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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. 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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: _. 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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 <- transform(iris, id = seq_len(nrow(iris))) ) 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/teal-data-reproducibility.html","id":"reproducibility-of-teal_data-objects","dir":"Articles","previous_headings":"","what":"Reproducibility of teal_data objects","title":"teal_data reproducibility","text":"Reproducibility primary function qenv class, teal_data inherits . Every data modification teal_data object performed encapsulated environment, separate global environment. important note reproducibility object limited data-code relationship. aspects reliability data source, reproducibility R session (including package versions), creation use objects environments (e.g. .GlobalEnvironment) verified properly teal_data.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data-reproducibility.html","id":"verification-status","dir":"Articles","previous_headings":"Reproducibility of teal_data objects","what":"Verification status","title":"teal_data reproducibility","text":"teal_data objects instantiated empty created verified. Objects can modified eval_code() within() functions ensure code saved object always evaluated correct environment. Evaluating code teal_data object change verification status. Find teal_data() documentation.","code":"library(teal.data) my_data <- teal_data() my_data <- within(my_data, data <- data.frame(x = 11:20)) my_data <- within(my_data, data$id <- seq_len(nrow(data))) my_data # is verified ## ✅︎ verified teal_data object ## [L] ## Parent: ## Bindings: ## • data: [L]"},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data-reproducibility.html","id":"verification","dir":"Articles","previous_headings":"Reproducibility of teal_data objects","what":"Verification","title":"teal_data reproducibility","text":"teal_data objects instantiated data code run risk code reproducible. objects created unverified state. confirm code exactly reproduces variables stored object, one must run verify() function. verification succeeds, object’s state changed verified, otherwise error raised. retrieving code, unverified objects always add warning code stating passed verification.","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data-reproducibility.html","id":"verified","dir":"Articles","previous_headings":"Reproducibility of teal_data objects > Verification","what":"verified","title":"teal_data reproducibility","text":"","code":"library(teal.data) data <- data.frame(x = 11:20) data$id <- seq_len(nrow(data)) data_right <- teal_data( data = data, code = quote({ data <- data.frame(x = 11:20) data$id <- seq_len(nrow(data)) }) ) (data_right_verified <- verify(data_right)) # returns verified object ## ✅︎ verified teal_data object ## [L] ## Parent: ## Bindings: ## • data: [L]"},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data-reproducibility.html","id":"unverified","dir":"Articles","previous_headings":"Reproducibility of teal_data objects > Verification","what":"unverified","title":"teal_data reproducibility","text":"","code":"data_wrong <- teal_data( data = data, code = quote({ data <- data.frame(x = 11:20) }) ) verify(data_wrong) # fails verification, raises error ## Error: Code verification failed. ## Object(s) recreated with code that have different structure in data_wrong: ## • data"},{"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. teal_data class inherits qenv meant used reproducibility purposes.","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":"create teal_data class object, use teal_data function. teal_data number methods allow set get relevant information private class slots.","code":"library(teal.data) ## Loading required package: teal.code my_data <- teal_data() my_data <- within( my_data, { data1 <- data.frame(id = 1:10, x = 11:20) data2 <- data.frame(id = 1:10, x = 21:30) } ) # get variables from teal_data environment my_data[[\"data1\"]] my_data[[\"data1\"]] # get reproducible code get_code(my_data) # set/get datanames datanames(my_data) <- c(\"data1\", \"data2\") datanames(my_data) # concise print print(my_data)"},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data.html","id":"teal_data-characteristics","dir":"Articles","previous_headings":"Introduction","what":"teal_data characteristics","title":"Introduction to teal.data","text":"teal_data class object keeps following information: - env - environment containing data. - code - string containing code reproduce env (details teal_data reproducibility). - datanames - character vector names datasets. - join_keys - join_keys object defining relationships datasets (details Join Keys).","code":""},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data.html","id":"reproducibility","dir":"Articles","previous_headings":"Introduction > teal_data characteristics","what":"Reproducibility","title":"Introduction to teal.data","text":"primary function teal_data provide reproducibility data. recommend initialize empty teal_data, marks object verified, create data sets code evaluated object, using within eval_code. Read teal_data Reproducibility.","code":"my_data <- teal_data() my_data <- within(my_data, data <- data.frame(x = 11:20)) my_data <- within(my_data, data$id <- seq_len(nrow(data))) my_data # is verified ## ✅︎ verified teal_data object ## [L] ## Parent: ## Bindings: ## • data: [L]"},{"path":"https://insightsengineering.github.io/teal.data/articles/teal-data.html","id":"relational-data-models","dir":"Articles","previous_headings":"Introduction > teal_data characteristics","what":"Relational data models","title":"Introduction to teal.data","text":"teal_data class can extended support relational data. join_keys function can used specify relationships datasets. See join_keys.","code":"my_data <- teal_data() my_data <- within(my_data, { data <- data.frame(id = 1:10, x = 11:20) child <- data.frame(id = 1:20, data_id = c(1:10, 1:10), y = 21:30) }) join_keys(my_data) <- join_keys( join_key(\"data\", \"data\", key = \"id\"), join_key(\"child\", \"child\", key = \"id\"), join_key(\"child\", \"data\", key = c(\"data_id\" = \"id\")) ) join_keys(my_data) ## A join_keys object containing foreign keys between 2 datasets: ## data: [id] ## <-> child: [data_id] ## child: [id] ## <-> data: [id]"},{"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 0.3.0.9026, 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 0.3.0.9026, 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/TealData.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated TealData class and related functions — TealData","title":"Deprecated TealData class and related functions — TealData","text":"function deprecated. Please see teal_data() cdisc_data() instead. Find information Migration guide.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated TealData class and related functions — TealData","text":"","code":"as_cdisc(...) callable_code(...) callable_function(...) code_dataset_connector(...) code_cdisc_dataset_connector(...) csv_dataset_connector(...) csv_cdisc_dataset_connector(...) python_code(...) python_dataset_connector(...) python_cdisc_dataset_connector(...) cdisc_data_connector(...) cdisc_dataset(...) cdisc_dataset_connector(...) cdisc_dataset_connector_file(...) cdisc_dataset_file(...) dataset(...) dataset_connector(...) dataset_connector_file(...) dataset_file(...) data_connection(...) fun_dataset_connector(...) fun_cdisc_dataset_connector(...) relational_data_connector(...) mae_dataset(...) get_attrs(...) get_dataset_label(...) get_dataset(...) get_datasets(...) get_dataname(...) get_key_duplicates(...) get_keys(...) get_raw_data(...) is_pulled(...) load_dataset(...) load_datasets(...) mutate_data(...) mutate_dataset(...) set_args(...) rds_dataset_connector(...) rds_cdisc_dataset_connector(...) script_dataset_connector(...) script_cdisc_dataset_connector(...) set_keys(...) read_script(...) to_relational_data(...) validate_metadata(...) get_cdisc_keys(...) cdisc_data_file(...) teal_data_file(...)"},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated TealData class and related functions — TealData","text":"... argument supported TealData related functions.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/TealData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated TealData class and related functions — TealData","text":"nothing","code":""},{"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":"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/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":"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":"https://insightsengineering.github.io/teal.data/reference/col_labels-set.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Label Attributes of All Variables in a data.frame — col_labels<-","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"Variable labels can stored label attribute variable. functions sets non-missing (non-NA) variable labels data.frame","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels-set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"","code":"col_labels(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels-set.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Set Label Attributes of All 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-set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"x data.frame object value new variable labels, NA removes variable label","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels-set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"modifies variable labels x","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/reference/col_labels-set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Label Attributes of All 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\" 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 — get_labels","title":"Get Label Attributes of Variables in a data.frame — get_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 — get_labels","text":"","code":"get_labels(data, fill = TRUE) 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 — get_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 — get_labels","text":"data data.frame object fill boolean case label attribute exist TRUE variable names returned, otherwise NA x data.frame object","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 — get_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 — get_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":"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":"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":"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/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/get_code-teal_data-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Code from teal_data — get_code,teal_data-method","title":"Get Code from teal_data — get_code,teal_data-method","text":"Retrieve code teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code-teal_data-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Code from teal_data — get_code,teal_data-method","text":"","code":"# S4 method for teal_data get_code(object, deparse = TRUE, datanames = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code-teal_data-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Code from teal_data — get_code,teal_data-method","text":"object (teal_data) deparse (logical) flag specifying whether return code character (deparse = TRUE) expression (deparse = FALSE). datanames (character) vector data set names return code .","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code-teal_data-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Code from teal_data — get_code,teal_data-method","text":"Either string expression representing code used create requested data sets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code-teal_data-method.