[adegenet-forum] DAPC group choice
t.jombart at imperial.ac.uk
Thu Feb 23 15:08:58 CET 2012
so I think the in the DAPC vignette, the example based on H3N2 data (section 3.4) uses the year of sampling as group factor in DAPC. Also, in the same document, the microbov example (p25-34) uses the cattle breeds as group factor in DAPC. The H3N2 example was also presented in the original paper.
So yes, it does make sense. DAPC provides the best achievable reduced space representation of between-group diversity (in the sense of a F statistic, var between / var within). It is comparable to STRUCTURE or any other similar method when the same groups are used, to the extent that the methods give comparable outputs - in this case, the only common thing is group membership probabilities.
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of J. Richardson [jrichardson4 at gmail.com]
Sent: 22 February 2012 22:30
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] DAPC group choice
Hi Dr. Jombart and Adegenet users,
I have a question related to DAPC that I have not found in the manual, tutorials or forum archive.
I am wondering what the DAPC operation is doing (i.e. how it is configuring clusters relative to each other) when you
do not use the groups created in "find.clusters" (i.e. grp$grp output), but rather use the population of origin as the
group designation (i.e. dataset$pop)?
I ran "find.clusters" and performed the DAPC with these created groups. I also performed a DAPC with the groups set
as the sampling sites (populations of origin) using the number of clusters derived from k-means. Interestingly, the DAPC using the k-means
groupings don't make a lot of intuitive sense. However, the DAPC results using the sampling sites/populations of origin for the group
designation make sense and correspond closely to the output from STRUCTURE using their location prior.
So I am wondering if using the sampling site/population designation as the group designation is (A) analogous to the
STRUCTURE operation using the location prior or "population flags", and (B) if this is valid if you have good a priori information on
your population delineations (e.g. a species breeding in discrete, contained habitats)?
Thank you so much in advance for any insight you can provide.
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