADSL","text":"object class tbl_df (inherits tbl, data.frame) 400 rows 55 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADSL.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random patient listing — rADSL","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTR.html","id":null,"dir":"Reference","previous_headings":"","what":"Random data rADTR — rADTR","title":"Random data rADTR — rADTR","text":"Random data rADTR","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random data rADTR — rADTR","text":"","code":"rADTR"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTR.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random data rADTR — rADTR","text":"object class data.frame 2800 rows 76 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random data rADTR — rADTR","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTTE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Time to Event Analysis Dataset — rADTTE","title":"Random Time to Event Analysis Dataset — rADTTE","text":"Random Time Event Analysis Dataset","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTTE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Time to Event Analysis Dataset — rADTTE","text":"","code":"rADTTE"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTTE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Time to Event Analysis Dataset — rADTTE","text":"object class tbl_df (inherits tbl, data.frame) 2000 rows 67 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADTTE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Time to Event Analysis Dataset — rADTTE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADVS.html","id":null,"dir":"Reference","previous_headings":"","what":"Random data rADVS — rADVS","title":"Random data rADVS — rADVS","text":"Random data rADVS","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADVS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random data rADVS — rADVS","text":"","code":"rADVS"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADVS.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random data rADVS — rADVS","text":"object class tbl_df (inherits tbl, data.frame) 16800 rows 87 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rADVS.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random data rADVS — rADVS","text":"internal","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rds_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"","code":"rds_dataset_connector( dataname, file, keys = character(0), label = character(0), code = character(0), script = character(0), metadata = list(type = \"rds\", file = file), ... ) rds_cdisc_dataset_connector( dataname, file, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), metadata = list(type = \"rds\", file = file), ... )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rds_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) path (.rds .R) contains data.frame object code source keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... (optional) additional arguments applied base::readRDS() function parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rds_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"Create TealDatasetConnector RDS file. Create CDSICTealDatasetConnector RDS file keys automatically assigned dataname","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/rds_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RDS TealDatasetConnector — rds_dataset_connector","text":"","code":"if (FALSE) { x <- rds_dataset_connector( dataname = \"ADSL\", file = \"path/to/file.RDS\" ) x$get_code() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/read_script.html","id":null,"dir":"Reference","previous_headings":"","what":"Read .R file into character — read_script","title":"Read .R file into character — read_script","text":"Comments excluded","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/read_script.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read .R file into character — read_script","text":"","code":"read_script(file, dataname = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/read_script.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read .R file into character — read_script","text":"file (character) File parsed code dataname (character) dataset name subset code chunks","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/read_script.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read .R file into character — read_script","text":"(character) vector code","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/read_script.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read .R file into character — read_script","text":"","code":"file_example <- tempfile() writeLines(c(\"x <- 2\", \"#second line comment\", \"x <- x + 2\"), file_example) read_script(file_example) #> [1] \"x <- 2\\nx <- x + 2\""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/relational_data_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"","code":"relational_data_connector(connection, connectors)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/relational_data_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"connection (TealDataConnection) connection data source connectors (list TealDatasetConnector elements) list dataset connectors","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/relational_data_connector.