darmitage

############################################################################
#CODE FOR ANALYZING NESTEDNESS OF A COMMUNITY MATRIX & PLOTTING THE RESULTS#
############################################################################

require(vegan)
require(ade4)

#Here, samp_85 is simply a community matrix of my 85% OTU cyano bins. The [5:9] just chooses
#specific rows for analysis (here, a depth gradient).
samp <- samp_85[c(5:9),]

darmitage

#This is code for those plots I made using the MPD and MNTD metrics. You need to organize them into a table such as the one below#

require(ggplot2)
data = read.csv("data.csv", header = TRUE, sep = "")
s <- c("NM1","NM2","NM3", "NM4", "NM5", "Green", "Pink", "Brown", "S1", "S2", "G1", "G2")
data$OTU <- factor(data$OTU)
cyanos = subset(data, group == "cyano")
PSBs = subset(data, group == "PSB")
closts = subset(data, group == "clost")

darmitage

#This code uses a community matrix a'la VEGAN to make a bipartite network of how your taxa are organized into a particular habitat#
#Gets really messy with >100 species#

samp <- samp[c(4,10,1,11,12),]

require(bipartite)

visweb(samp, type="nested", prednames=TRUE, preynames=TRUE, labsize=1,
plotsize=12, square="black", text="no", frame=NULL, textsize=1,
textcol="red", pred.lablength=NULL, prey.lablength = NULL, clear=TRUE,

darmitage

#Example for calculating diversity profiles of Part of the Eectronic Supplementary Material for Leinster, T. & Cobbold C.A. 2011
#"Measuring diversity: the importance of species similarity" #
#URL: www.esajournals.org/doi/abs/10.1890/10-2402.1 #

require(picante)

#assumes you already have a phylogeny (called "phylo") and a community matrix (called "samp")#
#where rows = sites, columns = taxa (the way VEGAN and PICANTE like them).#

samp <- t(samp)

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)

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

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

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

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


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

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