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Thank you.
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<div class="">I have said it before and will say it again: your efforts are very much appreciated by many.</div>
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<div class="">dlc<br class="">
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<blockquote type="cite" class="">
<div class="">On Jun 14, 2017, at 7:47 AM, Thibaut Jombart <<a href="mailto:thibautjombart@gmail.com" class="">thibautjombart@gmail.com</a>> wrote:</div>
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<div class="">
<div class="">Hi again,<br class="">
<br class="">
OK, so it looks like there was a problem with C routine registration,<br class="">
following some new policies enforced by CRAN, which could have created<br class="">
issue with genlight objects. Not related to your problem, but<br class="">
basically you wouldn't have been able to use genlight objects in the<br class="">
first place. This is fixed in the devel now.<br class="">
<br class="">
As for youR problem, after installing the devel version of adegenet,<br class="">
things should work simply with 'tab'. Here's a toy example:<br class="">
<br class="">
<blockquote type="cite" class="">dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e3, prob=c(.5, .49, .01), replace=TRUE))<br class="">
x <- new("genlight", dat, pop = rep(1:2, each = 25))<br class="">
x<br class="">
</blockquote>
/// GENLIGHT OBJECT /////////<br class="">
<br class="">
// 50 genotypes, 1,000 binary SNPs, size: 76.5 Kb<br class="">
530 (1.06 %) missing data<br class="">
<br class="">
// Basic content<br class="">
@gen: list of 50 SNPbin<br class="">
<br class="">
// Optional content<br class="">
@pop: population of each individual (group size range: 25-25)<br class="">
@other: a list containing: elements without names<br class="">
<br class="">
<blockquote type="cite" class="">X <- tab(x, NA.method = "mean")<br class="">
xval1 <- xvalDapc(X, grp = pop(x))<br class="">
</blockquote>
<br class="">
<br class="">
Best<br class="">
Thibaut<br class="">
<br class="">
--<br class="">
Dr Thibaut Jombart<br class="">
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London<br class="">
Head of RECON: <a href="http://repidemicsconsortium.org" class="">repidemicsconsortium.org</a><br class="">
WHO Consultant - outbreak analysis<br class="">
<a href="http://sites.google.com/site/thibautjombart/" class="">sites.google.com/site/thibautjombart/</a><br class="">
Twitter: @TeebzR<br class="">
+44(0)20 7594 3658<br class="">
<br class="">
<br class="">
On 14 June 2017 at 12:15, Thibaut Jombart <thibautjombart@gmail.com> wrote:<br class="">
<blockquote type="cite" class="">Hello,<br class="">
<br class="">
this should work with the devel version using 'tab' on the genlight<br class="">
object, but I have just seen an issue accessing C functions underlying<br class="">
genlight on most recent R. Investigating. Will post back soon.<br class="">
<br class="">
Best<br class="">
Thibaut<br class="">
<br class="">
--<br class="">
Dr Thibaut Jombart<br class="">
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London<br class="">
Head of RECON: repidemicsconsortium.org<br class="">
WHO Consultant - outbreak analysis<br class="">
sites.google.com/site/thibautjombart/<br class="">
Twitter: @TeebzR<br class="">
+44(0)20 7594 3658<br class="">
<br class="">
<br class="">
On 13 June 2017 at 02:41, Crawford, Douglas L <dcrawford@rsmas.miami.edu> wrote:<br class="">
<blockquote type="cite" class="">Good Afternoon,<br class="">
I cannot get results from “xialdapc”. I apologize for the long list of<br class="">
attempts.<br class="">
In general, I have followed the advice in the "A tutorial for<br class="">
Discriminant Analysis of Principal Components (DAPC) using adegenet 2.0.0”,<br class="">
"https://urldefense.proofpoint.com/v2/url?u=https-3A__grunwaldlab.github.io_Population-5FGenetics-5Fin-5FR_DAPC.html&d=DwIFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=BpG6K2k1Rl1JP8zpH3Kivhq29ZS4KUsaaEDq0PE3O4A&m=xWOBcPJ7sxqTwQME6kgKFJbsiua_iZdhojC_48YZSgY&s=dOvQ0Yp8vrw_M9sTQ29-UpiUtWKZc6K-TIcjx9A_45Y&e=
” and<br class="">
thibautjombart commented on May 9 • edited about Replace NA in genlight<br class="">
file for xvalDapc #168<br class="">
<br class="">
Mydata;<br class="">
Using penlight object:<br class="">
/// GENLIGHT OBJECT /////////<br class="">
<br class="">
