[adegenet-forum] xvalDapc, help for arguments "x" and "grp"

[Roman Luštrik]

Hi Maïlis, 

in xvalDapc `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 

xvalDapc(tab(dapc1), grp = grp$grp) 

I omitted `x =` which is personal preference of always omitting first argument in a function call. 
Let us know if this works. 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 

----- Original Message -----

From: "Maïlis" <mailis at kwata.net> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, January 26, 2016 12:01:31 PM 
Subject: [adegenet-forum] xvalDapc, help for arguments "x" and "grp" 

Hello, 

I am contacting you because I use the DAPC fonction of adegenet package without encountering any particular problems. However , I would like to use the cross validation, and that 's when it no longer works.. 

> database<-read.table(file.choose("C:/Users/.../XXX.txt"), header=TRUE, sep=",",na.strings="-9") 
> x<- df2genind(data.frame(database), sep="/", ncode=3, p=NULL, NA.char="-9", ploidy=2, type=c("codom"),strata=NULL, hierarchy=NULL) 
/// GENIND OBJECT ///////// 

// 341 individuals; 7 loci; 164 alleles; size: 264.9 Kb 

// Basic content 
@tab: 341 x 164 matrix of allele counts 
@loc.n.all: number of alleles per locus (range: 13-30) 
@loc.fac: locus factor for the 164 columns of @tab 
@all.names: list of allele names for each locus 
@ploidy: ploidy of each individual (range: 2-2) 
@type: codom 
@call: df2genind(X = data.frame(database), sep = "/", ncode = 3, pop = NULL, 
NA.char = "-9", ploidy = 2, type = c("codom"), strata = NULL, 
hierarchy = NULL) 

// Optional content 
- empty - 
Warning message: 
In df2genind(data.frame(database), sep = "/", ncode = 3, p = NULL, : 
duplicate labels detected for some individuals; using generic labels 

> grp<-find.clusters(x, max.n.clust=9) 
Choose the number PCs to retain (>=1): 140 
Choose the number of clusters (>=2): 6 
> dapc1<-dapc(x,grp$grp) 
Choose the number PCs to retain (>=1): 40 
Choose the number discriminant functions to retain (>=1): 5 

It works but, for using xvalDapc 
I don't know what to choose as an argument for " x" and " grp ". I tried severals things but that didn't work. 
Can you advise me on the arguments to use? 


Thank you in advance for your reply, 

Best regards, 

Maïlis 

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