Tracking phylogenetic dependence for bird species

Introduction

In this script, we create random lists of bird species assigned to clusters in order to create a random phylogeny for each cluster and compare these randomly generated phylogenies between clusters.

Packages

library(methClust)
library(CountClust)
library(rasterVis)
library(gtools)
library(sp)
library(rgdal)
library(ggplot2)
library(maps)
library(mapdata)
library(mapplots)
library(scales)
library(ggthemes)

Load the data

Wallacea Region data

datalist <- get(load("../data/wallace_region_pres_ab_breeding_with_seabirds.rda"))
latlong <- datalist$loc
data <- datalist$dat
if(nrow(latlong) != nrow(data)) stop("dimensions matching error")

topics_clust <- get(load("../output/methClust_wallacea_w_seabirds.rda"))

K = 2

topics <- topics_clust[[2]]
freq <- topics$freq
order1 <- order(freq[,1] - freq[,2], decreasing = TRUE)[1:250]
order2 <- order(freq[,2] - freq[,1], decreasing = TRUE)[1:250]
rand_freq <- freq[union(order1, order2), ]
rand_freq_norm <- t(apply(rand_freq, 1, function(x) return(x/sum(x))))

ll <- list()
for(m in 1:1000){
  blocks <- apply(rand_freq_norm, 1, function(x) {
  if(runif(1, 0, 1) < x[1]) {return (1)}
  else {return(2)}
  })
  ll[[m]] <- list()
  ll[[m]][[1]] <- names(blocks)[which(blocks == 1)]
  ll[[m]][[2]] <- names(blocks)[which(blocks == 2)]
}

save(ll, file = "../output/bird_lists_for_phylogeny_clusters_2_wallacea.rda")