I also get this warning message when a taxon is listed twice because there is MNI and NISP data. The result is the count number is the NISP + MNI for that taxon.

Okay, I think that this might be a bit more complicated to resolve, because it means we need to rethink the way the taxa are represented in the count objects. For your purposes are NISP and MNI both 'Presence'? If so then you could just write a short function:

set_to_one <- function(x){
  x$counts[x$counts > 1] <- 1
  x
}

and then lapply on a download_list object.

It's not the prettiest solution but I think it ought to work. Would columns Martes nobilis_NISP and Martes_nobilis_MNI work? I'm not in love with it, but I'd need to think a bit more about how to make the taxon_list interact with the actual count table.

For our purposes right now, we can treat NISP and MNI as presences so I can use a function to convert them but in the future it will be better to keep the original NISP and MNI information. Having two columns or two rows for taxa with NISP and MNI would work. Or an additional column that indicates if the count is an NISP or MNI, although I don't know how much of a pain this is. Thanks for your help.