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Package bio

Convenience functions to facilitate installation and management of required resources for course unit Biostatistics (BS).


This package is intended to be used with RStudio 2026.08 or newer
and R 4.6.1 or newer.
 Functions may not work correctly with the previous versions of RStudio and R.


Bug reports and your feedback are welcome at https://github.com/mokymai/bio/issues. In the report, indicate what operating system you are using.

Install

To install this package from CRAN-like repository, use code (recommended):

repos <- c("https://mokymai.github.io/download/", getOption("repos"))
install.packages("bio", repos = repos)
Install from GitHub

To install this package from GitHub:

if (!require(remotes)) install.packages("remotes")
remotes::install_github("mokymai/bio", dependencies = TRUE)

Note: installation from GitHub may require Rtools on Windows.

Examples

Check information about OS and user

Check information about the operating system (OS) and R-related user information.

bio::check_user_info()
## # A tibble: 9 × 2
##   Setting          Value
##   <chr>            <fs::path>
## 1 Operating system Windows 10 x64 (build 19045)
## 2 Platform         x86_64-w64-mingw32/x64
## 3 LOGNAME
## 4 USERNAME         user
## 5 USERPROFILE      C:/Users/user
## 6 HOME             C:/Users/user
## 7 R_USER           C:/Users/user
## 8 R_HOME           C:/PROGRA~1/R/R-4.6.1
## 9 R_LIBS_USER      C:/Users/user/AppData/Local/R/win-library/4.6

Check information about programs

Check the versions and availability of installed R-related and other programs. Options:

  • "main" (default) – checks for “R”, “RStudio”, “Quarto”, and “Rtools” (“Windows” only) or “R Build Tools” (non-“Windows” only).
  • "all" – additionally checks for presence of “XQuartz” (“Mac” only), “Git” (all systems), and (sometimes) “Meld”.

Installation and release information is maintained by the R Project, RStudio IDE, and Quarto projects. Windows users who build packages from source should also consult the Rtools documentation.

bio::check_installed_programs()
## ✔ Program R (4.6.1) is installed (4.6.1 is available online).
## ✔ Program RStudio (2026.8.1.195) is installed (2026.8.1.195 is available online).
## ✔ Tool Quarto (1.10.18) is installed (1.10.18 is available online).
bio::check_installed_programs("all")
## ✔ Program R (4.6.1) is installed (4.6.1 is available online).
## ✔ Program RStudio (2026.8.1.195) is installed (2026.8.1.195 is available online).
## ✔ Tool Quarto (1.10.18) is installed (1.10.18 is available online).
## ✔ Tool Rtools is installed.
## ✔ Program Git is installed.
## ✔ Program Meld is installed.

RStudio settings and user preferences

Make sure that you understand what you are doing when using functions that reset RStudio key bindings (shortcut keys), settings, or snippets. You may lose all your previous settings.

Dictionaries

This function downloads or updates hunspell spelling-checking dictionaries (including Lithuanian) that can be used by RStudio or by tools from the wellspell.addin package. See Posit’s guide to spelling dictionaries.

Shortcut keys

This function changes shortcut keys in RStudio.

Run the function without arguments to see the available options.

bio::rstudio_reset_keybindings()
## Error: The value of argument 'to' is missing.
## Possible options: 'bio-default', 'rstudio-default'.

Options:

  • "bio-default" – shortcut keys recommended for BS course.
  • "rstudio-default" – RStudio defaults.
bio::rstudio_reset_keybindings(to = "bio-default")
## ✔ Back up copy of shortcut keys was saved as  'C:/Users/User/.R/_backup/keybindings/addins__backup_260824_212734.json'
## ✔ Shortcut keys were reset to bio-default.

Table 1. Some examples of shortcut keys set with the "bio-default" option.

