Peter Beerli's Classes

Geneland tutorial

(if you need to still install see Installation:)

Tutorial

I have prepared 3 sample data files with increasing migration rate 1 is low and 3 is high, all use the same coordinate file (in fact the data was simulated using two populations and the coordinates are assigned randomly to the samples -- this is NOT how real data is collected because this destroys any geography within a population, but since there was no geography to start with this will be OK, I expect that geneland will cope well with sample1 and less well with sample3.

• start R

library('Geneland')
Geneland.GUI()

• fill in the output directory and the coordinates and the sampled data (use codominated markers)
• run the analysis using at least 10000 steps (more would be better), do also a few replicates
• postprocess using the defaults
• run the graphics section and look at some of the plots (we will discuss these in class)

Installation:

On a mac:

• Install XQuartz (you may already have it) download and install: http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.7.dmg
• Install R for your system (on my mac I run R.app, but every OS has one or more working R installations) for example use this: https://cran.r-project.org/bin/macosx/R-3.2.2.pkg and install
• install the geneland library into R: in the R.app installer get the package 'Geneland' using the package manager otherwise fire up R and then do: install.packages("Geneland")

if this works do (!! capitalization !!) library("Geneland") You may need to follow the prompt to install command line tools, otools or similar.

• if all worked then you should be set: in R try (again): library('Geneland') Geneland.GUI()

On UNIX systems:

• install R (use apt-get if your system supports that)
• in R:

install.packages("Geneland",method="wget")
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* you should be set: in R try: 
<pre>
library('Geneland') 
Geneland.GUI()

on Windows:

• Go to the Windows binary repository http://cran.r-project.org/bin/windows/base/
• Download the executable R-x.x.x-win32.exe
• Launch this executable.
• type

install.packages("Geneland").

• follow the instructions.