rethomics manuscript

The sweave (R + latex) files used to generate the rethomics manuscript. Curently available under the CC-BY license as a preprint on biorxiv

IMPORTANT do not modify the .tex files (see below).

Set up

1. Clone this repo
2. check you have the arch packages texlive-most gcc-fortran r
3. Install the R packages required:

# these should take a few min
install.packages(c("devtools", 
					"knitr", 
					"cowplot",
					"ggetho",
					"zeitgebr",
					"damr"),
				repos = c(CRAN = "http://cran.rstudio.com"))
	
# sleepr installed from github (ignore the warning about submodule)
devtools::install_github("rethomics/sleepr")

Building the whole manuscript

Once the necessary packages are installed, we can compile the whole manuscript with a makefile using make all.

The generates two targets:

• geissmann_et_al_2018.pdf -- The whole formated manuscript
• manuscript-changes.pdf -- The manuscript with track changes for revisions (made with latexdiff)

To clean the project, one can run make clean

Editing the manuscript

IMPORTANT do not modify the .tex files. Tex files are compiled from the .Rnw files. The text of the manuscript is contained in two files:

• manuscript.Rnw -- All the text, except the result section
• results.Rnw -- The result section only