pairwise.WCfst(genind2hierfstat(x)) and genet.dist(x, method = "WC84") do not yield the same result about hierfstat

[jgx65]

I'm puzzled, it does for me? (see below). Could you provide an example?

> library(hierfstat)
> data(gtrunchier)
> pairwise.WCfst(gtrunchier[,-2])
          1         2         3         4
1        NA 0.4695425 0.4194788 0.4486061
2 0.4695425        NA 0.7795719 0.7648904
3 0.4194788 0.7795719        NA 0.6321912
4 0.4486061 0.7648904 0.6321912        NA
5 0.3356973 0.5994008 0.5688411 0.5199231
6 0.3992087 0.7563057 0.5308519 0.4776794
          5         6
1 0.3356973 0.3992087
2 0.5994008 0.7563057
3 0.5688411 0.5308519
4 0.5199231 0.4776794
5        NA 0.5065197
6 0.5065197        NA

> genet.dist(gtrunchier[,-2],method="WC84")
          1         2         3         4         5
2 0.4695425                                        
3 0.4194788 0.7795719                              
4 0.4486061 0.7648904 0.6321912                    
5 0.3356973 0.5994008 0.5688411 0.5199231          
6 0.3992087 0.7563057 0.5308519 0.4776794 0.5065197

[DaniEstevezBarcia]

do you add the [, -2] to remove the population column?

[DaniEstevezBarcia]

Also, in the genet.dist option I used a genind object. When changed to hierfstat it works, but I thought it also did with genind (it does actually provide a result but it is different)

[jgx65]

gtuncatula contains 2 populations column (hierarchical design), the [,-2] is just to remove one of them. With nancycats, the following give me TRUE:

all.equal(mat2vec(pairwise.WCfst(genind2hierfstat(nancycats))),mat2vec(as.matrix(genet.dist(nancycats,method="WC84"))))

[jgx65]

Note that if you update hierfstat with the current version on github, you won't need the extra genind2hierfstat in pairwise.WCfst (see #56)

[DaniEstevezBarcia]

The new version is not on cran yet right?

Thank you for the answers

[jgx65]

no, on github

[DaniEstevezBarcia]

Ok, the problem was that the version on cran for some reason was doing something odd with the genind (it did not return error though). With the github version it works.