Template for R Markdown manuscript

To use this repository

Click Use this template from the GitHub interface. Choose a name for your new repository. You will get a copy of this repository with all the files but none of the commit history.

I recommend that you peruse the bookdown documentation.

Required R packages

It is probably helpful to make sure all of your packages are up to date!

At the very least:

• bookdown
• rmarkdown
• knitr

Steps to get your own paper started.

1. Rename Manscript.Rmd to whatever you want it to be
2. Rename the value of the PAPERFILENAME variable in Makefile to match your new Rmd file name.
3. Update Makefile to reflect removing Model.png
4. Write your paper!

If you add external images to this repository that will be graphics for slides:

1. Commit them!
2. Add them to the IMAGES variable in Makefile so that your slides rebuild if they change.

The supporting material document is SupportingInformation.Rmd. Any figures and tables added here start counting again from 1 and have an S prepended to their labels. If you add supplemental equations, you'll want to do similar tricks for equation numbers and labels. This document also gets a separate bibliography, but it uses the same .bib file as the main manuscript file. The supporting material is a build dependency for the main manuscript. Thus, any changes there will cause the main manuscript to be re-processed when a make command is issued. This file also uses a separate preamble, sipreamble.tex.

Managing the bibliography

Add new Bibtex records to references.bib. The file references.bib is a build dependency in the Makefile.

Those of you using vim-like editors will benefit greatly from the following plugins:

• vim-pandoc
• vim-pandoc-syntax
• vim-rmarkdown

These plugins give you auto completion of citations via the bibliography file declared in the YAML. For this repository, that file is references.bib. The auto completion works using the same <C-X-O> that is used throughout vim for auto completion. For example, vimtex auto-completes \cite commands this way. If the bibliography file contains a citation key AuthorYear, then the citation code in the markdown will be [@AuthorYear] or @AuthorYear. To use auto completion, typing @A<C-X-O> will bring up a completion list of all citation keys starting with A. You then select the correct key from that list.

The default citation code ([@AuthorYear]) results in a parenthetical citation, equivalent to \citep. The code @AuthorYear is equivalent to \citet. To the best of my knowledge, there is no equivalent to \citeyearpar. However, you may use that command "manually", as you may enter any valid LaTeX in your markdown file.

Generating the pdf of your paper

Execute make. If you use a vim-like editor, then execute this command when in normal mode:

:make

The build step saves the intermediate .tex file.

Changing the preamble

The Makefile includes preamble.tex as a build requirement. You may add the usual LaTeX stuff to this file to configure various things. Alternately, you can do a lot of configuration via the YAML.

Configuring the R environment

1. Make the changes to the r setup block near the top of the Rmd file.