darmitage

require(AICcmodavg)
require(mgcv)
require(boot)
require(car)
require(MASS)
require(repmis)
require(pscl)

#Read in data from my public dropbox folder
dropURL <- "https://dl.dropboxusercontent.com/u/26280366/Papers/EcoLetts/AreaNrgPseudoFinal.csv"

darmitage

require(kernlab)
require(caret)
require(e1071)
require(nnet)
require(randomForest)

set.seed(34873458)

#Open call library (needs name (eg. MYLU), and parameters)
setwd = ("Dropbox/Anabat files/Dave's Florida Bat Calls/")

darmitage

require(picante)
require(gtools)
require(reshape)




###########################################################
### For calculation of Naiive (Z = I)  diversity profiles ###
###########################################################

darmitage

phy = read.tree("mytree.tre")
samp = read.table("OTUtable.txt", head = T, sep = "")

#lists taxa in OTU table that are not in the phylogeny, and removes them
samp = (samp[rowSums(samp) != 0, , drop=FALSE])
samp = t(samp)
phy = prune.sample(samp, phy)
labs <- phy$tip.label
length(labs)
ncol(samp)

darmitage

require(picante)
require(gtools)
require(reshape)


###########################################################
###              Utility functions                      ###
###########################################################

internal2tips.self = function (phy, int.node){

darmitage

############Here's a function that calculates Hill number diversity using a phylogeny from the Leinster and Cobbold (2012) paper

#Requires a phylogeny with tip labels and a community matrix (rows = samples, columns = species)
Phylo.Z <- function(phy,samp){

#packages required for this to work:
  require(reshape)
  require(picante)
  require(ape)
  require(gtools)

darmitage

require(reshape)
require(picante)
require(gtools)

#Function that lists all terminal tip labels descended from ancestral node
internal2tips.self = function (phy, int.node){
  #require(picante); require(ape)
  Ntaxa = length(phy$tip.label)
  Nnode = phy$Nnode
  if ((Ntaxa + Nnode - 1) != nrow(phy$edge)) {

darmitage

nodes2root <-
  function(phy,int.node) {
    Ntaxa = length(phy$tip.label) + phy$Nnode
    Nnode = phy$Nnode
    tips = c()
    nodes = int.node
    repeat {
      nodes = phy$edge[which(phy$edge[,2]%in%nodes),1]
      if (length(nodes)==0) break
      tips = c(tips,nodes)

darmitage

#Code to collapse a phylogeny by a tree's support values, when nodes have support value names
#tree = phylogenetic tree, cutoff = support value cutoff (can be changed or made into a vector)

require(ape)
h <- which(tree$node.label < cutoff)
nodes <- matrix(h + Ntip(tree))
nodes <- nodes[-1]
k <- matrix(tree$edge[,2])

j <- matrix(nrow = length(i), ncol = 1)

darmitage

require(picante)

#function that maps dissimilarity to similarity & scales between 0 and 1
range01 <- function(x){exp((-1/max(x))*x)}

#Calculate branch lengths bewteen taxa
dist <- cophenetic(tree)

#calculate similarity between taxa from 0 to 1
Z <- range01(dist)