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Code from teal_data — get_code,teal_data-method","text":"Retrieve code stored @code, (principle) can used recreate objects found @env. Use datanames limit code one data sets enumerated @datanames. code passed verification (verify()), warning prepended.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code-teal_data-method.html","id":"notes-for-developers","dir":"Reference","previous_headings":"","what":"Notes for Developers","title":"Get Code from teal_data — get_code,teal_data-method","text":"learn subset code needed reproduce specific data set extracted code, see get_code_dependency().","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code-teal_data-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Code from teal_data — get_code,teal_data-method","text":"","code":"tdata1 <- teal_data() tdata1 <- within(tdata1, { a <- 1 b <- a^5 c <- list(x = 2) }) get_code(tdata1) #> [1] \"a <- 1\\nb <- a^5\\nc <- list(x = 2)\" datanames(tdata1) <- c(\"a\", \"b\", \"c\") get_code(tdata1, datanames = \"a\") #> [1] \"a <- 1\" get_code(tdata1, datanames = \"b\") #> [1] \"a <- 1\\nb <- a^5\" tdata2 <- teal_data(x1 = iris, code = \"x1 <- iris\") get_code(tdata2) #> [1] \"warning('Code was not verified for reproducibility.')\\nx1 <- iris\" get_code(verify(tdata2)) #> [1] \"x1 <- iris\""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Code Dependency of an Object — get_code_dependency","title":"Get Code Dependency of an Object — get_code_dependency","text":"Extract subset code required reproduce specific object(s), including code producing side-effects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Code Dependency of an Object — get_code_dependency","text":"","code":"get_code_dependency(code, names, check_names = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Code Dependency of an Object — get_code_dependency","text":"code character code. names character vector object names. check_names logical(1) flag specifying warning non-existing names displayed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Code Dependency of an Object — get_code_dependency","text":"Character vector, subset code. Note subsetting actually done calls code, necessarily elements vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/get_code_dependency.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Code Dependency of an Object — get_code_dependency","text":"Given character vector code, function extract part code responsible creating variables specified names. includes final call creates variable(s) question well parent calls, .e. calls create variables used final call parents, etc. Also included calls create side-effects like establishing connections. assumed object dependency established using three assignment operators: <-, =, -> . assignment methods (assign, <<-) non-standard-evaluation methods supported. Side-effects detected automatically must marked code. Add # @linksto object end line side-effect occurs specify line required reproduce variable called object.","code":""},{"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":"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":[]},{"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 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/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/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":"https://insightsengineering.github.io/teal.data/reference/show-teal_data-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Show teal_data object — show,teal_data-method","title":"Show teal_data object — show,teal_data-method","text":"Prints teal_data object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/show-teal_data-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show teal_data object — show,teal_data-method","text":"","code":"# S4 method for teal_data show(object)"},{"path":"https://insightsengineering.github.io/teal.data/reference/show-teal_data-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show teal_data object — show,teal_data-method","text":"object (teal_data)","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/show-teal_data-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show teal_data object — show,teal_data-method","text":"Input teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/show-teal_data-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show teal_data object — show,teal_data-method","text":"","code":"teal_data() #> ✅︎ verified teal_data object #> [L] #> Parent: teal_data(x = iris, code = \"x = iris\") #> ✖ unverified teal_data object #> [L] #> Parent: #> Bindings: #> • x: [L] verify(teal_data(x = iris, code = \"x = iris\")) #> ✅︎ verified teal_data object #> [L] #> Parent: #> Bindings: #> • x: [L]"},{"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) vector