Beta div using binary distance?

[d-callan]

From microbiomeComputations created by asizemore: VEuPathDB/microbiomeComputations#30

For bray and jaccard we use dist <- try(vegan::vegdist(df[, -..allIdColumns], method=method, binary=TRUE)) but the shiny apps used phyloseq (which wrapped vegdist) and in their method had binary=F.

Either let's remind ourselves why we changed to binary (so just assuming presence/absence) or change the params to use binary=F.