My R & RStudio Setup | 2024

The code and the ‘why’ behind my setup, as well as some shoutouts.

1 Intro

This is a hybrid blog post/README/code file where it is the actual code file I use when I update my R environment/computer, but also I wrote some descriptions along the way so if somebody else stumbles upon this and likes what they see, they can copy it or maybe even find something new that they didn’t know about before. The link to my GitHub repo is on the right panel. Feel free to fork and customize it for your own use!

2 r-and-rstudio-setup.R

First, we begin with the R file that makes everything after it possible.

2.1 Packages

These are the packages I most frequently use, loosely grouped into the categories below. This does not include dependency packages. So for example, I use quarto to render Quarto documents via R code, but I don’t directly use the markdown package myself, so it is not listed below.

You can find the info page for each package at https://cran.r-project.org/web/packages/[package_name]/index.html where [package_name] is the name of the package.

r-and-rstudio-setup.R

install.packages(c(
  # Meta Packages
  'tidyverse',  # Easily Install and Load the "Tidyverse" packages | https://tidyverse.tidyverse.org
  'tidymodels', # Easily Install and Load the "Tidymodels" packages | https://tidymodels.tidymodels.org/
  
  # Programming & Development
  'purrr',    # Functional Programming Tools | https://purrr.tidyverse.org/
  'forcats',  # Tools for Working with Categorical Variables (Factors) | https://forcats.tidyverse.org/
  'keyring',  # Package for accessing OS's credential store | https://keyring.r-lib.org/
  'fs',       # Cross-Platform File System Operations Based on 'libuv' | https://fs.r-lib.org/
  'renv',     # Project Environments | https://rstudio.github.io/renv/index.html

  # Import
  'readr',    # Read Rectangular Data | https://readr.tidyverse.org/
  'httr2',    # Perform HTTP Requests and Process the Responses | https://httr2.r-lib.org/
  'readxl',   # Read Excel Files | https://readxl.tidyverse.org/
  'rvest',    # Easily Harvest (Scrape) Web Pages | https://rvest.tidyverse.org/
  'jsonlite', # A Simple and Robust JSON Parser and Generator for R | https://jeroen.r-universe.dev/jsonlite
  
  # Tidy/Transform
  'dplyr',     # A Grammar of Data Manipulation | https://dplyr.tidyverse.org/
  'tidyr',     # Tidy Messy Data | https://tidyr.tidyverse.org/
  'tibble',    # Simple Data Frames | https://tibble.tidyverse.org/
  'stringr',   # Simple, Consistent Wrappers for Common String Operations | https://stringr.tidyverse.org/
  'lubridate', # Make Dealing with Dates a Little Easier | https://lubridate.tidyverse.org/
  'janitor',   # Simple Tools for Examining and Cleaning Dirty Data | https://sfirke.github.io/janitor/index.html 

  # Visualize
  'ggplot2',   # Create Elegant Data Visualizations Using the Grammar of Graphics | https://ggplot2.tidyverse.org/
  'gt',        # Easily Create Presentation-Ready Display Tables | https://gt.rstudio.com/
  'skimr',     # Compart and Flexible Summaries of Data | https://docs.ropensci.org/skimr/
  
  # Model
  'rsample',   # General Re-sampling Infrastructure | https://rsample.tidymodels.org/
  'parsnip',   # A Common API to Modeling and Analysis Functions | https://parsnip.tidymodels.org/
  'recipes',   # Pre-processing and Feature Engineering Steps for Modeling | https://recipes.tidymodels.org/
  'workflows', # Modeling Workflows | https://workflows.tidymodels.org/
  'tune',      # Tidy Tuning Tools | https://tune.tidymodels.org/
  'yardstick', # Tidy Characterizations of Model Performance | https://yardstick.tidymodels.org/
  'broom',     # Convert Statistical Objects into Tidy Tibbles | https://broom.tidymodels.org/
  'dials',     # Tools for Creating Tuning Parameter Values | https://dials.tidymodels.org/
  'infer',     # Tidy Statistical Inference | https://infer.tidymodels.org/
  'corrr',     # Correlations in R | https://corrr.tidymodels.org/
  
