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.
It is probably helpful to make sure all of your packages are up to date!
At the very least:
bookdown
rmarkdown
knitr
Manscript.Rmd
to whatever you want it to bePAPERFILENAME
variable in Makefile
to match your new Rmd
file name.Makefile
to reflect removing Model.png
If you add external images to this repository that will be graphics for slides:
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
.
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:
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.
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.
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
.
r setup
block near the top of the Rmd
file.