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"TealDataConnector object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/relational_data_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The constructor for TealDataConnector class. — relational_data_connector","text":"","code":"library(magrittr) random_data_connector <- function(dataname) { fun_dataset_connector( dataname = dataname, fun = teal.data::example_cdisc_data, fun_args = list(dataname = dataname), ) } open_fun <- callable_function(library) open_fun$set_args(list(package = \"teal.data\")) con <- data_connection(open_fun = open_fun) con$set_open_server( function(id, connection) { moduleServer( id = id, module = function(input, output, session) { connection$open(try = TRUE) return(invisible(connection)) } ) } ) x <- relational_data_connector( connection = con, connectors = list( random_data_connector(dataname = \"ADSL\"), random_data_connector(dataname = \"ADLB\") ) ) x$set_ui( function(id, connection, connectors) { ns <- NS(id) tagList( connection$get_open_ui(ns(\"open_connection\")), numericInput(inputId = ns(\"n\"), label = \"Choose number of records\", min = 0, value = 1), do.call( what = \"tagList\", args = lapply( connectors, function(connector) { div( connector$get_ui( id = ns(connector$get_dataname()) ), br() ) } ) ) ) } ) x$set_server( function(id, connection, connectors) { moduleServer( id = id, module = function(input, output, session) { # opens connection connection$get_open_server()(id = \"open_connection\", connection = connection) if (connection$is_opened()) { for (connector in connectors) { set_args(connector, args = list(n = input$n)) # pull each dataset connector$get_server()(id = connector$get_dataname()) if (connector$is_failed()) { break } } } } ) } ) if (FALSE) { x$launch() x$get_datasets() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the lines of code needed to reproduce the object. — return_code","title":"Return the lines of code needed to reproduce the object. — return_code","text":"Return lines code needed reproduce object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the lines of code needed to reproduce the object. — return_code","text":"","code":"return_code(object, occur, cooccur, eff, parent = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the lines of code needed to reproduce the object. — return_code","text":"object character object name occur result code_dependency()$occurrence cooccur result code_dependency()$cooccurrence eff result code_dependency()$effects parent NULL numeric vector - recursive call, possible needed drop parent object indicator omit dependency cycles","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the lines of code needed to reproduce the object. — return_code","text":"numeric vector indicating lines parsed_code calls required build object numeric vector number lines input pd returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code_for_effects.html","id":null,"dir":"Reference","previous_headings":"","what":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"Return lines code needed reproduce side-effects impact object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code_for_effects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"","code":"return_code_for_effects(object, calls_pd, occur, cooccur, eff)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code_for_effects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"object character object name calls_pd list data.frames, result get_children(utils::getParseData(), parent = 0) applied parse(text = code, keep.source = TRUE) code_dependency(code). occur result code_dependency()$occurrence cooccur result code_dependency()$cooccurrence","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/return_code_for_effects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return the lines of code needed to reproduce the side-effects having an impact on the object. — return_code_for_effects","text":"numeric vector indicating lines parsed_code calls required build side-effects impact object numeric vector number lines input pd returned effects.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/script_dataset_connector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Script TealDatasetConnector — script_dataset_connector","text":"","code":"script_dataset_connector( dataname, file, keys = character(0), label = character(0), code = character(0), script = character(0), metadata = NULL, ... ) script_cdisc_dataset_connector( dataname, file, keys = get_cdisc_keys(dataname), parent = if (identical(dataname, \"ADSL\")) character(0L) else \"ADSL\", label = character(0), code = character(0), script = character(0), metadata = NULL, ... )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/script_dataset_connector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Script TealDatasetConnector — script_dataset_connector","text":"dataname (character) given name dataset may contain spaces file (character) file location containing code evaluated connector. Object obtained last call file returned connector - source(file = file)$value keys optional, (character) vector dataset primary keys column names label (character) Label describe dataset. code (character) character string defining code modify raw_data dataset. modify current dataset code contain least one assignment object defined dataname argument. example dataname = ADSL example code contain ADSL <- . used simultaneously script script (character) Alternatively code - location file containing modification code. used simultaneously script. metadata (named list, NULL CallableFunction) Field containing either metadata dataset (element list atomic length one) CallableFuntion pull metadata connection. return list object can converted list .list. ... Additional arguments applied pull function. case object code depends raw_data TealDataset, TealDatasetConnector object(s) constant value, /object(s) included. Please note vars included object local vars modified within another dataset. parent (character, optional) parent dataset name","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/script_dataset_connector.