From goatsrunfaster at gmail.com  Fri Jun  9 14:03:45 2017
From: goatsrunfaster at gmail.com (Spencer Bruce)
Date: Fri, 9 Jun 2017 08:03:45 -0400
Subject: [adegenet-forum] Dictating group membership for DAPC plot
Message-ID: <CAGjKGeaa-hrXFNV+eJ8T59H3mOZsQr7iR3N-EL3UzHY69SMWGg@mail.gmail.com>

Good Morning,

I'm interested in creating a DAPC scatter plot for some hatchery fish
populations where several of the populations are known F1 hybrids. When I
go through the process of defining the clusters these admixed F1
individuals are sometimes assigned to their own cluster, but some
individuals are often assigned to either of the two parental clusters. That
being said, is there a way to dictate what clusters individuals are
assigned to based on prior knowledge of their origin, rather than depending
on the inferred grouping?

Any help is greatly appreciated.

Best,
Spencer

-- 
Spencer A Bruce
113 Hill St.
Troy, NY 12180
518 225 0787
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From thibautjombart at gmail.com  Mon Jun 12 13:00:14 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Mon, 12 Jun 2017 12:00:14 +0100
Subject: [adegenet-forum] Dictating group membership for DAPC plot
In-Reply-To: <CAGjKGeaa-hrXFNV+eJ8T59H3mOZsQr7iR3N-EL3UzHY69SMWGg@mail.gmail.com>
References: <CAGjKGeaa-hrXFNV+eJ8T59H3mOZsQr7iR3N-EL3UzHY69SMWGg@mail.gmail.com>
Message-ID: <CANPRA+oSGfw2Tv3DkhYsgtsTS4HS-Xs7W92ho1h3VWx-hKxr1g@mail.gmail.com>

Hi there,

changing the group membership for dapc scatterplot has been discussed
repeatedly on this forum, and is documented in ?scatter.dapc - see
argument 'grp'.

For identifying hybrids, the new method 'genclust' will be much more
appropriate - in the devel version for now, paper under review. As a
rule I don't think DAPC is appropriate at identifying hybrids. In
fact, models which classify individuals in parental populations will
most likely assign F1 fully to one of the parental populations (based
on geometric criteria or likelihood approaches).

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 9 June 2017 at 13:03, Spencer Bruce <goatsrunfaster at gmail.com> wrote:
> Good Morning,
>
> I'm interested in creating a DAPC scatter plot for some hatchery fish
> populations where several of the populations are known F1 hybrids. When I go
> through the process of defining the clusters these admixed F1 individuals
> are sometimes assigned to their own cluster, but some individuals are often
> assigned to either of the two parental clusters. That being said, is there a
> way to dictate what clusters individuals are assigned to based on prior
> knowledge of their origin, rather than depending on the inferred grouping?
>
> Any help is greatly appreciated.
>
> Best,
> Spencer
>
> --
> Spencer A Bruce
> 113 Hill St.
> Troy, NY 12180
> 518 225 0787
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

From dcrawford at rsmas.miami.edu  Tue Jun 13 03:41:57 2017
From: dcrawford at rsmas.miami.edu (Crawford, Douglas L)
Date: Tue, 13 Jun 2017 01:41:57 +0000
Subject: [adegenet-forum] adegenet - a.score.opt vs. xvalDAPC
Message-ID: <5EFBAF16-A696-4DE7-8AF6-C63DE8C581DE@miami.edu>

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://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html? 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://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html<http://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html>

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<mailto:dcrawford at miami.edu>
http://www.funhe-evol.org/


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From thibautjombart at gmail.com  Wed Jun 14 13:15:15 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Wed, 14 Jun 2017 12:15:15 +0100
Subject: [adegenet-forum] adegenet - a.score.opt vs. xvalDAPC
In-Reply-To: <5EFBAF16-A696-4DE7-8AF6-C63DE8C581DE@miami.edu>
References: <5EFBAF16-A696-4DE7-8AF6-C63DE8C581DE@miami.edu>
Message-ID: <CANPRA+pEY4FUyjjbdoCsNoEaD_9f+8Gckw_G6Pn9msv02QJRTQ@mail.gmail.com>

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://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html? 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://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html
>
> 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
> http://www.funhe-evol.org/
>
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

From thibautjombart at gmail.com  Wed Jun 14 13:47:32 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Wed, 14 Jun 2017 12:47:32 +0100
Subject: [adegenet-forum] adegenet - a.score.opt vs. xvalDAPC
In-Reply-To: <CANPRA+pEY4FUyjjbdoCsNoEaD_9f+8Gckw_G6Pn9msv02QJRTQ@mail.gmail.com>
References: <5EFBAF16-A696-4DE7-8AF6-C63DE8C581DE@miami.edu>
 <CANPRA+pEY4FUyjjbdoCsNoEaD_9f+8Gckw_G6Pn9msv02QJRTQ@mail.gmail.com>
Message-ID: <CANPRA+p3DnzcFN5bsr8MrOkqy=9GYixekJ_2AfA028LvG7VGvA@mail.gmail.com>