representing code necessary reproduce contents @env. Access get_code(). setter provided. Evaluate code append code slot. id (integer) random identifier assigned element @code. Used internally. warnings (character) vector warnings raised evaluating code. Access get_warnings(). messages (character) vector 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(). verified (logical(1)) flag signifying code @code proven yield contents @env. Used internally. See verify() details.","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) #> ✖ unverified teal_data object #> [L] #> Parent: #> Bindings: #> • x1: [L] #> • x2: [L]"},{"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_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/verify.html","id":null,"dir":"Reference","previous_headings":"","what":"Verify Code Reproducibility — verify","title":"Verify Code Reproducibility — verify","text":"Checks whether code teal_data reproduces stored objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/verify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Verify Code Reproducibility — verify","text":"","code":"verify(x)"},{"path":"https://insightsengineering.github.io/teal.data/reference/verify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Verify Code Reproducibility — verify","text":"x teal_data object","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/verify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Verify Code Reproducibility — verify","text":"Input teal_data object error.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/verify.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Verify Code Reproducibility — verify","text":"objects created code @code slot x all_equal contents @env slot, function updates @verified slot TRUE returned teal_data object. verified, slot always set TRUE. @code fails recreate objects teal_data@env, error raised.","code":""},{"path":"https://insightsengineering.github.io/teal.data/reference/verify.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Verify Code Reproducibility — verify","text":"","code":"tdata1 <- teal_data() tdata1 <- within(tdata1, { a <- 1 b <- a^5 c <- list(x = 2) }) verify(tdata1) #> ✅︎ verified teal_data object #> [L] #> Parent: #> Bindings: #> • a: [L] #> • b: [L] #> • c: [L] tdata2 <- teal_data(x1 = iris, code = \"x1 <- iris\") verify(tdata2) #> ✅︎ verified teal_data object #> [L] #> Parent: #> Bindings: #> • x1: [L] verify(tdata2)@verified #> [1] TRUE tdata2@verified #> [1] FALSE if (FALSE) { tdata3 <- teal_data() tdata3 <- within(tdata3, { stop(\"error\") }) verify(tdata3) a <- 1 b <- a + 2 c <- list(x = 2) d <- 5 tdata4 <- teal_data( a = a, b = b, c = c, d = d, code = \" a <- 1 b <- a c <- list(x = 2) e <- 1 \" ) tdata4 verify(tdata4) }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"enhancements-0-3-0-9026","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.data 0.3.0.9026","text":"Simplified join_key better support primary keys. JoinKey R6 object removed favor list-like object class name join_keys. Subset operators assignments supported ([, [[, [<- [[<-) join_keys function works constructor, getter setter.","code":""},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"breaking-changes-0-3-0-9026","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.data 0.3.0.9026","text":"teal_data() cdisc_data() return now teal_data class object replaces TealData class object. teal_data becomes standard input entire teal framework. TealDataset, TealDatasetConnector TealDataConnector classes removed. Delayed-data-loading longer supported teal.data. called connectors now supported teal package (see ?teal::teal_data_module). join_keys() join_key() return now join_keys object replace JoinKeys class.","code":""},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"miscellaneous-0-3-0-9026","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.3.0.9026","text":"Specified minimal version package dependencies. Upgraded teal.code dependency Imports Depends. Deprecated get_labels function removed supporting function data_labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"enhancements-0-3-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.data 0.3.0","text":"Removed scda package dependency examples. Added col_labels function removed formatters dependency.","code":""},{"path":"https://insightsengineering.github.io/teal.data/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/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/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/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/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. Replaced argument name archive_name comply latest version synthetic_cdisc_dataset function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"bug-fixes-0-1-2","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.data 0.1.2","text":"Fixed get_raw_data examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.1.1","text":"Added template pkgdown site. Removed usage .Globalenv Python code execution. Updated package authors. Added package vignettes.","code":""},{"path":"https://insightsengineering.github.io/teal.data/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/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$get_metadata(\"<>\") can pulled added directly datasets derived TealDatasetConnectors.","code":""},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"breaking-changes-0-1-0","dir":"Changelog","previous_headings":"Changes (from behavior when functionality was part of teal)","what":"Breaking changes","title":"teal.data 0.1.0","text":"get_key_duplicates