R/create.matrix.R

In fossil: Palaeoecological and Palaeogeographical Analysis Tools

`create.matrix` <-
function(x, tax.name="genus", locality="locality", time.col=NULL, time=NULL, abund=FALSE, abund.col="abundance")
{
if (is.null(time.col)==FALSE & is.null(time)==FALSE) x<-x[which(x[,time.col]==time),]
a <- tax.name
nr <- length(levels(as.factor(x[,a])))
rn <- levels(as.factor(x[,a]))
z <- locality
cn <- levels(as.factor(x[,z]))
nc <- length(cn)
nm<-matrix(0,nr,nc,dimnames=list(rn,cn))
for (i in 1:length(x[,1])) {
  m<-as.character(x[i,a])
  n<-as.character(x[i,z])
  if (is.na(m)==TRUE | is.null(m)==TRUE | is.na(n)==TRUE | is.null(n)==TRUE) next (i)
  if (m=='' | m==' ' | n=='' | n==' ') next (i)
  if (abund==TRUE) nm[m,n]<-nm[m,n]+x[i,abund.col]
  else nm[m,n]<-1
  }
fm<-nm[rowSums(nm)>0,]
return(fm)
}