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Script TealDatasetConnector — script_dataset_connector","text":"Create TealDatasetConnector .R file. Create CDISCTealDatasetConnector script file keys assigned automatically dataname.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/script_dataset_connector.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Script TealDatasetConnector — script_dataset_connector","text":"","code":"if (FALSE) { x <- script_dataset_connector( dataname = \"ADSL\", file = \"path/to/script.R\", keys = get_cdisc_keys(\"ADSL\") ) x$get_code() }"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_args.html","id":null,"dir":"Reference","previous_headings":"","what":"Set arguments of a CallableFunction — set_args","title":"Set arguments of a CallableFunction — set_args","text":"Set arguments CallableFunction","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_args.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set arguments of a CallableFunction — set_args","text":"","code":"set_args(x, args) # S3 method for CallableFunction set_args(x, args) # S3 method for CallableCode set_args(x, args) # S3 method for TealDatasetConnector set_args(x, args)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_args.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set arguments of a CallableFunction — set_args","text":"x CallableFunction TealDatasetConnector) args (NULL named list) dynamic arguments function","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_args.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set arguments of a CallableFunction — set_args","text":"nothing","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_args.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set arguments of a CallableFunction — set_args","text":"","code":"## Using CallableFunction fun <- callable_function(example_cdisc_data) set_args(fun, list(dataname = \"ADSL\")) ## Using CallableCode code <- callable_code(\"example_cdisc_data()\") set_args(code, list(df = \"adsl\")) #> Warning: 'CallableCode' is unchangable. Ignoring arguments set by 'set_args' ## Using TealDatasetConnector ds <- dataset_connector(\"x\", pull_callable = callable_function(data.frame)) set_args(ds, list(x = 1:5, y = letters[1:5]))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_keys.html","id":null,"dir":"Reference","previous_headings":"","what":"Set dataset primary keys — set_keys","title":"Set dataset primary keys — set_keys","text":"Set dataset primary keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_keys.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dataset primary keys — set_keys","text":"","code":"set_keys(x, ...) # S3 method for TealDataset set_keys(x, keys, ...) # S3 method for TealDatasetConnector set_keys(x, keys, ...) # S3 method for TealDataAbstract set_keys(x, dataname, keys, ...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_keys.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dataset primary keys — set_keys","text":"x object TealDataset TealDatasetConnector class ... used, support S3 keys optional, (character) vector primary keys dataname (character) name dataset set keys","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_keys.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dataset primary keys — set_keys","text":"(character) vector column names","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/set_keys.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set dataset primary keys — set_keys","text":"","code":"# TealDataset -------- set_keys( dataset( \"DF\", data.frame(ID = 1:10, x = runif(10)) ), keys = c(\"ID\") ) # TealDatasetConnector -------- pull_fun <- callable_function( function() { data.frame(ID = 1:10, x = runif(10)) } ) set_keys( dataset_connector( \"DF\", pull_fun ), keys = c(\"ID\") ) # TealData -------- set_keys( teal_data( dataset(\"x\", data.frame(x1 = 1:10, y1 = 11:20), keys = \"x1\"), dataset(\"y\", data.frame(x2 = 1:10, y2 = 11:20), keys = \"x2\") ), \"x\", c(\"x1\", \"y1\") )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal.data-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.data: Reproducible data model for teal applications — teal.data-package","title":"teal.data: Reproducible data model for teal applications — teal.data-package","text":"package extends teal applications module stores data relationships (keys) reproducible code. Package offers also load data files, databases easily extendable another data sources.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal.data-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.data: Reproducible data model for teal applications — teal.data-package","text":"Maintainer: Dawid Kaledkowski dawid.kaledkowski@roche.com Authors: Pawel Rucki pawel.rucki@roche.com Mahmoud Hallal mahmoud.hallal@roche.com Nikolas Burkoff Maciej Nasinski Konrad Pagacz Junlue Zhao contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Reproducible data. — teal_data-class","title":"Reproducible data. — teal_data-class","text":"Reproducible data container class. Inherits code tracking behavior teal.code::qenv.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reproducible data. — teal_data-class","text":"class provides isolated environment store process data code recorded. environment, code, data set names, data joining keys stored respective slots. slots never accessed directly, use provided get/set functions. code evaluated teal_data, messages warnings stored respective slots. errors raised, qenv.error object returned.