inst/extdata/scripts/impute_make_suit_layer.R

In stranda/holoSimCell: Linked demographic/genetic simulation

### imputed, popmap (individualID->pop mapping), pts (sample locations) and ashpred
### are now built into holoSimCell
### as built in dataframes (in data/ directory)

rownames(popmap) <- popmap[,1]
table(popmap[gsub("fp","",names(imputed)),2])
imputed.pruned=imputed[,-which(gsub("fp","",names(imputed))%in%popmap[popmap$abbrev=="Michigan","id"])]
imputed.pruned=imputed.pruned[,-which(gsub("fp","",names(imputed.pruned))%in%popmap[popmap$abbrev=="UNK","id"])]
imputed.pruned=imputed.pruned[,-which(gsub("fp","",names(imputed.pruned))%in%popmap[popmap$abbrev=="MO1","id"])]
imputed.pruned=imputed.pruned[,-which(gsub("fp","",names(imputed.pruned))%in%popmap[popmap$abbrev=="ON1","id"])]
imputed.pruned=imputed.pruned[,-which(gsub("fp","",names(imputed.pruned))%in%popmap[popmap$abbrev=="VA1","id"])]
imputed.pruned=imputed.pruned[,-which(gsub("fp","",names(imputed.pruned))%in%popmap[popmap$abbrev=="MB1","id"])]
removes <- c()
popids <- popmap[gsub("fp","",names(imputed.pruned)),2]
table(popids)
for (a in unique(popids))
{
    if (sum(popids==a)>14)
    {
        removes <- c(removes,sample(which(popids==a),1))
    }
}
imputed.pruned <- imputed.pruned[,-1*removes]

poptbl <- table(popmap[gsub("fp","",names(imputed.pruned)),2])

samppts <- pts[pts$abbrev %in% names(poptbl),]