#Example of diversity decomposition using the dataset "phylocom" (R-package picante) #Librairies library(picante) library(ade4) library(geiger) #Data preparation data(phylocom) spxp <- phylocom$sample phy <- phylocom$phylo is.missing<- !(phy$tip.label %in% colnames(spxp)) phy <- drop.tip(phy, phy$tip.label[is.missing]) spxp <- spxp[, phy$tip.label] #Functions source("abgFunctions.R") #Parametrization of the similarity effect for delta = 0.5 phy0.5 <- rescale(phy, model = "delta", 0.5) #Taxonomic alpha, beta, gamma decomposition abgDecompQ(spxp, Z = NULL, q = 0) abgDecompQ(spxp, Z = NULL, q = 1) abgDecompQ(spxp, Z = NULL, q = 2) abgDecompQ(spxp, Z = NULL, q = Inf) #alpha, beta, gamma decomposition using Leinster & Cobbold 2012 dis <- cophenetic(phy0.5) Z <- 1 - dis/max(dis) abgDecompQ(spxp, Z, q = 0) abgDecompQ(spxp, Z, q = 1) abgDecompQ(spxp, Z, q = 2) abgDecompQ(spxp, Z, q = Inf) #alpha beta gamma decomposition using Chao et al. 2010 chao.objs <- chaoObjects(spxp, phy0.5) abgDecompQ(chao.objs$pi, chao.objs$Z, q = 0) abgDecompQ(chao.objs$pi, chao.objs$Z, q = 1) abgDecompQ(chao.objs$pi, chao.objs$Z, q = 2) abgDecompQ(chao.objs$pi, chao.objs$Z, q = Inf) # Pairwise beta-diversity (minus 1) between sites using Leinster & Cobbold 2012 beta.dis <- BetaDisQ(spxp, Z, q = 1) scatter(dudi.pco(as.dist(beta.dis), scannf = F)) #Visualisation of the pairwise beta-diversity pattern # Pairwise beta-diversity (minus 1) between sites using Chao and al. 2010 beta.dis <- BetaDisQ(chao.objs$pi, chao.objs$Z, q = 1) scatter(dudi.pco(as.dist(beta.dis), scannf = F))#Visualisation of the pairwise beta-diversity pattern