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-[{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"First , thank taking time contribute! ✌️ 🎉 love input regardless size, content scope - whether issue, feature request, bug-fix documentation enhancement. Thanks 🙏 rock 🤘","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 🐛 report bug? 💡 request change? 🚩 submit change? 👗 Style guide 🧐 Recognition model ❓ questions","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"introduction, please read README file. can also find vignettes . Usually find “Getting started” article. Please also see package manual form pkgdown website.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"project governed Code Conduct. participating, expected follow rules outlined .","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"code changes license covers project.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"how-to-report-a-bug","dir":"","previous_headings":"","what":"How to report a bug?","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests well bugs. opening new issue please double-check ’s already reported (don’t worry duplicate - manage). already - -vote ⬆️. look faster! kindly ask write good issue minimal reproducible example demonstrates problem. also great know local environment (R session info) well. find template issues opening bug ticket. speed fixing process lot! 📈.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"how-to-request-the-change","dir":"","previous_headings":"","what":"How to request the change?","title":"Contribution Guidelines","text":"notice missing feature idea enhance existing functionalities - please let us know creating new issue. opening new issue please double-check ’s already reported (don’t worry occurs duplicate - manage). already - -vote ⬆️. look faster! Please elaborate “?” - ’s context, ’s benefit . find template opening feature request ticket. help us prioritize submit meaningful changes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"How to submit a change?","what":"GitHub Flow","title":"Contribution Guidelines","text":"following GitHub Flow collaborate repository. order submit changes please following: Open branch Please see branch naming convention . don’t write access please fork first. Make changes. Make sure code passes checks well documented tested decrease existing test coverage 💪. Create PR(s) Please link issue make good change description. Include development assumptions necessary. Give details reviewer efficiently check changes. Address review comments Please apply changes necessary. disagree reviewer - please explain . approved - merge PR(s) delete branch","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"branching-convention","dir":"","previous_headings":"How to submit a change?","what":"Branching convention","title":"Contribution Guidelines","text":"case working task inside one specific repository, please name branch _ lowercase. Multiple words description divided underscore (_). E.g. 15_fix_spelling_error case try solve spelling mistake mentioned issue number 15. case working task one repository affects multiple repositories, please always name branches: __ lowercase. Multiple words description divided underscore (_). E.g. 15_abc_fix_spelling_error case try solve spelling mistake inside xyz closes issue 15 inside abc.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"How to submit a change?","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. configuration already staged_dependencies.yaml file. just need name feature branches identically. exception branch naming convention described . Please read package manual details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"How to submit a change? > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version well given package dependencies. recommend set-working environment way. can find details given GitHub Action execution log - step prints session info. find bugs older version dependencies - please create appropriate bug ticket.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"How to submit a change? > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend pre-commit tool combined R hooks pre-commit execute checks prior committing pushing. configuration already repository (). Please, follow installation guide official pre-commit page GitHub readme page R hooks.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide ’s checked lintr. slight modifications default settings available .lintr file. Although allows flexibility - recommend sticking style existing code. Please note style also lintr check place validate code.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"contribution highly welcomed appreciated. contribution data already GitHub repository insights feature, introduced objective rules recognize significant contribution became package author: Minimum 5% lines code authored (determined git blame query) top 5 contributors terms number commits lines added lines removed. package maintainer also reserves rights manually adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/CONTRIBUTING.html","id":"any-questions","dir":"","previous_headings":"","what":"Any questions","title":"Contribution Guidelines","text":"questions regarding contribution - please reach repository maintainer(s)!","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Sabanés Bové. Author, maintainer. Samer Mouksassi. Author. wrote original Kaplan-Meier code Michael Sachs. Author. wrote original Kaplan-Meier code F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Mouksassi S, Sachs M (2024). ggplot2.utils: Selected Utilities Extending 'ggplot2'. R package version 0.3.2.9001, https://insightsengineering.github.io/ggplot2.utils/.","code":"@Manual{, title = {ggplot2.utils: Selected Utilities Extending 'ggplot2'}, author = {Daniel {Sabanés Bové} and Samer Mouksassi and Michael Sachs}, year = {2024}, note = {R package version 0.3.2.9001}, url = {https://insightsengineering.github.io/ggplot2.utils/}, }"},{"path":"https://insightsengineering.github.io/ggplot2.utils/index.html","id":"ggplot2utils-","dir":"","previous_headings":"","what":"Selected Utilities Extending ggplot2","title":"Selected Utilities Extending ggplot2","text":"ggplot2.utils package simplifies access utility functions adding functionality ggplot2. package imports functions across multiple extensions packages exports , user needs load package instead multiple others. addition, package provides layers Kaplan-Meier lines ticks additions plots. functions tested make sure work reliably.