Shortcut Action
Shift+Alt+S Insert inline LaTeX equation (Quarto).
Shift+Alt+A Use “Tidyverse” style on selected lines of R code. Package styler must be installed (R code).
Ctrl+Shift+Alt+S Check spelling in selected text. Package wellspell.addin must be installed.
Ctrl+Shift+Alt+P Align parts of selected lines at a custom pattern.
Ctrl+Shift+] Change heading one level down (Quarto) [!].
Ctrl+Shift+[ Change heading one level up or remove heading (Quarto) [!].
Ctrl+Shift+; Insert lower opening quotes „.
Ctrl+Shift+’ Insert upper closing quotes “.
Ctrl+R Insert/Enclose with R code block (Quarto) [!] .
Ctrl+Alt+T Insert inline code highlighted as R code (Quarto).
Ctrl+Alt+NumPad8 Insert operator %*% (R code).
Ctrl+Alt+NumPad7 Insert operator %in% (R code).
Alt+Shift+D Document R package (that you are building).

For more information, see Customizing Keyboard Shortcuts in RStudio.

RStudio settings

This function resets RStudio user preferences and settings.

RStudio documents the corresponding point-and-click options in its Custom Settings guide and explains editor themes in the Themes guide.

Run the function without arguments to see the available options.

bio::rstudio_reset_user_settings()
#> Error: The value of argument 'to' is missing.
#> Possible choices: 'bio-default', 'bio-dark-blue', 'bio-black', 'rstudio-default'.

The options:

  • "bio-default" – recommended bio settings (and light theme “Textmate (default)”);
  • "bio-dark-blue" – recommended bio settings (and dark blue theme “Cobalt”);
  • "bio-black" – recommended bio settings (and black theme “Chaos”);
  • "rstudio-default" – default RStudio settings.
bio::rstudio_reset_user_settings(to = "bio-default")

To check how your settings differ from the defaults in a particular list, use:

bio::rstudio_compare_user_settings(to = "bio-default")
## ℹ Show differences between current and bio-default setting lists.
## ✔ No differences

Settings that are not in the list will not be displayed. The available options for to are “bio-default” and “rstudio-default”. The default source = "auto" reads settings from a running RStudio session when available, otherwise it compares the saved rstudio-prefs.json file. Use source = "file" to always inspect saved preferences, or source = "live" to require a running RStudio session. The default concise output summarizes differences; use output = "minimal" for counts only or output = "verbose" for the complete technical comparison.

RStudio installation scope

Use get_rstudio_install_scope() to determine whether the installed RStudio Desktop application is a per-user or system-wide installation. This affects the location of RStudio application files only; personal settings and keybindings remain per-user in either case.

bio::get_rstudio_install_scope()
## [1] "user"

Snippets

The function replaces the current R and Quarto snippets with those from the “snippets” package.

snippets::install_snippets_from_package("snippets", backup = TRUE)
## ✔ File with markdown snippets was updated:
##   'C:/Users/User/AppData/Roaming/RStudio/snippets/markdown.snippets'
## ✔ File with r snippets was updated:
##   'C:/Users/User/AppData/Roaming/RStudio/snippets/r.snippets'
##
## ℹ You will be able to use the snippets after RStudio is closed and reopened.

For more information, see RStudio’s Code Snippets guide and the snippets package website.

Restart R and RStudio

If you want to see the effect of the changed settings, reload RStudio. You can use this function to reload RStudio without closing it:

However, in some cases, it is recommended that you close and reopen RStudio.

To restart the R session without closing RStudio, use:

bio::restart_r()

Useful to apply before trying to install R packages.

The following projects overlap with or complement parts of bio. They are listed to help users choose a narrower or more general tool when appropriate:

  • rstudio.prefs, by S.A. van der Wulp and Daniel D. Sjoberg, is the closest CRAN alternative for managing RStudio preferences and addin shortcuts across devices.
  • rstudioapi, by Kevin Ushey, JJ Allaire, Hadley Wickham, and Gary Ritchie, exposes the supported API for interacting with a running RStudio session. bio uses it for live IDE operations.
  • renv, by Kevin Ushey and Hadley Wickham, manages reproducible project-local package libraries and lockfiles. This complements bio’s package discovery helpers.
  • styler, by Kirill Müller, Lorenz Walthert, and Indrajeet Patil, formats R code and powers one of the optional course shortcuts.
  • drat, by Dirk Eddelbuettel and Carl Boettiger, creates and manages CRAN-like repositories; the mokymai repository used to distribute bio is built with this approach.

The GitHub-only wellspell.addin provides interactive spellchecking in RStudio. It is useful alongside the dictionaries installed by bio, but is not currently a CRAN package.