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EricArcher / strataG

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
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Error with genind2gtypes 'no ids in 'schemes' are in 'gen.data' or 'ind.names'' #46

Closed ksil91 closed 3 years ago

ksil91 commented 3 years ago

I was converting a genind to a gtype and got this error: 

Error: no ids in 'schemes' are in 'gen.data' or 'ind.names'
Traceback:

1. genind2gtypes(cp)
2. df2gtypes(x = gen.mat, ploidy = x@ploidy[1], id.col = NULL, strata.col = if (has.pop) 1 else NULL, 
 .     loc.col = if (has.pop) 2 else 1, schemes = x@strata, other = list(genind = adegenet::other(x)))
3. methods::new("gtypes", gen.data = gen.data, ploidy = ploidy, 
 .     ind.names = ind.names, strata = strata, schemes = schemes, 
 .     sequences = sequences, description = description, other = if (is.null(other)) list() else other)
4. initialize(value, ...)
5. initialize(value, ...)
6. .local(.Object, ...)
7. stop("no ids in 'schemes' are in 'gen.data' or 'ind.names'", 
 .     call. = FALSE)

These are the parameters of my genind object: 

/// GENIND OBJECT /////////

 // 605 individuals; 2,809 loci; 5,618 alleles; size: 14.6 Mb

 // Basic content
   @tab:  605 x 5618 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 2-2)
   @loc.fac: locus factor for the 5618 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 2-2)
   @type:  codom
   @call: repool(c(D, N, F, DFf1, DFf2, DFf1xD, DFf1xF, DFf1DxD, DFf1FxF, 
    DFf1xN, DNf1, DNf2, DNf1xD, DNf1DxD, DNf1xN, DNf1NxN, DNf1xF, 
    DNf1FxF, FNf1, FNf2, FNf1xF, FNf1FxF, FNf1xN, FNf1NxN, FNf1NNxN, 
    FNf1xD, FNf1DxD))

 // Optional content
   @pop: population of each individual (group size range: 20-40)
   @strata: a data frame with 2 columns ( INDIVIDUALS, POP_ID )

It seems like genind2gtype is setting the schemes parameter as as strata(genind), so it is getting an error because my strata(genind) columns have a different name than 'id' as required by schemes. I was able to avoid the error by changing the column name:
colnames(strata(sim.gind)) <- c("id","POP_ID")

EricArcher commented 3 years ago

Thanks for the heads up on this. I am wrapping up some bug fixes and major updates to strataG this month and will make sure this issue is addressed in that.