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Selected Utilities Extending ggplot2","text":"Typically want install release version. Developers beta-testers might want install development version.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/index.html","id":"release","dir":"","previous_headings":"Installation","what":"Release","title":"Selected Utilities Extending ggplot2","text":"can install current release version CRAN :","code":"install.packages(\"ggplot2.utils\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/index.html","id":"development","dir":"","previous_headings":"Installation","what":"Development","title":"Selected Utilities Extending ggplot2","text":"can install current development version R-Universe : Alternatively, can install current development version GitHub :","code":"install.packages( \"ggplot2.utils\", repos = c(\"https://insightsengineering.r-universe.dev\", \"https://cloud.r-project.org\") ) if (!require(\"remotes\")) { install.packages(\"remotes\") } remotes::install_github(\"insightsengineering/ggplot2.utils\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting Started","title":"Selected Utilities Extending ggplot2","text":"look package index explore available functionality:","code":"help(package = \"ggplot2.utils\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/index.html","id":"citing-ggplot2utils","dir":"","previous_headings":"","what":"Citing ggplot2.utils","title":"Selected Utilities Extending ggplot2","text":"cite ggplot2.utils please see .","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Kaplan-Meier Survival Curve — geom_km","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"Adds Kaplan-Meier survival curve.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"","code":"geom_km( mapping = NULL, data = NULL, stat = \"km\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, na.rm = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"geom_km() understands following aesthetics (required aesthetics bold): x: survival/censoring times, automatically mapped stat_km(). y: survival probability estimates, automatically mapped stat_km(). alpha color linetype linewidth","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"Inspired geom_km written Michael Sachs (ggkm) Samer Mouksassi (ggquickeda). directly use ggplot2::geom_step() instead general ggplot2::geom_path().","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex))) + geom_km()"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km_ticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"Adds tickmarks times censored observations events.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km_ticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"","code":"geom_km_ticks( mapping = NULL, data = NULL, stat = \"km_ticks\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, na.rm = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km_ticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km_ticks.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"geom_km_ticks() understands following aesthetics (required aesthetics bold): x: survival/censoring times, automatically mapped stat_km_ticks(). y: survival probability estimates, automatically mapped stat_km_ticks(). alpha color shape size stroke fill","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km_ticks.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"Michael Sachs (ggkm), Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_km_ticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex), group = factor(sex))) + geom_km() + geom_km_ticks(col = \"black\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Inset tables — geom_table","title":"Inset tables — geom_table","text":"See ggpp::geom_table() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/geom_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Inset tables — geom_table","text":"plot layer instance.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ggplot2.utils-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot2.utils Package — ggplot2.utils-package","title":"ggplot2.utils Package — ggplot2.utils-package","text":"ggplot2.utils provides simple access utility functions extending ggplot2.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ggplot2.utils-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"ggplot2.utils Package — ggplot2.utils-package","text":"Currently functions imported extension packages: ggpp: geom_table() associated functions. EnvStats: stat_n_text() associated functions. ggstats: stat_prop() associated functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ggplot2.utils-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ggplot2.utils Package — ggplot2.utils-package","text":"Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@rconis.com Authors: Samer Mouksassi (wrote original Kaplan-Meier code) Michael Sachs (wrote original Kaplan-Meier code) contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ggproto.html","id":null,"dir":"Reference","previous_headings":"","what":"New ggproto Objects — GeomKm","title":"New ggproto Objects — GeomKm","text":"Additional ggplot2::ggproto objects used custom geom stat functions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ggproto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"New ggproto Objects — GeomKm","text":"","code":"GeomKm GeomKmTicks StatKm StatKmTicks"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ggproto.