Package List and First Steps

Getting R

If you have never used or heard of R before, I suggest you start by reading about data science in R and installing RStudio. Only once you have done that can we continue.

The rethomics packages

Rethomics works as a collection of interconnected packages. Here is a list of all our packages so far (as well as their individual PDF documentation, description and status).

Package	Doc	Description	Travis	Coverage	CRAN
behavr		Canonical Data Structure for Behavioural Data
ggetho		Visualisation of High-Throughput Behavioural (i.e. Ethomics) Data
damr		Interface to Drosophila Activity Monitor System Result Files
scopr		Read Ethoscope Data
sleepr		Analyse Activity and Sleep Behaviour
zeitgebr		Analysis of Circadian Behaviours

Installation

CRAN

You may have noticed, in the table above, that some packages are on the CRAN (the official R package repository). Therefore, we can use R’s default tools to install them. For instance, behavr, can simply be installed with:

install.packages("behavr")

devtools

For packages that are not on CRAN, or if you want the very latest snapshot of a package, you can use devtools. First, install and load it:

install.packages("devtools")
library(devtools)

You should see a warning message saying something like "GitHub repo contains submodules, [...]", which is fine. Beyond that, ensure you have no error messages. devtool is a package that simplifies installation of unofficial packages (for instance hosted on github) like rethomics ones. To install behavr, you would run:

install_github("rethomics/behavr")

In the same way, you could install other rethomics packages by changing "behavr" for another package name. For instance, you could install ggetho with install_github("rethomics/ggetho").