R/hyp.ordi.breadth.R

In butterflyology/ordiBreadth: Ordinated Diet Breadth

hyp.ordi.breadth <- function(dat, grouping, dist.method = "jaccard", distance = FALSE){
  type="centroid"
  if(is.numeric(grouping) == TRUE){
    grouping[grouping == 0] <- FALSE
    grouping[grouping == 1] <- TRUE
      }
    dat.by.host <- t(dat)
    dismatrix <- vegdist(dat.by.host, method = dist.method, binary = TRUE)
    tempdisper <- betadisperF(dismatrix, group = grouping, type = type)
    tot.breadth <- sum(tempdisper$distances[which(grouping == TRUE)])
    if(dim(tempdisper$centroids)[1] == 1){rownames(tempdisper$centroids) = TRUE}
    if(distance == FALSE){return(tot.breadth)}else{return(list(tot.breadth = tot.breadth, distances = tempdisper$distances[which(grouping == "TRUE")], centroid = tempdisper$centroids[which(rownames(tempdisper$centroids) == TRUE), ]))}
  }