[adegenet-forum] any change in find.clusters and/or dapc functions from V1.4-2 to V2.0.1 ?

[Thibaut Jombart]

Hello,

yes, a lot has changed in between the two versions; see ChangeLog:
https://cran.r-project.org/web/packages/adegenet/ChangeLog

Besides, are you using the same version of R for both packages? Knowing if
and what change(s) specifically could cause the results to differ is going
to be difficult, we would have to finely compare the analyses. The first
thing to check would be verify that the matrices of allele frequencies are
the same. I think this would have been 'scaleGen' in the older version
(specify scale=FALSE, center=FALSE, do not replace NA). This is 'tab' in
the current version (use 'freq = TRUE, do not replace NA). Then check if
the matrices are the same. A change in the default treatment of NA, or in
scaling could explain the difference.

Cheers
Thibaut



--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 10 February 2017 at 10:47, flefevre <francois.lefevre.2 at inra.fr> wrote:

> Dear adegenet team,
>
> has something changed in the find.clusters and/or dapc functions from
> V1.4-2 and V2.01 of adegenet?
>
> I am re-doing an analysis that was first done in 2014 (with V1.4-2) on a
> genind object of 158 diploid individuals and 70 snp and the results are
> quite different (synthesis of 20 analyses using CLUMPP, highly consistent
> in each case). Exactly the same dataset and the same script. The only
> difference I can see between the 2 analyses is the version of adegenet: has
> something changed in these 2 functions?
>
> Actually the individuals belong to an admixed population, we look for the
> number of components and assignment of the individuals. The difference is
> as follows:
> 2014 analysis => 3 clear groups (136 individuals out of 158 have a mean
> assignment probability >0.95 to one of the groups), one group is more
> "compact" and consists of very related individuals
> 2017 analysis => 2 clear groups (111 individuals with assignment >0.95),
> all individuals previously assigned to the compact group are still assigned
> to the same new group but now associated with others, the other 2 previous
> groups do not relate well with the new ones.
>
> Any suggestion to interprete this discrepancy is welcome,
> Thank you,
>
> François
> francois.lefevre.2 at inra.fr
>
> --
>
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