  # Communicate
  'quarto', # R Interface to 'Quarto' Markdown Publishing System

  # Database
  'DBI',     # R Database Interface | https://dbi.r-dbi.org/index.html
  'odbc',    # Connect to ODBC Compatible Databases (using the {DBI} Interface) | https://odbc.r-dbi.org/
  'dbplyr',  # A {dplyr} Back End for Databases | https://dbplyr.tidyverse.org/
  'duckdb',  # {DBI} Package for the DuckDB Database Management System | https://r.duckdb.org/
  'duckplyr' # A DuckDB-backed Version of {dplyr} | https://duckdblabs.github.io/duckplyr/
))

install.packages(
  "rsthemes",
  repos = c(gadenbuie = 'https://gadenbuie.r-universe.dev', getOption("repos"))
)

rsthemes::install_rsthemes()

# Other packages I'm interested in:
# 'profvis'  # Interactive Visualizations for Profiling R Code | https://rstudio.github.io/profvis/
# 'targets'  # Pipelining Tools in R | https://docs.ropensci.org/targets/
# 'testthat' # Unit Testing for R | https://testthat.r-lib.org
# 'usethis'  # Automate Package and Project Setup | https://usethis.r-lib.org/
# 'devtools' # Tools to Make Developing R Packages Easier | https://devtools.r-lib.org/
# 'zoo'      # S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations) | https://zoo.R-Forge.R-project.org/

After these are installed, close and open RStudio again so that the addins from the packages also load.

2.2 RStudio Configuration

As I’ve been using R & RStudio, I’ve learned which custom settings I like the most. This section of code takes the respective files and copies them to where the base files for R and RStudio are. I created this repo because of my job where we log into different virtual machines. I got sick of resetting all of these options by hand, so now I just pull this repo from GitHub and run the code.

The directories don’t exist by default, they are created when you manually change the respective settings, so this chunk takes care of that, especially if it’s a fresh install of RStudio.

r-and-rstudio-setup.R

purrr::walk(
  .x = c('themes', 'keybindings', 'snippets'),
  .f = \(directory) stringr::str_c("C:/Users/", {Sys.info()[['user']]}, "/AppData/Roaming/RStudio/", directory) |> fs::dir_create()
)

Then we copy the files from this folder to their appropriate locations.

r-and-rstudio-setup.R

purrr::pwalk(
  .l = tibble::tribble(
    ~file,                   ~destination,
    'rstudio_bindings.json',  stringr::str_glue("C:/Users/{Sys.info()[['user']]}/AppData/Roaming/RStudio/keybindings/rstudio_bindings.json"),
    'addins.json',            stringr::str_glue("C:/Users/{Sys.info()[['user']]}/AppData/Roaming/RStudio/keybindings/addins.json"),
    'r.snippets',             stringr::str_glue("C:/Users/{Sys.info()[['user']]}/AppData/Roaming/RStudio/snippets/r.snippets"),
    'rstudio-prefs.json',     stringr::str_glue("C:/Users/{Sys.info()[['user']]}/AppData/Roaming/RStudio/rstudio-prefs.json"),
    '.Rprofile',              stringr::str_glue("C:/Users/{Sys.info()[['user']]}/Documents/.Rprofile")),
  .f = \(file, destination) fs::file_copy(path = file, new_path = destination, overwrite = TRUE)
)

2.3 R Themes

I hate that when you use dark mode in RStudio, it’s just this dark blue shade for the UI, not actually dark/black. Also, I’m really not a fan of any of the themes that come with RStudio. To some extent, I think Garrick Aden-Buie also agreed with my sentiment and created this awesome package, {rsthemes}.

2.3.1 {rthemes}

This package comes with a bunch of awesome themes that complete change the way RStudio looks and feels, and I would recommend it to anybody looking to modernize their RStudio interface. You can see the usage in the docs, and the settings I’m using in my .Rprofile, which I talk about below.

Right now, I really like the Elm light and Elm dark themes, and I switch between the two depending on the brightness of the room.

2.3.2 {darkstudio}

I’m now using the {rsthemes} package, but I have to give a huge shoutout to GitHub user rileytwo. I used rileytwo’s work below for more than a year, and I can’t not shout it out.

• {darkstudio} is a package that turns the IDE elements to shades of black whenever you are using a theme with rs-theme-is-dark: TRUE.
• Kiss: Keep It Stupid Simple is a theme from Riley that just looks so good, it’s been my go to for over a year now.

If either of these interest you, please go check them out. They were a staple to my R experience and I would like to support the creator as best as I can.

devtools::install_github('rileytwo/darkstudio')
darkstudio::activate() # This requires admin privileges

3 Settings Files

All of the settings for R & RStudio that I customized are controlled with the following files:

• .Rprofile
• r.snippets
• rstudio_bindings.json
• addins.json
• rstudio-prefs.json

3.1 .Rprofile

The .Rprofile file is an R script that runs each time R starts up that lets you to customize your R environment. It can be used to set global options, load packages, define functions, and customize the R startup process. Or in my case, have some fun 😁

3.1.1 Options

options() lets you set the global options for R. All of them have a default, and these are the ones I’ve changed for my preference. You can use ?options to view the full list.

.Rprofile

options(
  scipen = 999999,               # A penalty to be applied to turning regular values to scientific notation
  setWidthOnResize = TRUE,       # If set and TRUE, the terminal resize when the terminal pane is resized
  useFancyQuotes = FALSE,        # Turn off fancy quotes
  warn = 1,                      # Prints warnings as they happen instead of when the top function ends.
  warnPartialMatchArgs = TRUE,   # Warns if partial matching is used in argument matching.
  warnPartialMatchAttr = TRUE,   # Warns if partial matching is used in extracting attributes via attr.
  warnPartialMatchDollar = TRUE, # Warns if partial matching is used for extraction by $.
  prompt = 'R> ',                # This is complete personal preference
  continue = '+> ',              # This is complete personal preference
  rsthemes.theme_light = "Elm light {rsthemes}",
  rsthemes.theme_dark = "Elm dark {rsthemes}",
  rsthemes.theme_favorite = "Elm dark {rsthemes}"
)

3.1.2 R Completion Options

The rc.settings function is part of the utils package in R, which configures settings for the R completion mechanism. It can enable or disable specific completion features like inter-package completion, function argument completion, and fuzzy matching. You can use ?rc.settings to view the full list.

1. ipck (Inter-Package Completion):

   • Description: This option enables or disables completion of object names across all loaded packages.
   • Explanation: If you work with multiple packages, you can quickly access functions and objects from any loaded package without having to remember which package they belong to.

2. func (Function Argument Completion):

   • Description: This option enables or disables completion of function argument names.
   • Explanation: This helps you to write function calls more efficiently by providing argument suggestions, reducing the need to look up function documentation frequently.

3. fuzzy (Fuzzy Matching):

   • Description: This option enables or disables fuzzy matching for completion.
   • Explanation: This is useful when you cannot recall the exact name of a function or object. Fuzzy matching will suggest completions that closely resemble what you have typed, saving time and reducing frustration.

In short, the more help I can get coding, the better 😁

.Rprofile

rc.settings(ipck = TRUE, func = TRUE, fuzzy = TRUE)

3.1.3 Interactive Sessions

You can use this code section if you want things to enable in an interactive session, like auto-loading certain packages. Some people use it to load packages that they always use, like tidyverse, usethis, devtools, and so on, but I’m in the camp that every script should be very explicit in what packages are being used, so I use this feature to have some fun.