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Reproducible data. — teal_data-class","text":"env (environment) environment containing data sets possibly auxiliary variables Access variables get_var() [[[]. setter provided. Evaluate code add variables @env. code (character) representing code necessary reproduce contents @env. Access get_code(). setter provided. Evaluate code append code slot. id (integer) random identifier assigned line code @code. Used internally. warnings (character) warnings output evaluating code. warnings (character) warnings raised evaluating code. Access get_warnings(). messages (character) messages raised evaluating code. join_keys (join_keys) object specifying joining keys data sets @env. Access modify join_keys(). datanames (character) vector names data sets @env. Used internally distinguish auxiliary variables. Access modify datanames().","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Data — teal_data","title":"Teal Data — teal_data","text":"Universal function pass data teal application.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Data — teal_data","text":"","code":"teal_data( ..., join_keys = teal.data::join_keys(), code = character(0), check = FALSE )"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Data — teal_data","text":"... (TealDataConnector, TealDataset, TealDatasetConnector, ) Either 1) object Teal* class, deprecated removed next release, 2) number objects provided name = value pairs, available version 0.4.0. join_keys (join_keys) single (join_key_set) (optional) object dataset column relationships used joining. empty joins pairs objects code (character, language) code reproduce datasets. check (logical) reproducibility check - whether perform check pre-processing code included object definitions actually produces objects. check true preprocessing code empty error thrown.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Data — teal_data","text":"old data classes provided (TealDataset TealDatasetConnector, TealDataConnector), TealData object. Otherwise teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Data — teal_data","text":"","code":"teal_data(x1 = iris, x2 = mtcars) #> [L] #> Parent: #> Bindings: #> • x1: [L] #> • x2: [L]"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Load TealData object from a file — teal_data_file","title":"Load TealData object from a file — teal_data_file","text":"Please note script end call creating desired object. error raised otherwise.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load TealData object from a file — teal_data_file","text":"","code":"teal_data_file(path, code = get_code(path))"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load TealData object from a file — teal_data_file","text":"path (connection) (character) string giving pathname file URL read . \"\" indicates connection stdin. code (character) reproducible code re-create object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load TealData object from a file — teal_data_file","text":"TealData object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/teal_data_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load TealData object from a file — teal_data_file","text":"","code":"# simple example file_example <- tempfile(fileext = \".R\") writeLines( text = c( \"library(teal.data) x1 <- dataset(dataname = \\\"IRIS\\\", x = iris, code = \\\"IRIS <- iris\\\") x2 <- dataset(dataname = \\\"MTCARS\\\", x = mtcars, code = \\\"MTCARS <- mtcars\\\") teal_data(x1, x2)\" ), con = file_example ) teal_data_file(file_example, code = character(0)) #> A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (150 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa #> ... #> --> Element 2: #> A TealDataset object containing the following data.frame (32 rows and 11 columns): #> mpg cyl disp hp drat wt qsec vs am gear carb #> Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 #> Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 #> Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 #> Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 #> Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 #> Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 #> ..."},{"path":"https://insightsengineering.github.io/teal.data/main/reference/text_to_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Create call from string — text_to_call","title":"Create call from string — text_to_call","text":"Create call string","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/text_to_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create call from string — text_to_call","text":"","code":"text_to_call(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/text_to_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create call from string — text_to_call","text":"x (character) string containing code.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/text_to_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create call from string — text_to_call","text":"(call) object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/to_relational_data.html","id":null,"dir":"Reference","previous_headings":"","what":"S3 generic for to_relational_data function. — to_relational_data","title":"S3 generic for to_relational_data function. — to_relational_data","text":"function takes object converts TealData object, primary data object use teal applications.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/to_relational_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"S3 generic for to_relational_data function. — to_relational_data","text":"","code":"to_relational_data(data)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/to_relational_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"S3 generic for to_relational_data function. — to_relational_data","text":"data TealDataset, TealDatasetConnector, data.frame, MultiAssayExperiment, list function returning named list.