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://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html? 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://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html
>>
>> 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
>> http://www.funhe-evol.org/
>>
>>
>>
>> _______________________________________________
>> adegenet-forum mailing list
>> adegenet-forum at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

From dcrawford at rsmas.miami.edu  Wed Jun 14 14:27:14 2017
From: dcrawford at rsmas.miami.edu (Crawford, Douglas L)
Date: Wed, 14 Jun 2017 12:27:14 +0000
Subject: [adegenet-forum] adegenet - a.score.opt vs. xvalDAPC
In-Reply-To: <CANPRA+p3DnzcFN5bsr8MrOkqy=9GYixekJ_2AfA028LvG7VGvA@mail.gmail.com>
References: <5EFBAF16-A696-4DE7-8AF6-C63DE8C581DE@miami.edu>
 <CANPRA+pEY4FUyjjbdoCsNoEaD_9f+8Gckw_G6Pn9msv02QJRTQ@mail.gmail.com>
 <CANPRA+p3DnzcFN5bsr8MrOkqy=9GYixekJ_2AfA028LvG7VGvA@mail.gmail.com>
Message-ID: <8532F1A9-12AF-4FD0-8726-0932B91A9426@miami.edu>

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<mailto: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<http://repidemicsconsortium.org>
WHO Consultant - outbreak analysis
sites.google.com/site/thibautjombart/<http://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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From thibautjombart at gmail.com  Wed Jun 14 14:52:07 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Wed, 14 Jun 2017 13:52:07 +0100
Subject: [adegenet-forum] adegenet - a.score.opt vs. xvalDAPC
In-Reply-To: <8532F1A9-12AF-4FD0-8726-0932B91A9426@miami.edu>
References: <5EFBAF16-A696-4DE7-8AF6-C63DE8C581DE@miami.edu>
 <CANPRA+pEY4FUyjjbdoCsNoEaD_9f+8Gckw_G6Pn9msv02QJRTQ@mail.gmail.com>
 <CANPRA+p3DnzcFN5bsr8MrOkqy=9GYixekJ_2AfA028LvG7VGvA@mail.gmail.com>
 <8532F1A9-12AF-4FD0-8726-0932B91A9426@miami.edu>
Message-ID: <CANPRA+qLCp7sGsTMPg+pFoD8_GV=eEP5q-Dg1m1ed4GhACt+0g@mail.gmail.com>

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=
>
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> 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=
>
>

From stephanie.coster at gmail.com  Thu Jun 29 23:20:55 2017
From: stephanie.coster at gmail.com (Stephanie Coster)
Date: Thu, 29 Jun 2017 17:20:55 -0400
Subject: [adegenet-forum] When cross-validating DAPC (using web server),
 is it best to use 'group' or 'overall'?
Message-ID: <CAMeeibaeHjMTe1k+bA5CE41XxhwcwRSWmG_pHz9CgDh4ccK+Zw@mail.gmail.com>

Thanks in advance!

I have a dataset of genotypes from microsatellite loci and I'm looking to
analyze population structure. Program STRUCTURE shows essentially no
clusters, and I'd like to use DAPC to get another perspective.

I've run the 'find.clusters' code and the BIC suggests K=2, but the
assignments are unreliable (equal assignments across all sites to both
clusters). I am interpreting this to mean that K=1 and all samples likely
form a single cluster.

Now, I'd like to use my apriori site groupings to draw a scatterplot and am
using the DAPC web server to cross-validate and suggest the number of PCs
to retain. I get notably different scatterplots depending on whether I
choose 'group' or 'overall' to assess. The sites have more spatial
differentiation when using 'group', and essentially all overlap when using
'overall'. I understand that success is calculated by my groups or overall
depending on the choice, but what does this mean in application? Can
someone help explain why these plots differ and which is better to use?

Many thanks!

Stephanie
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From jean-luc.legras at inra.fr  Fri Jun  9 17:08:23 2017
From: jean-luc.legras at inra.fr (Jean-Luc Legras)
Date: Fri, 09 Jun 2017 15:08:23 -0000
Subject: [adegenet-forum] Varimax
Message-ID: <9DA8692B-B1B4-43FD-B568-C961F263308C@inra.fr>

Hi all

Adegenet is a fantastic tool for population genetic analysis.
 I used a  PCA on my dataset and populations are clearly clustered. However, in this case  they do not fit with the axis.  I was wondering if it was possible to setup a Varimax procedure after the PCA  (here centered, unscaled PCA) in order to make the main population dispersal fit the axis...


Best regards.

JL


scatter plot;

[cid:D9361326-297A-4A22-9067-F601280ED06C at supagro.inra.fr]
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