Nothing
filter.p <-
function(x,rare=TRUE,presen=1,persist=0.05)
{
{
if(rare==TRUE){
filter<-matrix(nrow=ncol(x),ncol=3,
dimnames=list(colnames(x),
c("n","n over minimum presence","quality")))
ifelse(x>0,1,0)->pres.abs
apply(pres.abs,2,sum)->filter[,1]
ifelse(x>presen,1,0)->presence
apply(presence,2,sum)->persistence
persistence->filter[,2]
a<-as.integer(persist*nrow(x))
ifelse(filter[,2]>=a,1,0)->filter[,3]
which(as.matrix(persistence)>=a)->filter1
x[,filter1]->filtered
matrix(nrow=3,ncol=1,dimnames=list(c("%","minimum n",
"# taxa"),"value"))->result
result[1,]<-presen
result[2,]<-a
result[3,]<-ncol(filtered)
}
else{
ifelse(x>0,1,0)->pres.abs
apply(pres.abs,2,sum)->filter1
a<-as.integer(persist*nrow(x))
names(which(filter1<=a))->filter2
x[,filter2]->filtered
matrix(nrow=2,ncol=1,dimnames=list(c("maximum n",
"#taxa"),"value"))->result
result[1,]<-a
result[2,]<-ncol(filtered)
}
}
if(rare==TRUE){
results<-list(filtered,filter,result)
names(results)<-c("filtered","filter","result")
return(results)
}
else{
results<-list(filtered,result)
names(results)<-c("filtered","result")
return(results)
}
}
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