R/null.breadth.R

In butterflyology/ordiBreadth: Ordinated Diet Breadth

null.breadth <- function(dat, dist.method = "jaccard", rep = 100, quantiles = c(0.025, 0.975), scaled = FALSE){
  hstrich <- sort(unique(apply(dat, 1, sum)))
  nulls <- array(dim = c(length(hstrich), rep))
  for(i in 1:length(hstrich)){
    tosamp<-rep(0, dim(dat)[2]); tosamp[1:hstrich[i]] <- 1
    cat("\n", i, "of", length(hstrich))
    for(j in 1:rep){
      nulls[i, j] <- hyp.ordi.breadth(dat, sample(tosamp, size = length(tosamp)))
        }
      }
      cat("\n")
      u.q <- NA
      l.q <- NA
      for(i in 1:dim(nulls)[1]){
        u.q[i] <- quantile(nulls[i, ], quantiles[2])
        l.q[i] <- quantile(nulls[i, ], quantiles[1])
      }
        if(scaled == TRUE){
          ug <- hyp.ordi.breadth(dat, rep(1, length(tosamp)), dist.method = dist.method)
          u.q <- u.q / ug; l.q <- l.q / ug
          }
      richness<-hstrich
      res<-cbind(richness, l.q, u.q)
      return(res)
    }