Installing R, RStudio, R Markdown, Latex

Supplement to POL90

For POL90, we require students shift away from word processors like Microsoft Word and use a workflow that involves R and a formatting language called R Markdown (as is done in some other stats classes). The two languages are glued together with another language called knitr. Certain kinds of advanced typography, like formulas, rely on yet another language called Latex. Installing and configuring all of this will impose a modest learning curve at the start but will make life much easier down the road.

The basic advantage of R + R Markdown + knitr + Latex is that you can easily braid together your prose, R code, formulas and R output (e.g., plots and tables) in a single document. This not only saves time and makes life easier by reducing the number of files that need to be managed, it also helps with creating better research such as when you write JPs or Senior Theses (we’ll discuss this more in class).

To get set up with R + R Markdown + knitr + Latex, please do the following before class:

Install software and packages

• Install R: http://www.r-project.org

• Install RStudio: https://rstudio.com/products/rstudio/download/#download

• Install course packages:

  • Copy and paste the following command to your R Console:

# opens a script to install R packages, do not restart R 
source("http://appliedstats.org/POL90_2022_packages.R")

• If prompted to restart R, click ‘No’
• If prompted with ‘Do you want to install from sources the package which needs compilation?’ type n and hit return

If necessary, install LaTeX

• If you did not install a suite of software called TeX in other stats classes, you’ll need to do that, too. If you did install either TinyTeX, MacTeX or MikTeX (or something similar) you can skip this step. Latex is the engine that helps with advanced typography, in cases like formulas or tables, or when converting documents into PDFs. You will only need to learn a little of the TeX formatting language to get started. The TeX downloads are large but, if your computer has sufficient storage, we recommend the complete versions.

TinyTeX

• Both Mac and Windows
  1. Open RStudio
  2. Run the following commands in RStudio:

install.packages('tinytex')
tinytex::install_tinytex()

3. To test if the installation worked, see Test your installation below:

TinyTex Issues

1. If, when installing TinyTex, you get an error like the following:

The directory /usr/local/bin is not writable. I recommend that you make it writable. See https://github.com/yihui/tinytex/issues/24 for more info.

• Hit Command-Spacebar and type Terminal to OPEN the TERMINAL application

• Once the Terminal application is open, copy and paste the following text into your Terminal and hit RETURN:

[ -e /usr/local/bin ] || sudo mkdir -p /usr/local/bin

• Again, copy and paste the following text into the TERMINAL application and hit RETURN (you may be prompted to type your password and it WILL NOT SHOW ANY CHARACTERS AS YOU TYPE THE PASSWORD)

sudo chown -R `whoami`:admin /usr/local/bin

• Finally, copy and paste this into the TERMINAL application

~/Library/TinyTeX/bin/*/tlmgr path add

• Open RStudio

• Copy and paste this command into the CONSOLE of RStudio (and hit RETURN)

tinytex::install_tinytex()

• See Test your installation below.

2. If you run tinytex::install_tinytex() and get an error like this:

curl failed to verify the legitimacy of the server       

Try the following slight modification:

tinytex::install_tinytex(version = "2021.10")

3. For Windows users, if you get an error like this:

Error in install.packages : cannot open file 'C:/Users/.../OneDrive/Documents/R/win-library/4.1/file666459c6cb3/distill/help/figures/logo.png': Permission denied

• Try (1) Run RStudio as administrator and (2) Under the Packages tab, click Install and change Install to Library option to C:/Program...../R/../library and select the desired package to install. See more of this solution at this StackExchange answer: https://stackoverflow.com/a/50787084/893399

If you have other issues or questions about TinyTex, see: - https://yihui.org/tinytex/ - Also try emailing your error to omar.wasow@pomona.edu

Alternate ways to install LaTeX

• Mac:
  • Lite: BasicTeX (~72MB): http://www.tug.org/mactex/morepackages.html
  • Or, Complete, MacTeX (~3.2Gb): http://www.tug.org/mactex/index.html
• Windows:
  • Lite, MikTeX (~194MB): http://miktex.org/download
  • Or, Complete, TeX Live (~2Gb): http://www.tug.org/texlive/acquire-netinstall.html

Test your installation

• Once you have installed TeX, if you already had RStudio open, quit and then re-open it.

• Once you have installed R, RStudio, knitr, and TeX and restarted RStudio, then, in RStudio do the following to compile a test R Markdown document:

• Create new document

  • File \(\rightarrow\) New File \(\rightarrow\) R Markdown
  • A pop-up window will appear. Give the document a title.
  • Click on the Knit icon (it’s a ball of blue wool with a knitting needle in it) and select Knit to HTML
  • Save the document when prompted
  • After saving a formatted HTML document should appear
  • Also try clicking on the Knit icon again and select Knit to PDF
  • If all goes well a PDF document will be created and you’re all set!

Troubleshooting

• This section is a work-in-progress The instructions below have worked for some students but not others. They will continue to be revised and improved as we identify additional solutions.

• Please email me ( omar.wasow@pomona.edu ) any errors you encounter so that this can be refined for future students.

For students who took other stats classes:

Mac

1. Hit command-space, type Terminal to open the Terminal app

2. Copy and paste the following text in to the command line prompt in the Terminal app and hit return

sudo chown -R `whoami`:admin /usr/local/bin

3. Copy and paste the following text in the Terminal app and hit return.

~/Library/TinyTeX/bin/x86_64-darwin/tlmgr path add

4. Try to run the following commands in R:

install.packages('tinytex')
tinytex::install_tinytex(force = TRUE)

Windows

1. Attempt to uninstall MikTek

• http://www.uninstallhelps.com/how-to-uninstall-miktex-2-9-4250.html

2. Try to run the following commands in R

install.packages('tinytex')
tinytex::install_tinytex(force = TRUE)