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"New ggproto Objects — GeomKm","text":"object class GeomKm (inherits GeomStep, GeomPath, Geom, ggproto, gg) length 4. object class GeomKmTicks (inherits Geom, ggproto, gg) length 6. object class StatKm (inherits Stat, ggproto, gg) length 5. object class StatKmTicks (inherits Stat, ggproto, gg) length 5.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ggproto.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"New ggproto Objects — GeomKm","text":"GeomKm, StatKm, GeomKmTicks StatKmTicks modified (particular certain functionality removed) code originally written Michael Sachs (ggkm) Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/h_surv_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for Common Kaplan-Meier Computations — h_surv_fit","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"Helper Common Kaplan-Meier Computations","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/h_surv_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"","code":"h_surv_fit(data)"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/h_surv_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"data (data.frame) time status numeric columns.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/h_surv_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"survival::survfit() result basis Kaplan-Meier estimate.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"stat computing Kaplan-Meier survival estimate right-censored data. requires aesthetic mapping time observation times status indicates event status, either 0 alive 1 dead, 1 alive 2 dead.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"","code":"stat_km( mapping = NULL, data = NULL, geom = \"km\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). geom geometric object use display data layer. using stat_*() function construct layer, geom argument can used override default coupling stats geoms. geom argument accepts following: Geom ggproto subclass, example GeomPoint. string naming geom. give geom string, strip function name geom_ prefix. example, use geom_point(), give geom \"point\". information ways specify geom, see layer geom documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"data.frame columns: time: time data. survival: survival estimate time.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"Logical status supported.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"Michael Sachs (ggkm), Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex))) + stat_km()"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_compute.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for stat_km — stat_km_compute","title":"Helper for stat_km — stat_km_compute","text":"Helper stat_km","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_compute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for stat_km — stat_km_compute","text":"","code":"stat_km_compute(data, scales)"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_compute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for stat_km — stat_km_compute","text":"data (data.frame) time status numeric columns. scales used.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_compute.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for stat_km — stat_km_compute","text":"data.frame time survival columns.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"stat computing location tick marks Kaplan-Meier survival estimate right-censored data. requires aesthetic mapping time observation times status indicates event status, either 0 alive 1 dead, 1 alive 2 dead.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"","code":"stat_km_ticks( mapping = NULL, data = NULL, geom = \"km_ticks\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). geom geometric object use display data layer. using stat_*() function construct layer, geom argument can used override default coupling stats geoms. geom argument accepts following: Geom ggproto subclass, example GeomPoint. string naming geom. give geom string, strip function name geom_ prefix. example, use geom_point(), give geom \"point\". information ways specify geom, see layer geom documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"data.frame columns: time: time data. survival: survival estimate time. n.risk: number patients risk. n.censor: number patients censored. n.event: number patients event.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"Logical status supported.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"Michael Sachs (ggkm), Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex))) + stat_km() + stat_km_ticks()"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks_compute.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for stat_km_ticks — stat_km_ticks_compute","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"Helper stat_km_ticks","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks_compute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"","code":"stat_km_ticks_compute(data, scales)"},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks_compute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"data (data.frame) time status numeric columns. scales used.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_km_ticks_compute.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"data.frame time, survival, n.risk, n.censor n.event columns.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_n_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Text Indicating the Sample Size to a ggplot2 Plot — stat_n_text","title":"Add Text Indicating the Sample Size to a ggplot2 Plot — stat_n_text","text":"See EnvStats::stat_n_text() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_n_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Text Indicating the Sample Size to a ggplot2 Plot — stat_n_text","text":"plot layer including sample size text.