8 Rstudio

8.1 Settings

It’s important for the team to all have the same settings in Rstudio. This will make it easier to help each other out and troubleshoot problems. Some settings can be personalized (ie, editor_theme), but others should be consistent across the team.

  1. Tools/global options/general/basic settings should be the same as the image below. It’s very important to have “Save workspace to .RData on exit” set to Never, and deselect “Restore .RData into workspace at startup”

  2. Another way we maintain the same settings is by all having the same settings in rstudio-prefs.json. You can find this file in Home/.config/rstudio/rstudio-prefs.json, use Cmd+shift+. to see your dotfiles. Replace your current rstudio-prefs.json with the one found in our dotfiles repo. This will give you the same settings as the rest of the team. Make sure to change the "document_author": to your name, and feel free to change the "editor_theme": to your preference.

8.2 Packages

  • Use pak to install packages when possible.

  • To get info about any function or package:

    • To see all functions in the package, run ls("package:package_name").
    • To pull up the documentation for a specific function, run ?function_name.
    • To see the raw function code in the console, run function_name

  • Here are some packages to become familiar with:

  • Introduction to Writing Packages in R

8.3 Helpful Resources

  • R for Data Science - A helpful resource for learning how to get your data into R, organize it, transform it, visualize it, and model it.

  • wtf is a good resource for learning more about R/Rstudio.

8.4 Rstudio Keyboard Shortcuts

See all keyboard shortcuts in Rstudio withTools/Keyboard Shortcuts Help` in the top menu.

Here is a list of some of the most common R studio keyboard shortcuts for Mac. Once you get used to these it will make script writing much quicker.

+ Commenting and uncommenting code: `Ctrl + Shift + C`
+ Pull up shortcuts cheat sheet in R: `Alt + Shift + K`
+ Insert pipe operator: `Ctrl + Shift + M`
+ Insert assignment operator: `Alt + -`
+ Make source pane full screen: `Ctrl + Shift + 1` 
+ Make console pane full screen: `Ctrl + Shift + 2` , 3 does `help` pane, 4 does `environment` pane.
+ Cursor-select multiple lines: `Ctrl + Alt + Up/Down/Click`
+ Find in files: `Ctrl + Shift + F`
+ Refresh R: `Ctrl + Shift + F10`
+ List recent commands: `Ctrl + ↑`
+ Execute command on currently selected line: `Ctrl + Enter`
+ Execute complete script: `Ctrl + Shift + S`

  • We have also created some of own shortcuts that are specific to our workspace. Here are a few examples:

    • Completely restart Rstudio (not just R) so you can do things like reload shrtcts: Shift+Cmd+9

  • You can find these shortcuts in the .shrtcts.R file in our dotfiles repo. To use these shortcuts:

    1. Install the shrtcts package by running pak::pkg_install("gadenbuie/shrtcts").
    2. Save the .shrtcts.R file in your home directory
    3. Add the following code to your .Rprofile file (also located in your home directory):
if (interactive() && requireNamespace("shrtcts", quietly = TRUE)) {
  shrtcts::add_rstudio_shortcuts(set_keyboard_shortcuts = TRUE)
}
  • More info on this can be found in the shrtcts github. Worth noting that weird glitches happen when there are conflicting shortcuts to the same call (.shrtcts.R vs manually added shortcuts in Tools/Modify Keyboard Shortcuts in Rstudio).

8.5 Rmarkdown

  • Rmarkdown is a great way to write reports, papers, and presentations. It allows you to write text and code in the same document. You can also create tables, figures, and equations. The document you are reading right now is in fact an .rmd (Rmarkdown) file! Checkout the Rmarkdown cheatsheet for a quick reference guide.

    • Take a look at the Remedy package for some nice Rmarkdown shortcuts.
    • You can use rsam to then manage addins such as Remedy and others.

  • Cross-referencing in Rmarkdown is really useful for referencing figures, tables, and sections. This can be done multiple ways using the bookdown package. Check out how to cross-reference here, specifically the pandoc auto-naming conventions if you are going to reference using header identifiers. Some examples of cross referencing are below:

    • To reference a figure: Figure \@ref(fig:label)
    • To reference a table: Table \@ref(tab:label)
    • To reference a section: Section \@ref(label)
    • To reference a section: [heading name]
    • Example: Section \@ref(git-and-github) makes Section 7
    • Example: [Git and Github] makes Git and Github

  • Super important to not use _ in your chunk labels, as it will not reference properly. Use - instead.

8.6 Dataframes

  • You can get lots of info about the structure of a dataframe just by looking at the details in the environment pane. For example, # of obs = number of rows, # variables = number of columns

  • When dataframes or tables have many columns (more than 50) Rstudio will only show you 50 at a time, so to see the rest you need to use the arrows located on the top left of the df/table view.

  • Hovering your mouse over the df will tell you what class the object is, in this example bcfishpass is of class sf (simple feature)

  • You can also check the class using:
class(bcfishpass)
  • You can glimpse the columns using
str(bcfishpass)

or

head(bcfishpass)
  • You can use the waldo package to compare columns
waldo::compare(bcfishpass$aggregated_crossings_id, bcfishpass$stream_crossing_id)

gives: old is a character vector ('1005400575', '1005400576', '1005400577', '1005400578', '1005400579', ...) new is an integer vector (NA, NA, NA, NA, NA, ...)