R/null.breadth.focal.R

In butterflyology/ordiBreadth: Ordinated Diet Breadth

null.breadth.focal <- function(dat, dist.method = "jaccard", reps = 100){
  res <- vector("list", dim(dat)[1])
for(focal.bug in 1:dim(dat)[1]){
  cat("\n", focal.bug, "of", dim(dat)[1])
  dat.null <- dat[-focal.bug, ]
  temp <- which(apply(dat.null, 2, sum) == 0)
    if(length(temp) != 0){
      dat.null <- dat.null[, -temp]
      focal.bug.m.f <- dat[focal.bug, -temp]
        }else{focal.bug.m.f <- dat[focal.bug, ]}
		#dat.null is the matrix minus the focal species
		#focal.bug.m.f is the focal vector minus unique plants
    ug.scale.factor <- hyp.ordi.breadth(dat.null, grouping = rep(TRUE, dim(dat.null)[2]))
    observed.breadth <- hyp.ordi.breadth(dat.null, grouping = as.numeric(focal.bug.m.f))
    null.breadth.reps <- NA
      for(i in 1:reps){
        null.breadth.reps[i] <- hyp.ordi.breadth(dat.null, grouping = sample(as.numeric(focal.bug.m.f), size = length(focal.bug.m.f)))}
      res[[focal.bug]]$species <- rownames(dat)[focal.bug]
      res[[focal.bug]]$observed.breadth <- observed.breadth
      res[[focal.bug]]$scale.factor <- ug.scale.factor
      res[[focal.bug]]$observed.breadth.scaled <- observed.breadth / ug.scale.factor
      res[[focal.bug]]$totalplantrichness <- sum(dat[focal.bug, ])
      res[[focal.bug]]$modplantrichness <- sum(focal.bug.m.f)
      res[[focal.bug]]$null <- null.breadth.reps
    }
    return(res)
  }