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/to_relational_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S3 generic for to_relational_data function. — to_relational_data","text":"TealData object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/to_relational_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S3 generic for to_relational_data function. — to_relational_data","text":"Passing TealData function leaves object unchanged.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/to_relational_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S3 generic for to_relational_data function. — to_relational_data","text":"","code":"to_relational_data(head(iris)) #> A TealData object containing 1 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa to_relational_data(dataset(\"IRIS\", head(iris))) #> A TealData object containing 1 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa to_relational_data(list(iris = head(iris), mtcars = head(mtcars))) #> A TealData object containing 2 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa #> --> Element 2: #> A TealDataset object containing the following data.frame (6 rows and 11 columns): #> mpg cyl disp hp drat wt qsec vs am gear carb #> Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 #> Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 #> Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 #> Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 #> Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 #> Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 d_connector <- dataset_connector(\"iris\", callable_function(function() head(iris))) d_connector$pull() to_relational_data(d_connector) #> A TealData object containing 1 TealDataset/TealDatasetConnector object(s) as element(s): #> --> Element 1: #> A TealDatasetConnector object, named iris, containing a TealDataset object that has been loaded/pulled: #> A TealDataset object containing the following data.frame (6 rows and 5 columns): #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.2 setosa #> 2 4.9 3.0 1.4 0.2 setosa #> 3 4.7 3.2 1.3 0.2 setosa #> 4 4.6 3.1 1.5 0.2 setosa #> 5 5.0 3.6 1.4 0.2 setosa #> 6 5.4 3.9 1.7 0.4 setosa"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/topological_sort.html","id":null,"dir":"Reference","previous_headings":"","what":"Topological graph sort — topological_sort","title":"Topological graph sort — topological_sort","text":"Graph list node contains vector child nodes returned list, parents appear children.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/topological_sort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Topological graph sort — topological_sort","text":"","code":"topological_sort(graph)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/topological_sort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Topological graph sort — topological_sort","text":"graph (named list) list node vector elements","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/topological_sort.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Topological graph sort — topological_sort","text":"Implementation Kahn algorithm modification maintain order input elements.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/topological_sort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Topological graph sort — topological_sort","text":"","code":"teal.data:::topological_sort(list(A = c(), B = c(\"A\"), C = c(\"B\"), D = c(\"A\"))) #> [[1]] #> [1] \"A\" #> #> [[2]] #> [1] \"B\" #> #> [[3]] #> [1] \"C\" #> #> [[4]] #> [1] \"D\" #> teal.data:::topological_sort(list(D = c(\"A\"), A = c(), B = c(\"A\"), C = c(\"B\"))) #> [[1]] #> [1] \"A\" #> #> [[2]] #> [1] \"D\" #> #> [[3]] #> [1] \"B\" #> #> [[4]] #> [1] \"C\" #> teal.data:::topological_sort(list(D = c(\"A\"), B = c(\"A\"), C = c(\"B\"), A = c())) #> [[1]] #> [1] \"A\" #> #> [[2]] #> [1] \"D\" #> #> [[3]] #> [1] \"B\" #> #> [[4]] #> [1] \"C\" #>"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/update_join_keys_to_primary.html","id":null,"dir":"Reference","previous_headings":"","what":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","title":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","text":"Add primary keys join_keys dataset self","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/update_join_keys_to_primary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","text":"","code":"update_join_keys_to_primary(data_objects, x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/update_join_keys_to_primary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add primary keys as join_keys to a dataset self — update_join_keys_to_primary","text":"data_objects (list) TealDataset, TealDatasetConnector TealDataConnector objects x (join_keys) object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/update_keys_given_parents.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"Updates keys datasets based parents.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/update_keys_given_parents.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"","code":"update_keys_given_parents(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/update_keys_given_parents.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"x (join_keys) object update keys.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/update_keys_given_parents.