doc: init R

.gitignore

@@ -42,4 +42,4 @@ testem.log
 Thumbs.db
 
 TextTestExe/
-data/
+data/

doc/.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

doc/.gitignore

@@ -0,0 +1,65 @@
+# Created by https://www.toptal.com/developers/gitignore/api/R
+# Edit at https://www.toptal.com/developers/gitignore?templates=R
+
+### R ###
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+### R.Bookdown Stack ###
+# R package: bookdown caching files
+/*_files/
+
+# End of https://www.toptal.com/developers/gitignore/api/R
+
+*.pdf
+*.html
+bib
+
+.env

doc/hci-doc.Rproj

@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

doc/renv.lock

@@ -0,0 +1,68 @@
+{
+  "R": {
+    "Version": "4.5.2",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://packagemanager.posit.co/cran/latest"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "1.1.6",
+      "Source": "Repository",
+      "Type": "Package",
+      "Title": "Project Environments",
+      "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.",
+      "License": "MIT + file LICENSE",
+      "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv",
+      "BugReports": "https://github.com/rstudio/renv/issues",
+      "Imports": [
+        "utils"
+      ],
+      "Suggests": [
+        "BiocManager",
+        "cli",
+        "compiler",
+        "covr",
+        "cpp11",
+        "curl",
+        "devtools",
+        "generics",
+        "gitcreds",
+        "jsonlite",
+        "jsonvalidate",
+        "knitr",
+        "miniUI",
+        "modules",
+        "packrat",
+        "pak",
+        "R6",
+        "remotes",
+        "reticulate",
+        "rmarkdown",
+        "rstudioapi",
+        "shiny",
+        "testthat",
+        "uuid",
+        "waldo",
+        "yaml",
+        "webfakes"
+      ],
+      "Encoding": "UTF-8",
+      "RoxygenNote": "7.3.3",
+      "VignetteBuilder": "knitr",
+      "Config/Needs/website": "tidyverse/tidytemplate",
+      "Config/testthat/edition": "3",
+      "Config/testthat/parallel": "true",
+      "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes",
+      "NeedsCompilation": "no",
+      "Author": "Kevin Ushey [aut, cre] (ORCID: <https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (ORCID: <https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
+      "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
+      "Repository": "CRAN"
+    }
+  }
+}

doc/renv/.gitignore

@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

doc/renv/settings.json

@@ -0,0 +1,20 @@
+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.dev": false,
+  "snapshot.type": "implicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}