Get started with bio

Lifecycle: experimental

bio is experimental. It is developed for a specific Biostatistics course and its user interface may change without a deprecation cycle. Several functions rewrite files that RStudio owns, so read Managing RStudio settings before running them on a machine you care about.

What `bio` is for

bio prepares and inspects the R and RStudio environment used in a Biostatistics course. It groups into three areas:

Area	Typical question	Vignette
Environment checks	Is my software new enough?	Checking your setup
RStudio configuration	Can I get the classroom defaults?	Managing RStudio settings
Projects and paths	Where does RStudio keep this file?	this vignette

Nothing in bio is required to use R — it exists to make a room full of laptops behave the same way.

Installation

bio and two of its dependencies are published through a drat repository rather than CRAN. The repository itself is available at mokymai/download:

repos <- c(
  mokymai = "https://mokymai.github.io/download/",
  CRAN = "https://cran.rstudio.com"
)

install.packages("bio", repos = repos)

DESCRIPTION declares that repository in Additional_repositories, so install.packages() resolves backup.tools and snippets from it too. See the R manual for details about installing packages.

A short tour

Start by confirming that the surrounding software is present:

bio::check_installed_programs()

Then look at where RStudio keeps the files bio may rewrite:

bio::get_path_rstudio_config_dir()
bio::get_path_rstudio_config_file(which = "current")
bio::get_path_rstudio_keybindings_dir()
bio::get_path_rstudio_snippets_dir()

The open_*() counterparts open the same locations in a file manager:

bio::open_rstudio_config_dir()
bio::open_rstudio_keybindings_dir()
bio::open_backup_dir()

Projects and project lists

RStudio keeps a list of recently opened projects. bio can read it, refresh the user-editable copy, and open a project by a name pattern:

bio::get_path_recent_proj_list()
bio::get_path_user_proj_list()

bio::update_rstudio_proj_list_user()
bio::read_projects(file = bio::get_path_user_proj_list())

bio::open_project("biostat", new_session = TRUE)

open_project() matches pattern against the project names. When several projects match, it asks which one to open, so it is interactive by design.

Restarting

bio::restart_r()
bio::restart_rstudio()
bio::rstudio_reload_ui()

These require a running RStudio session; outside RStudio they report that and return without doing anything.

Where to go next

Checking your setup — installed versions, packages, and what happens when the machine is offline.
Managing RStudio settings — presets, keybindings, dictionaries, backups, and the live-session caveats.

These projects overlap with or complement narrower parts of bio:

rstudio.prefs, by S.A. van der Wulp and Daniel D. Sjoberg, is the closest CRAN alternative for RStudio preference files and addin shortcuts.
rstudioapi, by Kevin Ushey, JJ Allaire, Hadley Wickham, and Gary Ritchie, provides the supported API for live RStudio integration.
renv, by Kevin Ushey and Hadley Wickham, manages reproducible project-local libraries and lockfiles; it complements bio::list_pkgs_used_in_dir().
styler, by Kirill Müller, Lorenz Walthert, and Indrajeet Patil, formats R code.
drat, by Dirk Eddelbuettel and Carl Boettiger, manages CRAN-like package repositories.

For the underlying platforms, use the official R manuals, RStudio IDE User Guide, and Quarto guide.

What bio is for