<html><body><div style="font-family: trebuchet ms,sans-serif; font-size: 12pt; color: #000000"><div><span style="font-family: 'trebuchet ms', sans-serif;">Hi Maïlis,</span></div><div><span style="font-family: 'trebuchet ms', sans-serif;"><br></span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;"><span style="font-family: 'trebuchet ms', sans-serif;">in xvalDapc</span> `x` argument is your DAPC result (`tab(dapc1)`) and `grp` is the membership of individuals in groups. The latter is sometimes found in // Optional content, but you appear to not have this. You will have to assign indviduals to a population some other way. You tried using `find.clusters` and you can access group membership by taking out a $grp element. In your case that would be</span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;"><br></span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;"> <span style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">xvalDapc(tab(dapc1), grp = grp$grp)</span></span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;"><br></span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;">I omitted `x =` which is personal preference of always omitting first argument in a function call.</span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;">Let us know if this works.</span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;"><br></span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;">Cheers,</span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;">Roman</span></div><div><span style="font-family: Helvetica, Arial, sans-serif;" data-mce-style="font-family: Helvetica, Arial, sans-serif;"><br></span></div><div><span name="x"></span>----<br>In god we trust, all others bring data.<span name="x"></span><br></div><div><br></div><hr id="zwchr"><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;"><b>From: </b>"Maïlis" <mailis@kwata.net><br><b>To: </b>adegenet-forum@lists.r-forge.r-project.org<br><b>Sent: </b>Tuesday, January 26, 2016 12:01:31 PM<br><b>Subject: </b>[adegenet-forum] xvalDapc, help for arguments "x" and "grp"<br><div><br></div>
Hello, <br>
<br>
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<span id="result_box" class="" lang="en"><span class="hps">I
am contacting</span> <span class="hps">you because</span>
<span class="hps">I use the</span> <span class="hps">DAPC
fonction</span> <span class="hps">of adegenet</span>
package <span class="hps">without encountering</span> <span class="hps">any particular problems.</span> <span class="hps">However</span><span>, I would</span> <span class="hps">like</span> <span class="hps">to use the</span>
<span class="hps">cross</span> <span class="hps">validation,</span>
<span class="hps">and that</span><span>'s when</span> <span class="hps">it</span> <span class="hps">no longer
works..</span></span></div>
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<br>
<small><i>>
database<-read.table(file.choose("C:/Users/.../XXX.txt"),
header=TRUE, sep=",",na.strings="-9")</i><i><br>
</i><i>> x<- df2genind(data.frame(database), sep="/",
ncode=3, p=NULL, NA.char="-9", ploidy=2,
type=c("codom"),strata=NULL, hierarchy=NULL)</i><i><br>
</i><i>/// GENIND OBJECT /////////</i><i><br>
</i><i><br>
</i><i> // 341 individuals; 7 loci; 164 alleles; size: 264.9 Kb</i><i><br>
</i><i><br>
</i><i> // Basic content</i><i><br>
</i><i> @tab: 341 x 164 matrix of allele counts</i><i><br>
</i><i> @loc.n.all: number of alleles per locus (range: 13-30)</i><i><br>
</i><i> @loc.fac: locus factor for the 164 columns of @tab</i><i><br>
</i><i> @all.names: list of allele names for each locus</i><i><br>
</i><i> @ploidy: ploidy of each individual (range: 2-2)</i><i><br>
</i><i> @type: codom</i><i><br>
</i><i> @call: df2genind(X = data.frame(database), sep = "/",
ncode = 3, pop = NULL, </i><i><br>
</i><i> NA.char = "-9", ploidy = 2, type = c("codom"), strata =
NULL, </i><i><br>
</i><i> hierarchy = NULL)</i><i><br>
</i><i><br>
</i><i> // Optional content</i><i><br>
</i><i> - empty -</i><i><br>
</i><i>Warning message:</i><i><br>
</i><i>In df2genind(data.frame(database), sep = "/", ncode = 3, p
= NULL, :</i><i><br>
</i><i> duplicate labels detected for some individuals; using
generic labels</i><i><br>
</i><i><br>
</i><i>> grp<-find.clusters(x, max.n.clust=9)</i><i><br>
</i><i>Choose the number PCs to retain (>=1): 140</i><i><br>
</i><i>Choose the number of clusters (>=2): 6</i><i><br>
</i><i>> dapc1<-dapc(x,grp$grp)</i><i><br>
</i><i>Choose the number PCs to retain (>=1): 40</i><i><br>
</i><i>Choose the number discriminant functions to retain
(>=1): 5</i></small><br>
<br>
It works but, for using xvalDapc
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<div dir="ltr" style="zoom:1"><span id="result_box" class="" lang="en"><span class="hps">I don't know</span> <span class="hps">what to choose</span> <span class="hps">as an
argument</span> <span class="hps atn">for "</span><span class="atn">x" and "</span><span>grp</span><span>". I tried
severals things but that didn't work. <br>
</span></span><span id="result_box" class="" lang="en"><span><span id="result_box" class="short_text" lang="en"><span class="hps">Can</span> <span class="hps">you advise me</span>
<span class="hps">on the arguments</span> <span class="hps">to use?<br>
<br>
</span></span></span></span><br>
<span id="result_box" class="" lang="en"><span><span id="result_box" class="short_text" lang="en"><span class="hps"><span id="result_box" class="short_text" lang="en"><span class="hps">Thank</span> <span class="hps">you in advance for</span> <span class="hps">your reply, <br>
<br>
Best regards, <br>
<br>
Maïlis<br>
</span></span><br>
</span></span></span></span></div>
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