README.md
In AsexGenomeEvol/AsexStats: The handy functions for analysis of asexual arthropods

The project is hosted at : https://github.com/AsexGenomeEvol

I will categorize functions by type (project specific will be somehow marked as well)

loading functions

filter_thetas - function for filtering thetas

plotting functions

sex_legend - plots a sex/asex legend
plot_log_hist - plots y-log histogram of sex/asex data

Misc

ssplit - split a string into vector of substring
make_data_frame - create a data.frame with predefined column names

data & variables

timema_pairs - useful descriptors of species pairs (labels, divergence_times, ...)
timemas - timema species labels stored in a list (codes, labels, ...)
asex_blue, sex_red - colours used for asexual and sexual species

get the package (clone or download the latest code)
open terminal in the folder of the package and run Rscript install.R,

or using devtools package, run R and type

library(devtools)
install_github("AsexGenomeEvol/AsexStats", build_vignettes=FALSE)

local installation

Users on clusters classically do not have a root access and therefore they won't be able to install R packages to the common folders of all the users. To access an R package without root access you need to install the package on some alternative place (like your home) and tell R that there will be an alternative place to look for packages.

The very beginning is the same, download this package, then create a place for your local R packages (/home/$USER/R in this example).

cd ~
git clone https://github.com/AsexGenomeEvol/AsexStats
mkdir -p /home/$USER/R
CMD INSTALL AsexStats -l /home/$USER/R

Now the package was installed to your home (~/R). To tell R about the alternative path you set an environmental variable by adding the line export R_LIBS=/home/$USER/R into your .bashrc file (the setting file of your bash)

echo "export R_LIBS=/home/$USER/R" >> ~/.bashrc

testing is done using testthat and it is integrated to installation (if test wont pass, installation fails)
documentation is generated using devtools and roxygen2
you can use make for rebuilding package - however, the Makefile is not fully portable (yet?), you need to modify path to your R package inside of the makefile.
use branches and pull requests for development of the new features

create an R script (*.R) in folder data-raw that will generate a *.rdata data file in data folder
add the name of data/scripts in R/data.R (use one of previous entries as template)
add the name to VARIABLES in the Makefile
document and reinstall package
before making a commit, check that data look as expected and check if the documentation of data (?mydata) looks as expected