Slides as PDF

You can save the slides as pdf by going to Print in a browser (Google Chrome works best) and then selecting save as pdf.

RStudio

  1. The command to clear all variables from the environment (workspace)

    rm(list=ls())

  2. In RStudio the keyboard shortcut for the pipe operator %>% is Ctrl+Shift+M (Windows) or Cmd+Shift+M (Mac).

  3. In RStudio the keyboard shortcut for the assignment operator <- is Alt + - (Windows) or Option + - (Mac).

  4. In RStudio use Ctrl+L to clear all the code from your console.

  5. If you’re typing in a script in the source editor pane but you want to move the curser to the console use Ctrl+2. You can also use Ctrl+1 to move the curser back to the source editor.

  6. To run a line of code from the source editor use Ctrl+Enter (Windows) or Cmd+Enter (Mac).

  7. You can “tear” code panes or data view panes out of the RStudio window which can be particularly useful on big screens or when using multiple monitors.

  8. You can scroll through your command history by clicking Ctrl + ↑ (Windows) or Cmd + ↑ (Mac). If you know what the line of code you’re looking for started with, type the first few characters and then press Ctrl/Cmd + ↑ and it will only search a matching subset of the history.

  9. You can rename all instances of a variable name by highlighting one instance of the variable name and then using Code > Rename in Scope. This is better than using Edit > Replace and Find because it only looks for whole word matches.

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. A useful guide to help you get started can be found here.

Rmarkdown is a great way to perform reproducible research and generate reports.

Super brief overview

  1. Create a new Rmd file. In RStudio File -> New File -> R Markdown...
  2. When you have a Rmd file open in RStudio there’s a Knit HTML button up the top of the source window. You click that button to turn the markdown into HTML (or PDF or Word).
  3. Text and R code can be combined in the Rmd file. Code chunks begin with three back ticks followed by r, the (optional) chunk name and any arugments: ```{r} or ```{r chunk_name, tidy=TRUE}. The chunk also ends with three back ticks ```. Examples can be seen in the template that opens along as a new file in RStudio.

The keyboard shortcut for inserting a chunk is Ctrl+Alt+I (Windows) or Cmd+Option+I (Mac).

Including Plots

You can embed static plots in an rmarkdown document without doing anything special. Important chunk options are fig.width and fig.height to set the figure width and height for example ```{r, fig.width=4, fig.height=6}.

Chunk options

Some useful chunk options:

  • tidy = TRUE makes the R code more readable (proper spacing)
  • results = 'hide' hide the results of the chunk output (i.e. don’t show them)
  • results = 'hold' hold the results of the chunk output until all commands in the chunk have been run
  • warning = FALSE don’t show any warning messages (e.g. when ggplot2 drops observations)
  • message = FALSE don’t show any messages (e.g. when packages load)
  • {r chunkname} you can name your chunks with text immediately after the r. This can be particularly useful when errors pop up as it makes it easier to identify which chunk the error occurs in.