Chapter 8 Creating documents in RMarkdown

8.1 Overview

In this practical you will create an RMarkdown (.Rmd) document in either html or PDF format. It can include anything, but the following things are included in RMarkdown document on the VLE (Rep_example.Rmd):

text in paragraphs
plots (e.g. scatterplots)
maps
tables
some hidden code
some visible code

NOTE

you may have to install the rmarkdown package on University computers - you should not have to but you never know! You should test this by running the code:

if (!is.element("rmarkdown", installed.packages()))
    install.packages("rmarkdown", dep = T)

You may need to use a simply named folder. This means removing any non-text characters in the name. So

not C:\Geocomp & Loc Anal\week9
instead C:\Geocomp\week9

8.2 Resources

This tutorial https://rmarkdown.rstudio.com/articles_intro.html may help and some other potentially useful resources include:

Also there are Cheatsheets

https://rmarkdown.rstudio.com/lesson-15.html
they can also be accessed through the Rstudio menu Help > Cheat Sheets > R Markdown Cheat Sheet

Documents created in this way allow you to connect the code, the analysis and the data in a single environment, supporting transparency and reproducibility.

8.3 Tasks

Task 1

This just gets you to create, save and compile a simple R Markdown document.

Open a new RMarkdown document:

File > New File > R Markdown

use HTML format.

Give it a name, save it with a name in your working folder, and try to run it by clicking on the “knit” icon. If you get an error here, you probably need to install the rmarkdown package for some reason.

Then change the 3rd line from

from output: html_document
to output: pdf_document

and compile the document again to create a PDF file. NOTE that if you are on a University PC you may get a ‘cannot compile PDF’ error message. In which case you may need to install a PDF compiler.

# only run this if you get the above errror!
tinytex::install_tinytex()

Task 2

Go through the Rep_Example.Rmd files on the VLE. I have chopped down a GWR Practical as a short example in the RMD file. You should

make sure that you can identify sections of words and code that produce text, plots, maps, hidden / visible code and tables as indicated above.
pay attention to the way that the code snippets presented, especially how the code blocks are bracketed by the backticks ( ` ).
try to create both PDF and HTML outputs by changing the outputs as below in the RMD header:
- output: pdf_document
- output: html_document