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_prop.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute Proportions According to Custom Denominator — stat_prop","title":"Compute Proportions According to Custom Denominator — stat_prop","text":"See ggstats::stat_prop() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/stat_prop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute Proportions According to Custom Denominator — stat_prop","text":"plot layer containing custom proportions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ttheme_gtdefault.html","id":null,"dir":"Reference","previous_headings":"","what":"Table themes — ttheme_gtdefault","title":"Table themes — ttheme_gtdefault","text":"See ggpp::ttheme_gtdefault() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ttheme_gtdefault.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Table themes — ttheme_gtdefault","text":"list object can used ttheme construction tables functions package 'gridExtra'.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ttheme_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Set default table theme — ttheme_set","title":"Set default table theme — ttheme_set","text":"See ggpp::ttheme_set() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ttheme_set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set default table theme — ttheme_set","text":"named list previous value option.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/reference/ttheme_set.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Set default table theme — ttheme_set","text":"testing function, found contrast original documentation, theme fixed plot object constructed. Instead, option setting affects rendering ready built plot objects.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-0329001","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.3.2.9001","title":"ggplot2.utils 0.3.2.9001","text":"Replaced dependency GGally ggstats original functions actually . also avoids corresponding overwrite messages coming GGally loading package.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-030","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.3.0","title":"ggplot2.utils 0.3.0","text":"CRAN release: 2023-06-24 Added geom_km geom_km_ticks (corresponding ggproto statistics layer functions) Kaplan-Meier lines ticks additions plots, respectively.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-021","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.2.1","title":"ggplot2.utils 0.2.1","text":"CRAN release: 2023-05-09 First publication CRAN release.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-015","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.5","title":"ggplot2.utils 0.1.5","text":"Removed dependency deprecated package test.nest.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-013","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.3","title":"ggplot2.utils 0.1.3","text":"Updated LICENCE README new package references. Remove cherry-picked code instead just import export relevant functions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-012","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.2","title":"ggplot2.utils 0.1.2","text":"Improved internal code style removed unnecessary functions imports.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-011","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.1","title":"ggplot2.utils 0.1.1","text":"Added stat_prop() variation stat_count allowing compute custom proportions according aesthetic defining denominator. Added stat_n_text() adds text indicating number y-values particular x-value. Added geom_table(), geom_table_npc() add textual table directly ggplot.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/news/index.html","id":"ggplot2utils-010","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.0","title":"ggplot2.utils 0.1.0","text":"Started package.","code":""}]
+[{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"First , thank taking time contribute! ✌️ 🎉 love input regardless size, content scope - whether issue, feature request, bug-fix documentation enhancement. Thanks 🙏 rock 🤘","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 🐛 report bug? 💡 request change? 🚩 submit change? 👗 Style guide 🧐 Recognition model ❓ questions","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"introduction, please read README file. can also find vignettes . Usually find “Getting started” article. Please also see package manual form pkgdown website.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"project governed Code Conduct. participating, expected follow rules outlined .","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"code changes license covers project.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"how-to-report-a-bug","dir":"","previous_headings":"","what":"How to report a bug?","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests well bugs. opening new issue please double-check ’s already reported (don’t worry duplicate - manage). already - -vote ⬆️. look faster! kindly ask write good issue minimal reproducible example demonstrates problem. also great know local environment (R session info) well. find template issues opening bug ticket. speed fixing process lot! 📈.