README.md

In kevin-allen/relectro: Analysis of electrophysiological data

relectro

R package to analyze electrophysiological data. The focus is on data from tetrode recording experiments in behaving animals. Most of the package is written in R but some sections are written in C for speed. Analysis can easily be run in parallel with the snow package.

Here is an example of figure you can generate using relectro. You can see the mean spike waveforms, the spike-time autocorrelations, instantaneous firing rate, spatial firing rate map and head-direction polar plot.

Install

• Get the source code with the git clone command: git clone http://github.com/kevin-allen/relectro.git

You will need to install the fftw3 C library to compute discrete Fourier transforms with relectro. You can install it on a linux machine.

• With Fedora: dnf install -y fftw3-devel

• With Ubuntu: apt-get install libfftw3-dev

• From R studio, click File/Open project... and select relectro.Rproj

If you just want to use the functions and objects of relectro, go in the terminal and run the following

• R CMD build relectro
• R CMD INSTALL relectro

You might need to add a few R packages to be able to build relectro. Here is a list of what was missing on a Fedora installation. In R, use install.packages().

• rmarkdown
• snow
• plotrix
• knitr
• abind
• testthat
• oce
• plyr
• circular

If you want to modify the code of relecto, I recommand using R studio together with the book "R Packages" by Hadley Wickham. Most of the tools used to develop relectro are presented in this book. You probably want to use the R package devtools for development.

Feedback

Please report any issues or suggestions at http://github.com/kevin-allen/relectro/issues.

Warning

There is no warranty that the code is bug-free. The tests run on the functions can be found in the tests directory.

kevin-allen/relectro documentation built on May 20, 2019, 9:06 a.m.