If in an interactive session, this code will output my message in the console everytime R starts. I’ve always wanted my own J.A.R.V.I.S., R is close enough 🥲

.Rprofile

if (interactive()) {
  message("Welcome Mr. Ozbeker, how may I be of assistance?")
}

3.2 r.snippets

RStudio lets you add custom snippets (pieces of code that can be quickly inserted, useful for repetitive code) and key bindings that can really help your code flow if you use them.

r.snippets

snippet user
  user = Sys.info()[['user']]

3.3 rstudio_bindings.json

This may seem like a simple change, but I though it was weird that you have to press 3 keys for arguably the most important operator in R. Also mapping to the actual pipe key, |, made more sense to me. (Well yes it’s technically mapping to \ but having to hit shift would’ve removed half the reason of remapping in the first place.)

rstudio_bindings.json

{
    "insertPipeOperator": "Ctrl+\\"
}

3.4 addins.json

RStudio uses a separate file for key bindings for addins, and the {rsthemes} package comes with a feature for toggling from light and dark modes, and a recommended key binding to follow:

addins.json

{
    "rsthemes::use_theme_toggle": "Ctrl+Alt+D"
}

3.5 rstudio-prefs.json

Last but not least, we have the file that began it all. rstudio-prefs.json holds all of your custom settings that you change in Tools > Global Options. Every time I had to setup RStudio on a new machine, I could never remember all the settings I liked, and I figured that there was a file somewhere which holds these settings that I could overwrite. That is exactly what this file is. These settings allow you to customize various aspects of the IDE, such as appearance, editor behavior, and default options for projects.

JSON files don’t have a great way of adding in-line comments, but the settings names are pretty descriptive of what they do. Since this is the last section of the blog post, I have no shame printing all 67 lines 😈

rstudio-prefs.json

{
    "restore_source_documents": false,
    "wrap_tab_navigation": false,
    "save_workspace": "never",
    "load_workspace": false,
    "initial_working_directory": "C:/Users/OzanO/Code",
    "default_open_project_location": "C:/Users/OzanO/Code",
    "always_save_history": false,
    "restore_last_project": false,
    "auto_detect_indentation": true,
    "insert_native_pipe_operator": true,
    "highlight_selected_line": true,
    "scroll_past_end_of_document": true,
    "highlight_r_function_calls": true,
    "rainbow_parentheses": true,
    "auto_append_newline": true,
    "strip_trailing_whitespace": true,
    "warn_if_no_such_variable_in_scope": true,
    "warn_variable_defined_but_not_used": true,
    "style_diagnostics": true,
    "show_diagnostics_other": true,
    "indent_guides": "gray",
    "syntax_color_console": true,
    "limit_visible_console": true,
    "auto_expand_error_tracebacks": true,
    "rmd_chunk_output_inline": false,
    "show_rmd_render_command": true,
    "rmd_viewer_type": "pane",
    "pdf_previewer": "none",
    "windows_terminal_shell": "win-ps",
    "full_project_path_in_window_title": true,
    "panes": {
        "quadrants": [
            "Source",
            "TabSet1",
            "Console",
            "TabSet2"
        ],
        "tabSet1": [
            "Environment",
            "History",
            "Connections",
            "Build",
            "VCS",
            "Presentation"
        ],
        "tabSet2": [
            "Files",
            "Plots",
            "Packages",
            "Help",
            "Viewer",
            "Presentations"
        ],
        "hiddenTabSet": [
            "Tutorial"
        ],
        "console_left_on_top": false,
        "console_right_on_top": true,
        "additional_source_columns": 0
    },
    "jobs_tab_visibility": "shown",
    "code_completion_characters": 1,
    "text_rendering": "geometricPrecision",
    "editor_theme": "Elm dark {rsthemes}",
    "margin_column": 96
}