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"how-to-request-the-change","dir":"","previous_headings":"","what":"How to request the change?","title":"Contribution Guidelines","text":"notice missing feature idea enhance existing functionalities - please let us know creating new issue. opening new issue please double-check ’s already reported (don’t worry occurs duplicate - manage). already - -vote ⬆️. look faster! Please elaborate “?” - ’s context, ’s benefit . find template opening feature request ticket. help us prioritize submit meaningful changes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"How to submit a change?","what":"GitHub Flow","title":"Contribution Guidelines","text":"following GitHub Flow collaborate repository. order submit changes please following: Open branch Please see branch naming convention . don’t write access please fork first. Make changes. Make sure code passes checks well documented tested decrease existing test coverage 💪. Create PR(s) Please link issue make good change description. Include development assumptions necessary. Give details reviewer efficiently check changes. Address review comments Please apply changes necessary. disagree reviewer - please explain . approved - merge PR(s) delete branch","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"branching-convention","dir":"","previous_headings":"How to submit a change?","what":"Branching convention","title":"Contribution Guidelines","text":"case working task inside one specific repository, please name branch _ lowercase. Multiple words description divided underscore (_). E.g. 15_fix_spelling_error case try solve spelling mistake mentioned issue number 15. case working task one repository affects multiple repositories, please always name branches: __ lowercase. Multiple words description divided underscore (_). E.g. 15_abc_fix_spelling_error case try solve spelling mistake inside xyz closes issue 15 inside abc.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"How to submit a change?","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. configuration already staged_dependencies.yaml file. just need name feature branches identically. exception branch naming convention described . Please read package manual details.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"How to submit a change? > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version well given package dependencies. recommend set-working environment way. can find details given GitHub Action execution log - step prints session info. find bugs older version dependencies - please create appropriate bug ticket.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"How to submit a change? > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend pre-commit tool combined R hooks pre-commit execute checks prior committing pushing. configuration already repository (). Please, follow installation guide official pre-commit page GitHub readme page R hooks.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide ’s checked lintr. slight modifications default settings available .lintr file. Although allows flexibility - recommend sticking style existing code. Please note style also lintr check place validate code.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"contribution highly welcomed appreciated. contribution data already GitHub repository insights feature, introduced objective rules recognize significant contribution became package author: Minimum 5% lines code authored (determined git blame query) top 5 contributors terms number commits lines added lines removed. package maintainer also reserves rights manually adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/CONTRIBUTING.html","id":"any-questions","dir":"","previous_headings":"","what":"Any questions","title":"Contribution Guidelines","text":"questions regarding contribution - please reach repository maintainer(s)!","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/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/ggplot2.utils/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/ggplot2.utils/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Sabanés Bové. Author, maintainer. Samer Mouksassi. Author. wrote original Kaplan-Meier code Michael Sachs. Author. wrote original Kaplan-Meier code F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Mouksassi S, Sachs M (2024). ggplot2.utils: Selected Utilities Extending 'ggplot2'. R package version 0.3.2.9001, https://insightsengineering.github.io/ggplot2.utils/main/.","code":"@Manual{, title = {ggplot2.utils: Selected Utilities Extending 'ggplot2'}, author = {Daniel {Sabanés Bové} and Samer Mouksassi and Michael Sachs}, year = {2024}, note = {R package version 0.3.2.9001}, url = {https://insightsengineering.github.io/ggplot2.utils/main/}, }"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/index.html","id":"ggplot2utils-","dir":"","previous_headings":"","what":"Selected Utilities Extending ggplot2","title":"Selected Utilities Extending ggplot2","text":"ggplot2.utils package simplifies access utility functions adding functionality ggplot2. package imports functions across multiple extensions packages exports , user needs load package instead multiple others. addition, package provides layers Kaplan-Meier lines ticks additions plots. functions tested make sure work reliably.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Selected Utilities Extending ggplot2","text":"Typically want install release version. Developers beta-testers might want install development version.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/index.html","id":"release","dir":"","previous_headings":"Installation","what":"Release","title":"Selected Utilities Extending ggplot2","text":"can install current release version CRAN :","code":"install.packages(\"ggplot2.utils\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/index.html","id":"development","dir":"","previous_headings":"Installation","what":"Development","title":"Selected Utilities Extending ggplot2","text":"can install current development version R-Universe : Alternatively, can install current development version GitHub :","code":"install.packages( \"ggplot2.utils\", repos = c(\"https://insightsengineering.r-universe.dev\", \"https://cloud.r-project.org\") ) if (!require(\"remotes\")) { install.packages(\"remotes\") } remotes::install_github(\"insightsengineering/ggplot2.utils\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting Started","title":"Selected Utilities Extending ggplot2","text":"look package index explore available functionality:","code":"help(package = \"ggplot2.utils\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/index.html","id":"citing-ggplot2utils","dir":"","previous_headings":"","what":"Citing ggplot2.utils","title":"Selected Utilities Extending ggplot2","text":"cite ggplot2.utils please see .","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Kaplan-Meier Survival Curve — geom_km","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"Adds Kaplan-Meier survival curve.