returns data.frame instead tibble. get_call() function CallableFunction now returns call namespace included. MultiAssayExperiment SummarizedExperiment now suggested packages, required. Objects dependent MultiAssayExperiment changed lazy-load now suggested packages. Minor changes interface TealDataset, example active fields replaced explicit “get” calls.","code":""},{"path":"https://insightsengineering.github.io/teal.data/news/index.html","id":"miscellaneous-0-1-0","dir":"Changelog","previous_headings":"Changes (from behavior when functionality was part of teal)","what":"Miscellaneous","title":"teal.data 0.1.0","text":"reticulate Suggests, added requireNamespace call whenever needed. dplyr moved imports suggests. Removed redundant calling JoinKeys$mutate method inside -loops. Removed rtables dependency package.","code":""}] +[{"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. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. 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 <- transform(iris, id = seq_len(nrow(iris))) ) 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/teal-data-reproducibility.html","id":"reproducibility-of-teal_data-objects","dir":"Articles","previous_headings":"","what":"Reproducibility of teal_data objects","title":"teal_data reproducibility","text":"Reproducibility primary function qenv class, teal_data inherits . Every data modification teal_data object performed encapsulated environment, separate global environment. important note reproducibility object limited data-code relationship. aspects reliability data source, reproducibility R session (including package versions), creation use objects environments (e.g. .GlobalEnvironment) verified properly teal_data.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data-reproducibility.html","id":"verification-status","dir":"Articles","previous_headings":"Reproducibility of teal_data objects","what":"Verification status","title":"teal_data reproducibility","text":"teal_data objects instantiated empty created verified. Objects can modified eval_code() within() functions ensure code saved object always evaluated correct environment. Evaluating code teal_data object change verification status. Find teal_data() documentation.","code":"library(teal.data) my_data <- teal_data() my_data <- within(my_data, data <- data.frame(x = 11:20)) my_data <- within(my_data, data$id <- seq_len(nrow(data))) my_data # is verified ## ✅︎ verified teal_data object ## [L] ## Parent: ## Bindings: ## • data: [L]"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data-reproducibility.html","id":"verification","dir":"Articles","previous_headings":"Reproducibility of teal_data objects","what":"Verification","title":"teal_data reproducibility","text":"teal_data objects instantiated data code run risk code reproducible. objects created unverified state. confirm code exactly reproduces variables stored object, one must run verify() function. verification succeeds, object’s state changed verified, otherwise error raised. retrieving code, unverified objects always add warning code stating passed verification.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data-reproducibility.html","id":"verified","dir":"Articles","previous_headings":"Reproducibility of teal_data objects > Verification","what":"verified","title":"teal_data reproducibility","text":"","code":"library(teal.data) data <- data.frame(x = 11:20) data$id <- seq_len(nrow(data)) data_right <- teal_data( data = data, code = quote({ data <- data.frame(x = 11:20) data$id <- seq_len(nrow(data)) }) ) (data_right_verified <- verify(data_right)) # returns verified object ## ✅︎ verified teal_data object ## [L] ## Parent: ## Bindings: ## • data: [L]"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data-reproducibility.html","id":"unverified","dir":"Articles","previous_headings":"Reproducibility of teal_data objects > Verification","what":"unverified","title":"teal_data reproducibility","text":"","code":"data_wrong <- teal_data( data = data, code = quote({ data <- data.frame(x = 11:20) }) ) verify(data_wrong) # fails verification, raises error ## Error: Code verification failed. ## Object(s) recreated with code that have different structure in data_wrong: ## • data"},{"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. teal_data class inherits qenv meant used reproducibility purposes.","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":"create teal_data class object, use teal_data function. teal_data number methods allow set get relevant information private class slots.","code":"library(teal.data) ## Loading required package: teal.code my_data <- teal_data() my_data <- within( my_data, { data1 <- data.frame(id = 1:10, x = 11:20) data2 <- data.frame(id = 1:10, x = 21:30) } ) # get variables from teal_data environment my_data[[\"data1\"]] my_data[[\"data1\"]] # get reproducible code get_code(my_data) # set/get datanames datanames(my_data) <- c(\"data1\", \"data2\") datanames(my_data) # concise print print(my_data)"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data.html","id":"teal_data-characteristics","dir":"Articles","previous_headings":"Introduction","what":"teal_data characteristics","title":"Introduction to teal.data","text":"teal_data class object keeps following information: - env - environment containing data. - code - string containing code reproduce env (details teal_data reproducibility). - datanames - character vector names datasets. - join_keys - join_keys object defining relationships datasets (details Join Keys).","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data.html","id":"reproducibility","dir":"Articles","previous_headings":"Introduction > teal_data characteristics","what":"Reproducibility","title":"Introduction to teal.data","text":"primary function teal_data provide reproducibility data. recommend initialize empty teal_data, marks object verified, create data sets code evaluated object, using within eval_code. Read teal_data Reproducibility.","code":"my_data <- teal_data() my_data <- within(my_data, data <- data.frame(x = 11:20)) my_data <- within(my_data, data$id <- seq_len(nrow(data))) my_data # is verified ## ✅︎ verified teal_data object ## [L] ## Parent: ## Bindings: ## • data: [L]"},{"path":"https://insightsengineering.github.io/teal.data/main/articles/teal-data.html","id":"relational-data-models","dir":"Articles","previous_headings":"Introduction > teal_data characteristics","what":"Relational data models","title":"Introduction to teal.data","text":"teal_data class can extended support relational data. join_keys function can used specify relationships datasets. See join_keys.","code":"my_data <- teal_data() my_data <- within(my_data, { data <- data.frame(id = 1:10, x = 11:20) child <- data.frame(id = 1:20, data_id = c(1:10, 1:10), y = 21:30) }) join_keys(my_data) <- join_keys( join_key(\"data\", \"data\", key = \"id\"), join_key(\"child\", \"child\", key = \"id\"), join_key(\"child\", \"data\", key = c(\"data_id\" = \"id\")) ) join_keys(my_data) ## A join_keys object containing foreign keys between 2 datasets: ## data: [id] ## <-> child: [data_id] ## child: [id] ## <-> data: [id]"},{"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 0.3.0.9026, 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 0.3.0.9026, 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/TealData.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated TealData class and related functions — TealData","title":"Deprecated TealData class and related functions — TealData","text":"function deprecated. Please see teal_data() cdisc_data() instead. Find information Migration guide.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated TealData class and related functions — TealData","text":"","code":"as_cdisc(...) callable_code(...) callable_function(...) code_dataset_connector(...) code_cdisc_dataset_connector(...) csv_dataset_connector(...) csv_cdisc_dataset_connector(...) python_code(...) python_dataset_connector(...) python_cdisc_dataset_connector(...) cdisc_data_connector(...) cdisc_dataset(...) cdisc_dataset_connector(...) cdisc_dataset_connector_file(...) cdisc_dataset_file(...) dataset(...) dataset_connector(...) dataset_connector_file(...) dataset_file(...) data_connection(...) fun_dataset_connector(...) fun_cdisc_dataset_connector(...) relational_data_connector(...) mae_dataset(...) get_attrs(...) get_dataset_label(...) get_dataset(...) get_datasets(...) get_dataname(...) get_key_duplicates(...) get_keys(...) get_raw_data(...) is_pulled(...) load_dataset(...) load_datasets(...) mutate_data(...) mutate_dataset(...) set_args(...) rds_dataset_connector(...) rds_cdisc_dataset_connector(...) script_dataset_connector(...) script_cdisc_dataset_connector(...) set_keys(...) read_script(...) to_relational_data(...) validate_metadata(...) get_cdisc_keys(...) cdisc_data_file(...) teal_data_file(...)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated TealData class and related functions — TealData","text":"... argument supported TealData related functions.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/TealData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated TealData class and related functions — TealData","text":"nothing","code":""},{"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":"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/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":"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":"https://insightsengineering.github.io/teal.data/main/reference/col_labels-set.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Label Attributes of All Variables in a data.frame — col_labels<-","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"Variable labels can stored label attribute variable. functions sets non-missing (non-NA) variable labels data.frame","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels-set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"","code":"col_labels(x) <- value"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels-set.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Set Label Attributes of All 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-set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"x data.frame object value new variable labels, NA removes variable label","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels-set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Label Attributes of All Variables in a data.frame — col_labels<-","text":"modifies variable labels x","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/reference/col_labels-set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Label Attributes of All 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\" 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 — get_labels","title":"Get Label Attributes of Variables in a data.frame — get_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 — get_labels","text":"","code":"get_labels(data, fill = TRUE) 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 — get_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 — get_labels","text":"data data.frame object fill boolean case label attribute exist TRUE variable names returned, otherwise NA x data.frame