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates the keys of the datasets based on the parents. — update_keys_given_parents","text":"(self) invisibly chaining","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/used_in_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Whether an object is used inside a function within a call — used_in_function","title":"Whether an object is used inside a function within a call — used_in_function","text":"Whether object used inside function within call","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/used_in_function.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Whether an object is used inside a function within a call — used_in_function","text":"","code":"used_in_function(call, object)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/used_in_function.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Whether an object is used inside a function within a call — used_in_function","text":"call element calls_pd list used detect_symbol. object character object name.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/used_in_function.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Whether an object is used inside a function within a call — used_in_function","text":"logical(1).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/validate_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","title":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","text":"validate metadata list length one atomic entries (NULL)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/validate_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","text":"","code":"validate_metadata(metadata)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/validate_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","text":"metadata object checked","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/validate_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","text":"NULL throw error","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/validate_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"validate metadata as a list of length one atomic entries (or NULL) — validate_metadata","text":"","code":"validate_metadata(NULL) #> NULL validate_metadata(list(A = TRUE, B = 10, C = \"test\")) #> NULL if (FALSE) { validate_metadata(list(a = 1:10)) }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"enhancements-0-3-0-9016","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.data 0.3.0.9016","text":"Simplified join_key better support primary keys. 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Added col_labels function removed formatters dependency.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"miscellaneous-0-3-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.3.0","text":"Update installation instructions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"enhancements-0-2-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.data 0.2.0","text":"Added ADQLQC, ADCSSRS, ADEQ5D5L supported data sets. Improved error message get_cdisc_keys. Examples now use scda.2022 instead scda.2021. Fixed help files TealDataset MAETealDataset. Added backstop missing reticulate package teal.data Python vignette.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"miscellaneous-0-2-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.2.0","text":"Modified teal.Dataset$print method less cluttered output. Transferred data hashing step TealDataset MAETealDataset teal. Removed CDISCTealData class updated TealData account removed functionality. Added datasets parents information JoinKeys class. Updated cdisc_data teal_data wrappers handle join_keys creation updating instead CDISCTealData TealData. Removed join_keys methods TealDataset, TealDatasetConnector.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"enhancements-0-1-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.data 0.1.2","text":"Updated vignettes README content.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"miscellaneous-0-1-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.1.2","text":"Exported validate_metadata function. 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Added package vignettes.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"tealdata-010","dir":"Changelog","previous_headings":"","what":"teal.data 0.1.0","title":"teal.data 0.1.0","text":"Initial release teal.data package data model used teal applications.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"Changes (from behavior when functionality was part of teal)","what":"New features","title":"teal.data 0.1.0","text":"Added metadata field TealDataset store named list metadata items. available module developers FilteredData$get_metadata(\"<>\") can pulled added directly datasets derived TealDatasetConnectors.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"breaking-changes-0-1-0","dir":"Changelog","previous_headings":"Changes (from behavior when functionality was part of teal)","what":"Breaking changes","title":"teal.data 0.1.0","text":"get_key_duplicates returns data.frame instead tibble. get_call() function CallableFunction now returns call namespace included. MultiAssayExperiment SummarizedExperiment now suggested packages, required. Objects dependent MultiAssayExperiment changed lazy-load now suggested packages. Minor changes interface TealDataset, example active fields replaced explicit “get” calls.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"miscellaneous-0-1-0","dir":"Changelog","previous_headings":"Changes (from behavior when functionality was part of teal)","what":"Miscellaneous","title":"teal.data 0.1.0","text":"reticulate Suggests, added requireNamespace call whenever needed. dplyr moved imports suggests. Removed redundant calling JoinKeys$mutate method inside -loops. Removed rtables dependency package.","code":""}]