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"","code":"geom_km( mapping = NULL, data = NULL, stat = \"km\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, na.rm = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"geom_km() understands following aesthetics (required aesthetics bold): x: survival/censoring times, automatically mapped stat_km(). y: survival probability estimates, automatically mapped stat_km(). alpha color linetype linewidth","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"Inspired geom_km written Michael Sachs (ggkm) Samer Mouksassi (ggquickeda). directly use ggplot2::geom_step() instead general ggplot2::geom_path().","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Kaplan-Meier Survival Curve — geom_km","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex))) + geom_km()"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km_ticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"Adds tickmarks times censored observations events.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km_ticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"","code":"geom_km_ticks( mapping = NULL, data = NULL, stat = \"km_ticks\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, na.rm = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km_ticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). stat statistical transformation use data layer. using geom_*() function construct layer, stat argument can used override default coupling geoms stats. stat argument accepts following: Stat ggproto subclass, example StatCount. string naming stat. give stat string, strip function name stat_ prefix. example, use stat_count(), give stat \"count\". information ways specify stat, see layer stat documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). na.rm FALSE, default, missing values removed warning. TRUE, missing values silently removed. ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km_ticks.html","id":"aesthetics","dir":"Reference","previous_headings":"","what":"Aesthetics","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"geom_km_ticks() understands following aesthetics (required aesthetics bold): x: survival/censoring times, automatically mapped stat_km_ticks(). y: survival probability estimates, automatically mapped stat_km_ticks(). alpha color shape size stroke fill","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km_ticks.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"Michael Sachs (ggkm), Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_km_ticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Tick Marks to a Kaplan-Meier Survival Curve — geom_km_ticks","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex), group = factor(sex))) + geom_km() + geom_km_ticks(col = \"black\")"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Inset tables — geom_table","title":"Inset tables — geom_table","text":"See ggpp::geom_table() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/geom_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Inset tables — geom_table","text":"plot layer instance.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ggplot2.utils-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot2.utils Package — ggplot2.utils-package","title":"ggplot2.utils Package — ggplot2.utils-package","text":"ggplot2.utils provides simple access utility functions extending ggplot2.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ggplot2.utils-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"ggplot2.utils Package — ggplot2.utils-package","text":"Currently functions imported extension packages: ggpp: geom_table() associated functions. EnvStats: stat_n_text() associated functions. ggstats: stat_prop() associated functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ggplot2.utils-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ggplot2.utils Package — ggplot2.utils-package","text":"Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@rconis.com Authors: Samer Mouksassi (wrote original Kaplan-Meier code) Michael Sachs (wrote original Kaplan-Meier code) contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ggproto.html","id":null,"dir":"Reference","previous_headings":"","what":"New ggproto Objects — GeomKm","title":"New ggproto Objects — GeomKm","text":"Additional ggplot2::ggproto objects used custom geom stat functions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ggproto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"New ggproto Objects — GeomKm","text":"","code":"GeomKm GeomKmTicks StatKm StatKmTicks"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ggproto.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"New ggproto Objects — GeomKm","text":"object class GeomKm (inherits GeomStep, GeomPath, Geom, ggproto, gg) length 4. object class GeomKmTicks (inherits Geom, ggproto, gg) length 6. object class StatKm (inherits Stat, ggproto, gg) length 5. object class StatKmTicks (inherits Stat, ggproto, gg) length 5.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ggproto.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"New ggproto Objects — GeomKm","text":"GeomKm, StatKm, GeomKmTicks StatKmTicks modified (particular certain functionality removed) code originally written Michael Sachs (ggkm) Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/h_surv_fit.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for Common Kaplan-Meier Computations — h_surv_fit","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"Helper Common Kaplan-Meier Computations","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/h_surv_fit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"","code":"h_surv_fit(data)"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/h_surv_fit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"data (data.frame) time status numeric columns.