[adegenet-forum] AFLP data format

[Jombart, Thibaut]

Dear Russell, 

I am afraid you have been viewing an outdated version of the tutorial. 

In the current version, there is a section titled "Handling presence/absence data" (section 3.13, p.49), which exactly answers your question, with a fake AFLP dataset remarkably similar to your data formatted as a table.

Best

Thibaut
--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of Pfau, Dr. Russell S. [PFAU at tarleton.edu]
Sent: 04 December 2010 03:03
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] AFLP data format

I have spent the past 5 hours reading the adegenet manual, tutorial, and forum and have yet to learn how to put my AFLP data into a file like the nancycats.RData file for use in analysis with adegenet.  How on earth does one do this?

I have my data in two format types, and have created simple test files showing the two format types that I have (see below).  Please help....where do I go from here!

Russell


table format:

                loc1    loc2    loc3    loc4
indA    pop1    1       0       1       1
indB    pop1    0       1       1       1
indC    pop1    1       1       0       1
indD    pop2    0       1       1       1
indE    pop2    1       1       0       0
indF    pop2    1       0       1       1
indG    pop2    0       1       1       0


STRUCTURE format:

                loc1    loc2    loc3    loc4
indA    pop1    1       0       1       1
indA    pop1    1       0       1       1
indB    pop1    0       1       1       1
indB    pop1    0       1       1       1
indC    pop1    1       1       0       1
indC    pop1    1       1       0       1
indD    pop2    0       1       1       1
indD    pop2    0       1       1       1
indE    pop2    1       1       0       0
indE    pop2    1       1       0       0
indF    pop2    1       0       1       1
indF    pop2    1       0       1       1
indG    pop2    0       1       1       0
indG    pop2    0       1       1       0


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