object","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 — get_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 — get_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":"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":"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":"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/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/get_code-teal_data-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Code from teal_data — get_code,teal_data-method","title":"Get Code from teal_data — get_code,teal_data-method","text":"Retrieve code teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code-teal_data-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Code from teal_data — get_code,teal_data-method","text":"","code":"# S4 method for teal_data get_code(object, deparse = TRUE, datanames = NULL)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code-teal_data-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Code from teal_data — get_code,teal_data-method","text":"object (teal_data) deparse (logical) flag specifying whether return code character (deparse = TRUE) expression (deparse = FALSE). datanames (character) vector data set names return code .","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code-teal_data-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Code from teal_data — get_code,teal_data-method","text":"Either string expression representing code used create requested data sets.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code-teal_data-method.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Code from teal_data — get_code,teal_data-method","text":"Retrieve code stored @code, (principle) can used recreate objects found @env. Use datanames limit code one data sets enumerated @datanames. code passed verification (verify()), warning prepended.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code-teal_data-method.html","id":"notes-for-developers","dir":"Reference","previous_headings":"","what":"Notes for Developers","title":"Get Code from teal_data — get_code,teal_data-method","text":"learn subset code needed reproduce specific data set extracted code, see get_code_dependency().","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code-teal_data-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Code from teal_data — get_code,teal_data-method","text":"","code":"tdata1 <- teal_data() tdata1 <- within(tdata1, { a <- 1 b <- a^5 c <- list(x = 2) }) get_code(tdata1) #> [1] \"a <- 1\\nb <- a^5\\nc <- list(x = 2)\" datanames(tdata1) <- c(\"a\", \"b\", \"c\") get_code(tdata1, datanames = \"a\") #> [1] \"a <- 1\" get_code(tdata1, datanames = \"b\") #> [1] \"a <- 1\\nb <- a^5\" tdata2 <- teal_data(x1 = iris, code = \"x1 <- iris\") get_code(tdata2) #> [1] \"warning('Code was not verified for reproducibility.')\\nx1 <- iris\" get_code(verify(tdata2)) #> [1] \"x1 <- iris\""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Code Dependency of an Object — get_code_dependency","title":"Get Code Dependency of an Object — get_code_dependency","text":"Extract subset code required reproduce specific object(s), including code producing side-effects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Code Dependency of an Object — get_code_dependency","text":"","code":"get_code_dependency(code, names, check_names = TRUE)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Code Dependency of an Object — get_code_dependency","text":"code character code. names character vector object names. check_names logical(1) flag specifying warning non-existing names displayed.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Code Dependency of an Object — get_code_dependency","text":"Character vector, subset code. Note subsetting actually done calls code, necessarily elements vector.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/get_code_dependency.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Code Dependency of an Object — get_code_dependency","text":"Given character vector code, function extract part code responsible creating variables specified names. includes final call creates variable(s) question well parent calls, .e. calls create variables used final call parents, etc. Also included calls create side-effects like establishing connections. assumed object dependency established using three assignment operators: <-, =, -> . assignment methods (assign, <<-) non-standard-evaluation methods supported. Side-effects detected automatically must marked code. Add # @linksto object end line side-effect occurs specify line required reproduce variable called object.","code":""},{"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":"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":[]},{"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 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/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/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":"https://insightsengineering.github.io/teal.data/main/reference/show-teal_data-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Show teal_data object — show,teal_data-method","title":"Show teal_data object — show,teal_data-method","text":"Prints teal_data object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/show-teal_data-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show teal_data object — show,teal_data-method","text":"","code":"# S4 method for teal_data show(object)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/show-teal_data-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show teal_data object — show,teal_data-method","text":"object (teal_data)","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/show-teal_data-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show teal_data object — show,teal_data-method","text":"Input teal_data object.