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/h_surv_fit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for Common Kaplan-Meier Computations — h_surv_fit","text":"survival::survfit() result basis Kaplan-Meier estimate.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"stat computing Kaplan-Meier survival estimate right-censored data. requires aesthetic mapping time observation times status indicates event status, either 0 alive 1 dead, 1 alive 2 dead.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"","code":"stat_km( mapping = NULL, data = NULL, geom = \"km\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). geom geometric object use display data layer. using stat_*() function construct layer, geom argument can used override default coupling stats geoms. geom argument accepts following: Geom ggproto subclass, example GeomPoint. string naming geom. give geom string, strip function name geom_ prefix. example, use geom_point(), give geom \"point\". information ways specify geom, see layer geom documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"data.frame columns: time: time data. survival: survival estimate time.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"Logical status supported.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"Michael Sachs (ggkm), Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adds a Kaplan-Meier Estimate of Survival Statistic — stat_km","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex))) + stat_km()"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_compute.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for stat_km — stat_km_compute","title":"Helper for stat_km — stat_km_compute","text":"Helper stat_km","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_compute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for stat_km — stat_km_compute","text":"","code":"stat_km_compute(data, scales)"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_compute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for stat_km — stat_km_compute","text":"data (data.frame) time status numeric columns. scales used.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_compute.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for stat_km — stat_km_compute","text":"data.frame time survival columns.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"stat computing location tick marks Kaplan-Meier survival estimate right-censored data. requires aesthetic mapping time observation times status indicates event status, either 0 alive 1 dead, 1 alive 2 dead.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"","code":"stat_km_ticks( mapping = NULL, data = NULL, geom = \"km_ticks\", position = \"identity\", show.legend = NA, inherit.aes = TRUE, ... )"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"mapping Set aesthetic mappings created aes(). specified inherit.aes = TRUE (default), combined default mapping top level plot. must supply mapping plot mapping. data data displayed layer. three options: NULL, default, data inherited plot data specified call ggplot(). data.frame, object, override plot data. objects fortified produce data frame. See fortify() variables created. function called single argument, plot data. return value must data.frame, used layer data. function can created formula (e.g. ~ head(.x, 10)). geom geometric object use display data layer. using stat_*() function construct layer, geom argument can used override default coupling stats geoms. geom argument accepts following: Geom ggproto subclass, example GeomPoint. string naming geom. give geom string, strip function name geom_ prefix. example, use geom_point(), give geom \"point\". information ways specify geom, see layer geom documentation. position position adjustment use data layer. can used various ways, including prevent overplotting improving display. position argument accepts following: result calling position function, position_jitter(). method allows passing extra arguments position. string naming position adjustment. give position string, strip function name position_ prefix. example, use position_jitter(), give position \"jitter\". information ways specify position, see layer position documentation. show.legend logical. layer included legends? NA, default, includes aesthetics mapped. FALSE never includes, TRUE always includes. can also named logical vector finely select aesthetics display. inherit.aes FALSE, overrides default aesthetics, rather combining . useful helper functions define data aesthetics inherit behaviour default plot specification, e.g. borders(). ... arguments passed layer()'s params argument. arguments broadly fall one 4 categories . Notably, arguments position argument, aesthetics required can passed .... Unknown arguments part 4 categories ignored. Static aesthetics mapped scale, fixed value apply layer whole. example, colour = \"red\" linewidth = 3. geom's documentation Aesthetics section lists available options. 'required' aesthetics passed params. Please note passing unmapped aesthetics vectors technically possible, order required length guaranteed parallel input data. constructing layer using stat_*() function, ... argument can used pass parameters geom part layer. example stat_density(geom = \"area\", outline.type = \"\"). geom's documentation lists parameters can accept. Inversely, constructing layer using geom_*() function, ... argument can used pass parameters stat part layer. example geom_area(stat = \"density\", adjust = 0.5). stat's documentation lists parameters can accept. key_glyph argument layer() may also passed .... can one functions described key glyphs, change display layer legend.