[adegenet-forum] Isolation by distance with adegenet

Serena Baini serenabaini at gmail.com
Sun Nov 24 20:41:33 CET 2019


I'am new to the mailing list. I hope I can find help here. I am trying to
perform Isolation by Distance through mantel.randtest()  from adegenet
package.I am working with this genepop dataset: /// GENPOP OBJECT /////////

 // 1 population; 23 loci; 221 alleles; size: 41 Kb

 // Basic content
   @tab:  1 x 221 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 4-16)
   @loc.fac: locus factor for the 221 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 2-2)
   @type:  codom
   @call: .local(x = x, i = i, j = j, drop = drop)

 // Optional content
   - empty -

The problem is that I can't figure out how to incorporate my lat/long
coordinates ($other$xy) in my dataset as shown in several tutorials. My
coordinates are in a separate file and when I run the test using distances
calculated from such dataset (e.g . dist(xy)) i get the following error: >
> ibd<-mantel.randtest(Dgen,Dgeo)
Error in if (n != attr(m2, "Size")) stop("Non convenient dimension") :
argument is of length zero.

I am wandering whether it is possible to run this test having coordinates
in a different files. I really hope you can hel me. Thanks in advice.

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