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”.

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.

bio::rstudio_install_spellcheck_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.

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”.

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 about Code Snippets in RStudio and on package snippets.

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:

bio::restart_rstudio()

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.

Package bio