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"data.frame columns: time: time data. survival: survival estimate time. n.risk: number patients risk. n.censor: number patients censored. n.event: number patients event.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"Logical status supported.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"Michael Sachs (ggkm), Samer Mouksassi (ggquickeda).","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adds Tick Marks to a Kaplan-Meier Estimate of Survival Statistic — stat_km_ticks","text":"","code":"library(ggplot2) sex <- rbinom(250, 1, .5) df <- data.frame( time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex ) ggplot(df, aes(time = time, status = status, color = factor(sex))) + stat_km() + stat_km_ticks()"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks_compute.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper for stat_km_ticks — stat_km_ticks_compute","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"Helper stat_km_ticks","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks_compute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"","code":"stat_km_ticks_compute(data, scales)"},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks_compute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"data (data.frame) time status numeric columns. scales used.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_km_ticks_compute.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper for stat_km_ticks — stat_km_ticks_compute","text":"data.frame time, survival, n.risk, n.censor n.event columns.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_n_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Text Indicating the Sample Size to a ggplot2 Plot — stat_n_text","title":"Add Text Indicating the Sample Size to a ggplot2 Plot — stat_n_text","text":"See EnvStats::stat_n_text() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_n_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Text Indicating the Sample Size to a ggplot2 Plot — stat_n_text","text":"plot layer including sample size text.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_prop.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute Proportions According to Custom Denominator — stat_prop","title":"Compute Proportions According to Custom Denominator — stat_prop","text":"See ggstats::stat_prop() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/stat_prop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute Proportions According to Custom Denominator — stat_prop","text":"plot layer containing custom proportions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ttheme_gtdefault.html","id":null,"dir":"Reference","previous_headings":"","what":"Table themes — ttheme_gtdefault","title":"Table themes — ttheme_gtdefault","text":"See ggpp::ttheme_gtdefault() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ttheme_gtdefault.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Table themes — ttheme_gtdefault","text":"list object can used ttheme construction tables functions package 'gridExtra'.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ttheme_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Set default table theme — ttheme_set","title":"Set default table theme — ttheme_set","text":"See ggpp::ttheme_set() details.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ttheme_set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set default table theme — ttheme_set","text":"named list previous value option.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/reference/ttheme_set.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Set default table theme — ttheme_set","text":"testing function, found contrast original documentation, theme fixed plot object constructed. Instead, option setting affects rendering ready built plot objects.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-0329001","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.3.2.9001","title":"ggplot2.utils 0.3.2.9001","text":"Replaced dependency GGally ggstats original functions actually . also avoids corresponding overwrite messages coming GGally loading package.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-030","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.3.0","title":"ggplot2.utils 0.3.0","text":"CRAN release: 2023-06-24 Added geom_km geom_km_ticks (corresponding ggproto statistics layer functions) Kaplan-Meier lines ticks additions plots, respectively.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-021","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.2.1","title":"ggplot2.utils 0.2.1","text":"CRAN release: 2023-05-09 First publication CRAN release.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-015","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.5","title":"ggplot2.utils 0.1.5","text":"Removed dependency deprecated package test.nest.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-013","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.3","title":"ggplot2.utils 0.1.3","text":"Updated LICENCE README new package references. Remove cherry-picked code instead just import export relevant functions.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-012","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.2","title":"ggplot2.utils 0.1.2","text":"Improved internal code style removed unnecessary functions imports.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-011","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.1","title":"ggplot2.utils 0.1.1","text":"Added stat_prop() variation stat_count allowing compute custom proportions according aesthetic defining denominator. Added stat_n_text() adds text indicating number y-values particular x-value. Added geom_table(), geom_table_npc() add textual table directly ggplot.","code":""},{"path":"https://insightsengineering.github.io/ggplot2.utils/main/news/index.html","id":"ggplot2utils-010","dir":"Changelog","previous_headings":"","what":"ggplot2.utils 0.1.0","title":"ggplot2.utils 0.1.0","text":"Started package.","code":""}]