<div dir="ltr">Hello, <div><br></div><div>yes, a lot has changed in between the two versions; see ChangeLog:<br><a href="https://cran.r-project.org/web/packages/adegenet/ChangeLog">https://cran.r-project.org/web/packages/adegenet/ChangeLog</a><br></div><div><br></div><div>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.</div><div><br></div><div>Cheers</div><div>Thibaut</div><div> </div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart</div><div style="font-size:small">Lecturer, Department of Infectious Disease Epidemiology, Imperial College London</div></div><div><span style="font-size:12.8px">Head of RECON: </span><span style="font-size:12.8px"><a href="http://repidemicsconsortium.org" target="_blank">repidemicsconsortium.org</a></span><br></div></div><div><a href="http://sites.google.com/site/thibautjombart/" style="font-size:12.8px" target="_blank">sites.google.com/site/thibautjombart/</a><br></div><div><a href="http://github.com/thibautjombart" target="_blank">github.com/thibautjombart</a></div>Twitter: <a href="http://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div><div dir="ltr">+44(0)20 7594 3658</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 10 February 2017 at 10:47, flefevre <span dir="ltr"><<a href="mailto:francois.lefevre.2@inra.fr" target="_blank">francois.lefevre.2@inra.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Dear adegenet team,<br>
<br>
has something changed in the find.clusters and/or dapc functions
from V1.4-2 and V2.01 of adegenet?<br>
<br>
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?<br>
<br>
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:<br>
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 <br>
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.<br>
<br>
Any suggestion to interprete this discrepancy is welcome,<br>
Thank you,<br>
<br>
François<br>
<a class="m_-6544450626097913501moz-txt-link-abbreviated" href="mailto:francois.lefevre.2@inra.fr" target="_blank">francois.lefevre.2@inra.fr</a><span class="HOEnZb"><font color="#888888"><br>
<br>
<div class="m_-6544450626097913501moz-signature">-- <br>
</div>
</font></span></div>
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