install.md

In yinscapital/retina-analysis-reference: Tools for plotting and analyzing vertebrate retinas.

Install

Developed and tested on R 3.1.1 with Windows 8.1

1. Setup:

Windows

Install R 3.1.2 Install RTools

Linux

Run in terminal:

sudo apt-get -y build-dep libcurl4-gnutls-dev
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libglu1-mesa-dev
sudo apt-get -y install r-base-core r-base r-cran-rgl libgtk2.0-dev

Mac

Install R 3.1.2 Run in the terminal:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install gtk+
export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig:$PKG_CONFIG_PATH
brew install caskroom/cask/brew-cask
brew cask install xquartz

Run in R

install.packages(c("cairoDevice", "RGtk2"), type="source")
install.packages('devtools')
devtools::install_github('bcohn12/retina')

Finally, install Xcode from the App Store

2. Load dependencies from the R console:

install.packages('retistruct') #if you have an issue, comment on it here to get it fixed: https://github.com/davidcsterratt/retistruct/issues/new
retistruct::retistruct() #On Windows, Accept the 'Install GTK+' popup
install.packages('devtools')
devtools::install_github('bcohn12/retina')

3. Load retina and plot the retina of a reef fish (Pseudodax moluccanus):

library(retina)
retinaplot(Pmol_753)

Full walkthrough tutorial to use your own retina

Link to Tutorial on Github

yinscapital/retina-analysis-reference documentation built on May 22, 2019, 12:40 p.m.