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/show-teal_data-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show teal_data object — show,teal_data-method","text":"","code":"teal_data() #> ✅︎ verified teal_data object #> [L] #> Parent: teal_data(x = iris, code = \"x = iris\") #> ✖ unverified teal_data object #> [L] #> Parent: #> Bindings: #> • x: [L] verify(teal_data(x = iris, code = \"x = iris\")) #> ✅︎ verified teal_data object #> [L] #> Parent: #> Bindings: #> • x: [L]"},{"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) vector representing code necessary reproduce contents @env. Access get_code(). setter provided. Evaluate code append code slot. id (integer) random identifier assigned element @code. Used internally. warnings (character) vector warnings raised evaluating code. Access get_warnings(). messages (character) vector 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(). verified (logical(1)) flag signifying code @code proven yield contents @env. Used internally. See verify() details.","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) #> ✖ unverified teal_data object #> [L] #> Parent: #> Bindings: #> • x1: [L] #> • x2: [L]"},{"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_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/verify.html","id":null,"dir":"Reference","previous_headings":"","what":"Verify Code Reproducibility — verify","title":"Verify Code Reproducibility — verify","text":"Checks whether code teal_data reproduces stored objects.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/verify.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Verify Code Reproducibility — verify","text":"","code":"verify(x)"},{"path":"https://insightsengineering.github.io/teal.data/main/reference/verify.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Verify Code Reproducibility — verify","text":"x teal_data object","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/verify.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Verify Code Reproducibility — verify","text":"Input teal_data object error.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/verify.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Verify Code Reproducibility — verify","text":"objects created code @code slot x all_equal contents @env slot, function updates @verified slot TRUE returned teal_data object. verified, slot always set TRUE. @code fails recreate objects teal_data@env, error raised.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/reference/verify.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Verify Code Reproducibility — verify","text":"","code":"tdata1 <- teal_data() tdata1 <- within(tdata1, { a <- 1 b <- a^5 c <- list(x = 2) }) verify(tdata1) #> ✅︎ verified teal_data object #> [L] #> Parent: #> Bindings: #> • a: [L] #> • b: [L] #> • c: [L] tdata2 <- teal_data(x1 = iris, code = \"x1 <- iris\") verify(tdata2) #> ✅︎ verified teal_data object #> [L] #> Parent: #> Bindings: #> • x1: [L] verify(tdata2)@verified #> [1] TRUE tdata2@verified #> [1] FALSE if (FALSE) { tdata3 <- teal_data() tdata3 <- within(tdata3, { stop(\"error\") }) verify(tdata3) a <- 1 b <- a + 2 c <- list(x = 2) d <- 5 tdata4 <- teal_data( a = a, b = b, c = c, d = d, code = \" a <- 1 b <- a c <- list(x = 2) e <- 1 \" ) tdata4 verify(tdata4) }"},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"enhancements-0-3-0-9026","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.data 0.3.0.9026","text":"Simplified join_key better support primary keys. JoinKey R6 object removed favor list-like object class name join_keys. Subset operators assignments supported ([, [[, [<- [[<-) join_keys function works constructor, getter setter.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"breaking-changes-0-3-0-9026","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.data 0.3.0.9026","text":"teal_data() cdisc_data() return now teal_data class object replaces TealData class object. teal_data becomes standard input entire teal framework. TealDataset, TealDatasetConnector TealDataConnector classes removed. Delayed-data-loading longer supported teal.data. called connectors now supported teal package (see ?teal::teal_data_module). join_keys() join_key() return now join_keys object replace JoinKeys class.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"miscellaneous-0-3-0-9026","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.3.0.9026","text":"Specified minimal version package dependencies. Upgraded teal.code dependency Imports Depends. Deprecated get_labels function removed supporting function data_labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"enhancements-0-3-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.data 0.3.0","text":"Removed scda package dependency examples. 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. Replaced argument name archive_name comply latest version synthetic_cdisc_dataset function.","code":""},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"bug-fixes-0-1-2","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"teal.data 0.1.2","text":"Fixed get_raw_data examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.data/main/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.data 0.1.1","text":"Added template pkgdown site. Removed usage .Globalenv Python code execution. Updated package authors. 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":""}]