List core taxa across groups

List the indices of all taxa that occur at least min.occ times in each group.

getCoreTaxa(x, groups = c(), min.occ = 1)

Arguments

x	an abundance matrix where rows are taxa and columns samples
groups	group membership vector with as many entries as abundances has samples
min.occ	minimal occurrence to count a taxon as present in each group

Value

indices of core taxa

Examples

abundances=cbind(c(1,2,2),c(0,1,1),c(0,0,3))
rownames(abundances)=c("taxon1","taxon2","taxon3")
rownames(abundances)[getCoreTaxa(abundances,groups=c(1,2,3))]
#> [1] "taxon3"