R/ordi.focal.drop.R

In butterflyology/ordiBreadth: Ordinated Diet Breadth

ordi.focal.drop <- function(dat,dist.method="jaccard"){
  res <- list()
  type.c = "centroid"
  res <- vector("list", dim(dat)[1])
  spnames <- rownames(dat)
  ODB <- ordi.breadth(dat, dist.method = dist.method)
  for(i in 1:length(spnames)){
    res[[i]]$species <- spnames[i]
    res[[i]]$ODB <- ODB$tot.breadth[i]
    res[[i]]$ODB.scaled <- ODB$scaled.breadth[i]
	}

  for(focal.bug in 1:length(spnames)){
    cat("\n", focal.bug, "of", length(spnames))
  dat.m.f <- dat[-focal.bug, ]
  temp <- which(apply(dat.m.f, 2, sum) == 0)
  if(length(temp) != 0){
    dat.m.f <- dat.m.f[, -temp]
    focal.bug.m.f <- dat[focal.bug, -temp]
      }else{focal.bug.m.f <- dat[focal.bug, ]}
  specialization.m.f <- ordi.breadth(dat.m.f, dist.method = dist.method)

  temp <- hyp.group.dist.m.f(dat.m.f, grouping = as.numeric(focal.bug.m.f), distances = TRUE)
  focal.breadth <- temp$distances.all
  total.breadth <- temp$tot.breath
#		cols<-rep(col[1],length(focal.breadth))
#		cols[which(focal.bug.m.f==1)]<-col[2]
      specdist <- focal.breadth#[which(focal.bug.m.f==1)]
#				cols<-cols[order(specdist)]
        specdisto <- specdist[order(specdist)]

  scale.factor <- hyp.group.dist.m.f(dat.m.f, grouping = rep("YES", dim(dat.m.f)[2]))

  res[[focal.bug]]$focal.distances <- specdisto
#	res[[focal.bug]]$cols<-cols
  res[[focal.bug]]$focal.breadth <- total.breadth
  res[[focal.bug]]$focal.scale.factor <- scale.factor
  res[[focal.bug]]$focal.scaled.breadth <- total.breadth / scale.factor
        }
  return(res)
      }