Difference between revisions of "GenelandTutorial"

Line 8: Line 8:
  
 
* start R
 
* start R
* library('Geneland')
+
<pre>
* Geneland.GUI()
+
library('Geneland')
 +
Geneland.GUI()
 +
</pre>
 
* fill in the output directory and the coordinates and the sampled data (use codominated markers)
 
* 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
 
* run the analysis using at least 10000 steps (more would be better), do also a few replicates
Line 30: Line 32:
  
 
* install R (use apt-get if your system supports that)
 
* install R (use apt-get if your system supports that)
* in R: install.packages(&quot;Geneland&quot;,method=&quot;wget&quot;)
+
* in R:  
* you should be set: in R try: library('Geneland') Geneland.GUI()
+
<pre>
 +
install.packages("Geneland",method="wget")
 +
</pre}
 +
* you should be set: in R try:  
 +
<pre>
 +
library('Geneland')  
 +
Geneland.GUI()
 +
</pre>
  
 
===on Windows:===
 
===on Windows:===
Line 38: Line 47:
 
* Download the executable R-x.x.x-win32.exe
 
* Download the executable R-x.x.x-win32.exe
 
* Launch this executable.
 
* Launch this executable.
* type install.packages(&quot;Geneland&quot;).
+
* type  
 +
<pre>
 +
install.packages("Geneland").
 +
</pre>
 
* follow the instructions.
 
* follow the instructions.

Revision as of 18:24, 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")
</pre}
* you should be set: in R try: 
<pre>
library('Geneland') 
Geneland.GUI()

on Windows:

install.packages("Geneland").
  • follow the instructions.