Difference between revisions of "GenelandTutorial"

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==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.
 
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.
  

Revision as of 19:22, 29 September 2015

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:

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")
  • you should be set: in R try: library('Geneland') Geneland.GUI()

on Windows: