Schefferville - transitions; Within and Among beta diversity comparisons of clusters

Tammy L. Elliott

Date: March 24, 2015

R version 3.1.0

# set global chunk options: 
library(knitr)
opts_chunk$set(cache=FALSE, fig.align='center')

Calculations for among cluster beta partitioning

The following shows how among cluster beta diversity is calculated.

#Among beta partitioning; analyzes with Hill number 1
sp.part.among.prep<-phyloDATA2014(tree0, abd.sp.allsp)
sp.part.among<-PhD2014(sp.part.among.prep$pAbun, sp.part.among.prep$pLength, 1)
sp.part.among$pCqN

## [1] 0.6459545

#Among beta partitioning for angiosperms only; analyzes with Hill number 1
sp.angio.part.among.prep<-phyloDATA2014(angiotree0, angio.sp.abd)
sp.angio.part.among<-PhD2014(sp.angio.part.among.prep$pAbun, sp.angio.part.among.prep$pLength, 1)
sp.angio.part.among$pCqN

## [1] 0.6545234

#Among phylogenetic beta partitioning; analyzes with Hill number 1
part.among.prep<-phyloDATA2014(tree, abd.sp.allsp)
part.among<-PhD2014(part.among.prep$pAbun, part.among.prep$pLength, 1)
part.among$pCqN

## [1] 0.9090127

#Among phylogenetic beta partitioning for angiosperms only; analyzes with Hill number 1
angio.part.among.prep<-phyloDATA2014(angiotree, angio.sp.abd)
angio.part.among<-PhD2014(angio.part.among.prep$pAbun, angio.part.among.prep$pLength, 1)
angio.part.among$pCqN

## [1] 0.8869543

---

Place different beta diversity distances into clusters formed by K-means clustering of environmental distance

In the following analyzes, I partition within and among beta and phylogenetic diversity. I do separate analyzes for Chao’s weighted and non-weighted beta diversity, as well as for both angiosperms and vasculars.

In these analyzes, the clusters are based on those groups from the environmental distance grouping using Gower’s distances. I first calculate 3,4, and 5 environmental distance clusters, and then I divide the plots according to those groups and do all subsequent beta diversity and phylogenetic analyzes based on those groupings. Therefore, the groupings remain the same for all analyzes.

According to Chao’s beta diversity partitioning, non-weighted beta partitioning compares species richness within a cluster to the overall richness.

Abundance-weighting to the order of 1 then compares overall Shannon’s diversity to within cluster diversity.

Chao’s phylogenetic beta diversity compares the branch lengths that are shared among groups to those branch lengths specific to a cluster.

head(vasc.env.clust.3$cluster)

## EA1 EB1 EC1 ED1 EE1 EF1 
##   2   2   2   2   2   2

str(vasc.env.clust.4$cluster)

##  Named int [1:176] 1 1 3 1 1 1 1 3 1 3 ...
##  - attr(*, "names")= chr [1:176] "EA1" "EB1" "EC1" "ED1" ...

str(vasc.env.clust.5$cluster)

##  Named int [1:176] 5 5 5 5 5 5 5 5 5 5 ...
##  - attr(*, "names")= chr [1:176] "EA1" "EB1" "EC1" "ED1" ...

# Three cluster groupings
abd.sp.groups.3<- cbind(t(abd.sp.allsp), vasc.env.clust.3$cluster)
colnames(abd.sp.groups.3)[which(colnames(abd.sp.groups.3) == "")] <- "Group"
Three.clust.1<-subset(abd.sp.groups.3,abd.sp.groups.3[,126]=="1")
Three.clust.2<-subset(abd.sp.groups.3,abd.sp.groups.3[,126]=="2") 
Three.clust.3<-subset(abd.sp.groups.3,abd.sp.groups.3[,126]=="3")

 # Check - the following should equal 176
nrow(Three.clust.1)+nrow(Three.clust.2)+nrow(Three.clust.3)

## [1] 176

# Four cluster groupings
abd.sp.groups.4<- cbind(t(abd.sp.allsp), vasc.env.clust.4$cluster)
colnames(abd.sp.groups.4)[which(colnames(abd.sp.groups.4) == "")] <- "Group"
Four.clust.1<-subset(abd.sp.groups.4,abd.sp.groups.4[,126]=="1")
Four.clust.2<-subset(abd.sp.groups.4,abd.sp.groups.4[,126]=="2")
Four.clust.3<-subset(abd.sp.groups.4,abd.sp.groups.4[,126]=="3")
Four.clust.4<-subset(abd.sp.groups.4,abd.sp.groups.4[,126]=="4")

# Five cluster groupings
abd.sp.groups.5<- cbind(t(abd.sp.allsp), vasc.env.clust.5$cluster)
colnames(abd.sp.groups.5)[which(colnames(abd.sp.groups.5) == "")] <- "Group"
Five.clust.1<-subset(abd.sp.groups.5,abd.sp.groups.5[,126]=="1")
Five.clust.2<-subset(abd.sp.groups.5,abd.sp.groups.5[,126]=="2")
Five.clust.3<-subset(abd.sp.groups.5,abd.sp.groups.5[,126]=="3")
Five.clust.4<-subset(abd.sp.groups.5,abd.sp.groups.5[,126]=="4")
Five.clust.5<-subset(abd.sp.groups.5,abd.sp.groups.5[,126]=="5")

---

Within beta partitioning; analyzes with Hill number 1 for group 1 in three group clustering (vasculars)

The following is sample code of show to calculate within cluster beta diversity.

sp.part.within.prep.1.3<-phyloDATA2014(tree0, t(Three.clust.1))
sp.part.within.1.3<-PhD2014(sp.part.within.prep.1.3$pAbun, sp.part.within.prep.1.3$pLength, 1)
sp.part.within.1.3$pCqN

## [1] 0.6343807

sp.part.within.prep.2.3<-phyloDATA2014(tree0, t(Three.clust.2))
sp.part.within.2.3<-PhD2014(sp.part.within.prep.2.3$pAbun, sp.part.within.prep.2.3$pLength, 1)
sp.part.within.2.3$pCqN

## [1] 0.6578618

sp.part.within.prep.3.3<-phyloDATA2014(tree0, t(Three.clust.3))
sp.part.within.3.3<-PhD2014(sp.part.within.prep.3.3$pAbun, sp.part.within.prep.3.3$pLength, 1)
sp.part.within.3.3$pCqN

## [1] 0.6271168

#Within phylogenetic beta partitioning; analyzes with Hill number 1 for group 1 in three group clustering (vasculars)
ph.part.within.prep.1.3<-phyloDATA2014(tree, t(Three.clust.1))
ph.part.within.1.3<-PhD2014(ph.part.within.prep.1.3$pAbun, ph.part.within.prep.1.3$pLength, 1)
ph.part.within.1.3$pCqN

## [1] 0.9266243

ph.part.within.prep.2.3<-phyloDATA2014(tree, t(Three.clust.2))
ph.part.within.2.3<-PhD2014(ph.part.within.prep.2.3$pAbun, ph.part.within.prep.2.3$pLength, 1)
ph.part.within.2.3$pCqN

## [1] 0.90829

ph.part.within.prep.3.3<-phyloDATA2014(tree, t(Three.clust.3))
ph.part.within.3.3<-PhD2014(ph.part.within.prep.3.3$pAbun, ph.part.within.prep.3.3$pLength, 1)
ph.part.within.3.3$pCqN

## [1] 0.8926333

---

Angiosperms comparisons

The following is sample code showing how groups are divided and within group beta diversity is partitioned.

# Three cluster groupings

angio.abd.sp.groups.3<- cbind(t(angio.sp.abd), vasc.env.clust.3$cluster)
colnames(abd.sp.groups.3)[which(colnames(angio.abd.sp.groups.3) == "")] <- "Group"
Three.clust.1.angio<-subset(angio.abd.sp.groups.3,angio.abd.sp.groups.3[,111]=="1")
Three.clust.2.angio<-subset(angio.abd.sp.groups.3,angio.abd.sp.groups.3[,111]=="2")
Three.clust.3.angio<-subset(angio.abd.sp.groups.3,angio.abd.sp.groups.3[,111]=="3")

 # Check - the following should equal 176
nrow(Three.clust.1.angio)+nrow(Three.clust.2.angio)+nrow(Three.clust.3.angio)

## [1] 176

# Four cluster groupings
angio.abd.sp.groups.4<- cbind(t(angio.sp.abd), vasc.env.clust.4$cluster)
colnames(angio.abd.sp.groups.4)[which(colnames(angio.abd.sp.groups.4) == "")] <- "Group"
Four.clust.1.angio<-subset(angio.abd.sp.groups.4,angio.abd.sp.groups.4[,111]=="1")
Four.clust.2.angio<-subset(angio.abd.sp.groups.4,angio.abd.sp.groups.4[,111]=="2")
Four.clust.3.angio<-subset(angio.abd.sp.groups.4,angio.abd.sp.groups.4[,111]=="3")
Four.clust.4.angio<-subset(angio.abd.sp.groups.4,angio.abd.sp.groups.4[,111]=="4")

# Five cluster groupings
angio.abd.sp.groups.5<- cbind(t(angio.sp.abd), vasc.env.clust.5$cluster)
colnames(angio.abd.sp.groups.5)[which(colnames(angio.abd.sp.groups.5) == "")] <- "Group"
Five.clust.1.angio<-subset(angio.abd.sp.groups.5,angio.abd.sp.groups.5[,111]=="1")
Five.clust.2.angio<-subset(angio.abd.sp.groups.5,angio.abd.sp.groups.5[,111]=="2")
Five.clust.3.angio<-subset(angio.abd.sp.groups.5,angio.abd.sp.groups.5[,111]=="3")
Five.clust.4.angio<-subset(angio.abd.sp.groups.5,angio.abd.sp.groups.5[,111]=="4")
Five.clust.5.angio<-subset(angio.abd.sp.groups.5,angio.abd.sp.groups.5[,111]=="5")


#Within phylogenetic beta partitioning; analyzes with Hill number 0 for group 1 in three group clustering
no.abd.sp.part.within.prep.1.3.angio<-phyloDATA2014(angiotree0, t(Three.clust.1.angio))
no.abd.sp.part.within.1.3.angio<-PhD2014(no.abd.sp.part.within.prep.1.3.angio$pAbun, no.abd.sp.part.within.prep.1.3.angio$pLength, 0)
no.abd.sp.part.within.1.3.angio$pCqN

## [1] 0.8506986

no.abd.sp.part.within.prep.2.3.angio<-phyloDATA2014(angiotree0, t(Three.clust.2.angio))
no.abd.sp.part.within.2.3.angio<-PhD2014(no.abd.sp.part.within.prep.2.3.angio$pAbun, no.abd.sp.part.within.prep.2.3.angio$pLength, 0)
no.abd.sp.part.within.2.3.angio$pCqN

## [1] 0.93257

no.abd.sp.part.within.prep.3.3.angio<-phyloDATA2014(angiotree0, t(Three.clust.3.angio))
no.abd.sp.part.within.3.3.angio<-PhD2014(no.abd.sp.part.within.prep.3.3.angio$pAbun, no.abd.sp.part.within.prep.3.3.angio$pLength, 0)
no.abd.sp.part.within.3.3.angio$pCqN

## [1] 0.8968521

Plot Chao’s beta and phylogenetic beta diversity for vasculars

#dev.new(width=11.8, height=5.5)
par(mfrow=c(1,3))
plot(no.abd.sp.line[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's beta diversity \nfor three grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:3,labels=c("Group 1", "Group 2", "Group 3"))
axis(2)
points(no.abd.ph.line[1,], col="gray70", pch=16, cex=1.25)
abline(h=no.abd.sp.part.among$pCqN, lwd=2, lty=2)
abline(h=no.abd.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")
plot(no.abd.sp.line.four[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's beta diversity \nfor four grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:4,labels=c("Group 1", "Group 2", "Group 3", "Group 4"))
axis(2)
points(no.abd.ph.line.four[1,], col="gray70", pch=16, cex=1.25)
abline(h=no.abd.sp.part.among$pCqN, lwd=2, lty=2)
abline(h=no.abd.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(no.abd.sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's beta diversity \nfor five grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(no.abd.ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=no.abd.sp.part.among$pCqN, lwd=2, lty=2)
abline(h=no.abd.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

Plot Chao’s weighted beta and phylogenetic beta diversity for vasculars

#dev.new(width=11.8, height=5.5)
par(mfrow=c(1,3))
plot(sp.line[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's weighted beta diversity \nfor three grouping based on environmental distances", ylim=c(0.3,1),cex.main=0.85, bty="c")
axis(1,1:3,labels=c("Group 1", "Group 2", "Group 3"))
axis(2)
points(ph.line[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.part.among$pCqN, lwd=2, lty=2)
abline(h=part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(sp.line.four[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's weighted beta diversity \nfor four grouping based on environmental distances", ylim=c(0.3,1),cex.main=0.85, bty="c")
axis(1,1:4,labels=c("Group 1", "Group 2", "Group 3", "Group 4"))
axis(2)
points(ph.line.four[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.part.among$pCqN, lwd=2, lty=2)
abline(h=part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's weighted beta diversity \nfor five grouping based on environmental distances", ylim=c(0.3,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.part.among$pCqN, lwd=2, lty=2)
abline(h=part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

Plot Chao’s beta and phylogenetic beta diversity for angiosperms

#dev.new(width=11.8, height=5.5)
par(mfrow=c(1,3))
plot(no.abd.sp.line.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's beta diversity \nfor three grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:3,labels=c("Group 1", "Group 2", "Group 3"))
axis(2)
points(no.abd.ph.line.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(no.abd.sp.line.four.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's beta diversity \nfor four grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:4,labels=c("Group 1", "Group 2", "Group 3", "Group 4"))
axis(2)
points(no.abd.ph.line.four.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(no.abd.sp.line.five.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's beta diversity \nfor five grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(no.abd.ph.line.five.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

Plot Chao’s weighted beta and phylogenetic beta diversity for angiosperms

#dev.new(width=11.8, height=5.5)
par(mfrow=c(1,3))
plot(abd.sp.line.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's weighted beta diversity \nfor three grouping based on environmental distances", ylim=c(0.35,1),cex.main=0.85, bty="c")
axis(1,1:3,labels=c("Group 1", "Group 2", "Group 3"))
axis(2)
points(abd.ph.line.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=abd.sp.abd.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=abd.angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(abd.sp.line.four.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's weighted beta diversity \nfor four grouping based on environmental distances", ylim=c(0.35,1),cex.main=0.85, bty="c")
axis(1,1:4,labels=c("Group 1", "Group 2", "Group 3", "Group 4"))
axis(2)
points(abd.ph.line.four.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=abd.sp.abd.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=abd.angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(abd.sp.line.five.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's weighted beta diversity \nfor five grouping based on environmental distances", ylim=c(0.35,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(abd.ph.line.five.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=abd.sp.abd.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=abd.angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=1,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

Compare five cluster within and among beta partitioning between Tammy’s classification an environmental distance groupings

The following sample code shows how I divide the clusters based on my classifications

# Make Tammy classifications
library(plyr)

## Warning: package 'plyr' was built under R version 3.1.1

hab<-site[,c(3:5), drop=FALSE]
hab.types<-hab[,1, drop=FALSE]
hab.types.smaller<-revalue(hab.types[,1], c("Spruce lichen - Shrubs"="Spruce lichen" , "Spruce moss - Spruce lichen"="Spruce lichen",
    "Spruce moss - Shrubs"="Spruce moss", "Spruce moss - Fen" = "Fen", "Tundra - Shrubs"="Tundra"))
table(hab.types.smaller)

## hab.types.smaller
##           Fen        Shrubs Spruce lichen   Spruce moss        Tundra 
##            33            31            10            71            31

hab.new<-cbind(hab.types.smaller,hab[,c(2:3)])

tam.class<-revalue(hab.types.smaller, c("Fen"="1", "Spruce lichen"="2", "Spruce moss"= "3", "Shrubs"= "4","Tundra"="5"))
 (tam.class.table<-table(tam.class))

## tam.class
##  1  4  2  3  5 
## 33 31 10 71 31

names(tam.class)<-colnames(abd.sp.allsp)

tam.class.groups.5<- cbind(t(abd.sp.allsp), tam.class)
colnames(tam.class.groups.5)[which(colnames(tam.class.groups.5) == "")] <- "Group"
Five.clust.1.tc<-subset(tam.class.groups.5,tam.class.groups.5[,126]=="1")
Five.clust.2.tc<-subset(tam.class.groups.5,tam.class.groups.5[,126]=="2")
Five.clust.3.tc<-subset(tam.class.groups.5,tam.class.groups.5[,126]=="3")
Five.clust.4.tc<-subset(tam.class.groups.5,tam.class.groups.5[,126]=="4")
Five.clust.5.tc<-subset(tam.class.groups.5,tam.class.groups.5[,126]=="5")

#Among beta partitioning for vasculars only; analyzes with Hill number 1
abd.sp.abd.part.among.prep.tc<-phyloDATA2014(tree0, t(tam.class.groups.5))
abd.sp.abd.part.among.tc<-PhD2014(abd.sp.abd.part.among.prep.tc$pAbun, abd.sp.abd.part.among.prep.tc$pLength, 1)
abd.sp.abd.part.among.tc$pCqN

## [1] 0.6459545

Show beta partitioning based on environmental distances (top) and my classifications (bottom) in vasculars

#dev.new(width=11.8, height=8)
par(mfrow=c(2,2))

plot(no.abd.sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's beta diversity \nfor five grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(no.abd.ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=no.abd.sp.part.among$pCqN, lwd=2, lty=2)
abline(h=no.abd.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's weighted beta diversity \nfor five grouping based on environmental distances", ylim=c(0.3,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.part.among$pCqN, lwd=2, lty=2)
abline(h=part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")


plot(tc.sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's beta diversity \nfor five grouping based on Tammy's classification", ylim=c(0.3,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(tc.ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.abd.part.among.tc$pCqN, lwd=2, lty=2)
abline(h=part.among.tc$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(tc.abd.sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (vasculars) using Chao's weighted beta diversity \nfor five grouping based on Tammy's classificatoin", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(tc.abd.ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=abd.sp.abd.part.among.tc$pCqN, lwd=2, lty=2)
abline(h=abd.part.among.tc$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

Show beta partitioning based on environmental distances (top) and my classifications (bottom) in angiosperms

#dev.new(width=11.8, height=8)
par(mfrow=c(2,2))
plot(no.abd.sp.line.five.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's beta diversity \nfor five grouping based on environmental distances", ylim=c(0.45,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(no.abd.ph.line.five.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(abd.sp.line.five.angio[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's weighted beta diversity \nfor five grouping based on environmental distances", ylim=c(0.35,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(abd.ph.line.five.angio[1,], col="gray70", pch=16, cex=1.25)
abline(h=abd.sp.abd.angio.part.among$pCqN, lwd=2, lty=2)
abline(h=abd.angio.part.among$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")


# These two are based on Tammy's classifications
plot(angio.tc.sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's beta diversity \nfor five grouping based on Tammy's classifications", ylim=c(0.3,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(angio.tc.ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=sp.abd.angio.part.among.tc$pCqN, lwd=2, lty=2)
abline(h=angio.part.among.tc$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")

plot(angio.tc.abd.sp.line.five[1,], axes=FALSE, col="black", pch=16, cex=1.25, ylab="Beta diversity", xlab="Group",las=1, cex.axis=1, cex.lab=1,
 main="Phylogenetic beta diversity compared to beta diversity within and \namong sampling bands (angiosperms) using Chao's weighted beta diversity \nfor five grouping based on Tammy's classifications", ylim=c(0.35,1),cex.main=0.85, bty="c")
axis(1,1:5,labels=c("Group 1", "Group 2", "Group 3", "Group 4", "Group 5"))
axis(2)
points(angio.tc.abd.ph.line.five[1,], col="gray70", pch=16, cex=1.25)
abline(h=abd.sp.abd.angio.part.among.tc$pCqN, lwd=2, lty=2)
abline(h=abd.angio.part.among.tc$pCqN, lwd=2, lty=2, col="gray70")
box(bty="l", lwd=3)
legend("bottomright", c("Beta diversity (among)", "Beta diversity (within)", "Phylogenetic beta diversity (among)", "Phylogenetic beta diversity (within)"), col = c("black","black", "gray70", "gray70"), cex=0.8,
      lty = c(2, 0,2,0),lwd=c(2,2,2,2), pch = c(NA, 16, NA, 16), bg = "white", bty="n")