// 69 genotypes, 3,243 binary SNPs, size: 487.6 Kb<br class="">
32430 (14.49 %) missing data<br class="">
<br class="">
// Basic content<br class="">
@gen: list of 69 SNPbin<br class="">
@ploidy: ploidy of each individual (range: 2-2)<br class="">
<br class="">
// Optional content<br class="">
@ind.names: 69 individual labels<br class="">
@loc.names: 3243 locus labels<br class="">
@pop: population of each individual (group size range: 4-22)<br class="">
@other: a list containing: sex phenotype pat mat<br class="">
<br class="">
COMMANDS & ERRORS:<br class="">
cmd:<br class="">
xval1 <- xvalDapc(CR_grp, grp, n.pca.max = 65, training.set = 0.9, result =<br class="">
"groupMean", center = TRUE, scale = FALSE, n.pca = NULL, n.rep = 30,<br class="">
xval.plot = TRUE)<br class="">
<br class="">
#error<br class="">
Error in sort.list(y) : 'x' must be atomic for 'sort.list'<br class="">
Have you called 'sort' on a list<br class="">
<br class="">
cmd:<br class="">
grp <- pop(CR_grp)<br class="">
cmd:<br class="">
xval1 <- xvalDapc(dapcCRg, grp, n.pca.max = 65, training.set = 0.9, result =<br class="">
"groupMean", center = TRUE, scale = FALSE, n.pca = NULL, n.rep = 30,<br class="">
xval.plot = TRUE)<br class="">
#error<br class="">
Error in as.data.frame.default(df) : cannot coerce class ""dapc"" to a<br class="">
data.frame<br class="">
<br class="">
Following DAPC tutorial 2.0.0<br class="">
Cmd:<br class="">
mat <- as.matrix(na.replace(CR_grp, method="mean"))<br class="">
# error<br class="">
Error in as.matrix(na.replace(CR_grp, method = "mean")) :<br class="">
error in evaluating the argument 'x' in selecting a method for function<br class="">
'as.matrix': Error: could not find function "na.replace"<br class="">
<br class="">
Following thibautjombart commented on May 9<br class="">
<br class="">
Cmd:<br class="">
mat <- as.matrix(CR_grp, NA.method = "mean")<br class="">
#ok<br class="">
Cmd:<br class="">
grp <- pop(CR_grp)<br class="">
#ok<br class="">
<br class="">
Cmd:<br class="">
xvalg <- xvalDapc(mat, grp, n.pca.max = 300, training.set = 0.9,<br class="">
result = "groupMean", center = TRUE, scale = FALSE,<br class="">
n.pca = NULL, n.rep = 30, xval.plot = TRUE)<br class="">
error:<br class="">
Error in dudi.pca(x, nf = n.pca.max, scannf = FALSE, center = center, :<br class="">
na entries in table<br class="">
<br class="">
<br class="">
Following https://urldefense.proofpoint.com/v2/url?u=https-3A__grunwaldlab.github.io_Population-5FGenetics-5Fin-5FR_DAPC.html&d=DwIFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=BpG6K2k1Rl1JP8zpH3Kivhq29ZS4KUsaaEDq0PE3O4A&m=xWOBcPJ7sxqTwQME6kgKFJbsiua_iZdhojC_48YZSgY&s=dOvQ0Yp8vrw_M9sTQ29-UpiUtWKZc6K-TIcjx9A_45Y&e=
<br class="">
<br class="">
CRgrpx <- xvalDapc(tab(CR_grp, NA.method = "mean"), pop(CR_grp))<br class="">
#Error in (function (classes, fdef, mtable) : unable to find an inherited<br class="">
method for function ‘tab’ for signature ‘"genlight"’<br class="">
CRgrpx <- xvalDapc(CR_grp, pop(CR_grp))<br class="">
#Error in dudi.pca(x, nf = n.pca.max, scannf = FALSE, center = center,: na<br class="">
entries in table<br class="">
<br class="">
Any suggestions would be appreciated.<br class="">
<br class="">
Douglas<br class="">
<br class="">
<br class="">
——************________*********————<br class="">
Douglas L. Crawford<br class="">
Professor, Marine Biology & Ecology<br class="">
Rosenstiel School of Marine & Atmospheric Science<br class="">
University of Miami<br class="">
4600 Rickenbacker Causeway<br class="">
Mami, FL 33149<br class="">
305-421-4121<br class="">
<br class="">
dcrawford@miami.edu<br class="">
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.funhe-2Devol.org_&d=DwIFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=BpG6K2k1Rl1JP8zpH3Kivhq29ZS4KUsaaEDq0PE3O4A&m=xWOBcPJ7sxqTwQME6kgKFJbsiua_iZdhojC_48YZSgY&s=3diONTc_po7Rti6_N2AMH7EI6XBXjunupS_xKoA3s6U&e=
<br class="">
<br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
adegenet-forum mailing list<br class="">
adegenet-forum@lists.r-forge.r-project.org<br class="">
https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.r-2Dforge.r-2Dproject.org_cgi-2Dbin_mailman_listinfo_adegenet-2Dforum&d=DwIFaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=BpG6K2k1Rl1JP8zpH3Kivhq29ZS4KUsaaEDq0PE3O4A&m=xWOBcPJ7sxqTwQME6kgKFJbsiua_iZdhojC_48YZSgY&s=Zb2bb0LD_77THMZ35JjMhQFqNbBXN-KrZV_4J0I4zt0&e=
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