[adegenet-forum] adegenet - a.score.opt vs. xvalDAPC

Wed Jun 14 14:52:07 CEST 2017

Well, thanks for the feedback, and apologies on this one: tutorials
are slightly outdated. Will recompile them today.

Best

Thibayt

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

On 14 June 2017 at 13:27, Crawford, Douglas L <dcrawford at rsmas.miami.edu> wrote:
> Thank you.
>
> I have said it before and will say it again:  your efforts are very much
> appreciated by many.
>
> dlc
>
>
> On Jun 14, 2017, at 7:47 AM, Thibaut Jombart <thibautjombart at gmail.com>
> wrote:
>
> Hi again,
>
> OK, so it looks like there was a problem with C routine registration,
> following some new policies enforced by CRAN, which could have created
> issue with genlight objects. Not related to your problem, but
> basically you wouldn't have been able to use genlight objects in the
> first place. This is fixed in the devel now.
>
> As for youR problem, after installing the devel version of adegenet,
> things should work simply with 'tab'. Here's a toy example:
>
> dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e3, prob=c(.5, .49, .01),
> replace=TRUE))
> x <- new("genlight", dat, pop = rep(1:2, each = 25))
> x
>
> /// GENLIGHT OBJECT /////////
>
> // 50 genotypes,  1,000 binary SNPs, size: 76.5 Kb
> 530 (1.06 %) missing data
>
> // Basic content
>   @gen: list of 50 SNPbin
>
> // Optional content
>   @pop: population of each individual (group size range: 25-25)
>   @other: a list containing: elements without names
>
> X <- tab(x, NA.method = "mean")
> xval1 <- xvalDapc(X, grp = pop(x))
>
>
>
> Best
> Thibaut
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
> London
> Head of RECON: repidemicsconsortium.org
> WHO Consultant - outbreak analysis
> sites.google.com/site/thibautjombart/
> Twitter: @TeebzR
> +44(0)20 7594 3658
>
>
> On 14 June 2017 at 12:15, Thibaut Jombart <thibautjombart at gmail.com> wrote:
>
> Hello,
>
> this should work with the devel version using 'tab' on the genlight
> object, but I have just seen an issue accessing C functions underlying
> genlight on most recent R. Investigating. Will post back soon.
>
> Best
> Thibaut
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
> London
> Head of RECON: repidemicsconsortium.org
> WHO Consultant - outbreak analysis
> sites.google.com/site/thibautjombart/
> Twitter: @TeebzR
> +44(0)20 7594 3658
>
>
> On 13 June 2017 at 02:41, Crawford, Douglas L <dcrawford at rsmas.miami.edu>
> wrote:
>
> Good Afternoon,
>    I cannot get results from “xialdapc”.   I apologize for the long list of
> attempts.
> In general,    I have followed the advice in the "A tutorial for
> Discriminant Analysis of Principal Components (DAPC) using adegenet 2.0.0”,
> "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
>
> thibautjombart commented on May 9 • edited  about Replace NA in genlight
> file for xvalDapc #168
>
> Mydata;
> Using penlight object:
> /// GENLIGHT OBJECT /////////
>
> // 69 genotypes,  3,243 binary SNPs, size: 487.6 Kb
> 32430 (14.49 %) missing data
>
> // Basic content
>   @gen: list of 69 SNPbin
>   @ploidy: ploidy of each individual  (range: 2-2)
>
> // Optional content
>   @ind.names:  69 individual labels
>   @loc.names:  3243 locus labels
>   @pop: population of each individual (group size range: 4-22)
>   @other: a list containing: sex  phenotype  pat  mat
>
> COMMANDS & ERRORS:
> cmd:
> xval1 <- xvalDapc(CR_grp, grp, n.pca.max = 65, training.set = 0.9, result =
> "groupMean", center = TRUE, scale = FALSE, n.pca = NULL, n.rep = 30,
> xval.plot = TRUE)
>
> #error
> Error in sort.list(y) : 'x' must be atomic for 'sort.list'
> Have you called 'sort' on a list
>
> cmd:
> grp <- pop(CR_grp)
> cmd:
> xval1 <- xvalDapc(dapcCRg, grp, n.pca.max = 65, training.set = 0.9, result =
> "groupMean", center = TRUE, scale = FALSE, n.pca = NULL, n.rep = 30,
> xval.plot = TRUE)
> #error
> Error in as.data.frame.default(df) : cannot coerce class ""dapc"" to a
> data.frame
>
> Following DAPC tutorial 2.0.0
> Cmd:
> mat <- as.matrix(na.replace(CR_grp, method="mean"))
> # error
> Error in as.matrix(na.replace(CR_grp, method = "mean")) :
>  error in evaluating the argument 'x' in selecting a method for function
> 'as.matrix': Error: could not find function "na.replace"
>
> Following thibautjombart commented on May 9
>
> Cmd:
> mat <- as.matrix(CR_grp, NA.method = "mean")
> #ok
> Cmd:
> grp <- pop(CR_grp)
> #ok
>
> Cmd:
> xvalg <- xvalDapc(mat, grp, n.pca.max = 300, training.set = 0.9,
>                 result = "groupMean", center = TRUE, scale = FALSE,
>                 n.pca = NULL, n.rep = 30, xval.plot = TRUE)
> error:
> Error in dudi.pca(x, nf = n.pca.max, scannf = FALSE, center = center,  :
>  na entries in table
>
>
> 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=
>
> CRgrpx <- xvalDapc(tab(CR_grp, NA.method = "mean"), pop(CR_grp))
> #Error in (function (classes, fdef, mtable) : unable to find an inherited
> method for function ‘tab’ for signature ‘"genlight"’
> CRgrpx <- xvalDapc(CR_grp, pop(CR_grp))
> #Error in dudi.pca(x, nf = n.pca.max, scannf = FALSE, center = center,: na
> entries in table
>
> Any suggestions would be appreciated.
>
> Douglas
>
>
> ——************________*********————
> Douglas L. Crawford
> Professor, Marine Biology & Ecology
> Rosenstiel School of Marine & Atmospheric Science
> University of Miami
> 4600 Rickenbacker Causeway
> Mami, FL 33149
> 305-421-4121
>
> dcrawford at miami.edu
> 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=
>
>
>
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