Schefferville - transitions; Beta diversity and phylogenetic beta diversity within and between clusters

Tammy L. Elliott

Date: March 8, 2015

R version 3.1.0

# set global chunk options: 
library(knitr)

## Warning: package 'knitr' was built under R version 3.1.2

opts_chunk$set(cache=TRUE, fig.align='center')

Within and between cluster beta diversity comparisons

#dev.new(width=11.8, height=6)
layout(matrix(1:2,ncol=2), width = c(1,1.75),height = c(1,1))
#par(mfrow=c(1,2))
barplot(as.matrix(vasc.within.bd), cex.lab=1.25, ylim=c(0,1), ylab="Beta diversity", xlab="Within cluster")
barplot(as.matrix(vasc.diff.bd), cex.lab=1.25, ylim=c(0,1), ylab="Beta diversity", xlab="Cluster combinations")

#dev.new(width=5.9, height=8)
par(mfrow=c(3,2))
barplot(as.matrix(vasc.within.between.1), cex.lab=1.25, ylim=c(0,1), ylab="Beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.between.2), cex.lab=1.25, ylim=c(0,1), ylab="Beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.between.3), cex.lab=1.25, ylim=c(0,1), ylab="Beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.between.4), cex.lab=1.25, ylim=c(0,1), ylab="Beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.between.5), cex.lab=1.25, ylim=c(0,1), ylab="Beta diversity", xlab="Clusters")
plot.new()

Phylogenetic beta diversity within and among clusters for vascular plants

#dev.new(width=11.8, height=6)
layout(matrix(1:2,ncol=2), width = c(1,1.75),height = c(1,1))
#par(mfrow=c(1,2))
barplot(as.matrix(vasc.within.ps.bd), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Within cluster")
barplot(as.matrix(vasc.diff.ps.bd), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Cluster combinations")

#dev.new(width=5.9, height=8)
par(mfrow=c(3,2))
barplot(as.matrix(vasc.within.ps.between.1), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.ps.between.2), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.ps.between.3), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.ps.between.4), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(vasc.within.ps.between.5), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
plot.new()

Angiosperm phylogenetic beta diversity within and between clusters

#dev.new(width=11.8, height=6)
layout(matrix(1:2,ncol=2), width = c(1,1.75),height = c(1,1))
#par(mfrow=c(1,2))
barplot(as.matrix(angio.within.ps.bd), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Within cluster")
barplot(as.matrix(angio.diff.ps.bd), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Cluster combinations")

#dev.new(width=5.9, height=8)
par(mfrow=c(3,2))
barplot(as.matrix(angio.within.ps.between.1), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(angio.within.ps.between.2), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(angio.within.ps.between.3), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(angio.within.ps.between.4), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
barplot(as.matrix(angio.within.ps.between.5), cex.lab=1.25, ylim=c(0,1), ylab="Phylogenetic beta diversity", xlab="Clusters")
plot.new()