Title: PCoA calculations

Name: Tammy L. Elliott

Date: October 10, 2017

R version 3.2

Table showing pseudo-r2 and variation explained by first two PCoA axes (presence-absence data)

write.table(pseudo.r2.pa)

## "pseudo r2" "PCoA 1" "PCoA 2"
## "SiteEnv" 0.95 0.8 0.15
## "BD - vasculars" 0.77 0.67 0.1
## "PhBD - vasculars" 0.78 0.42 0.36
## "BD - angiosperms" 0.74 0.61 0.13
## "PhBD - angiosperms" 0.9 0.59 0.32

# Table showing abundance-weighted values
site.env<-cbind(round(site.env.pseudo.r2,2), round(site.env.1,2), round(site.env.2,2))
raoD.abd.row<-cbind(round(raoD.abd.r2,2), round(raoD.abd.1,2), round(raoD.abd.2,2))
raoD.abd.phy.row<-cbind(round(raoD.abd.phy.r2.mean,2), round(raoD.abd.phy.1.mean,2), round(raoD.abd.phy.2.mean,2))
raoD.abd.angio.row<-cbind(round(raoD.abd.angio.r2,2), round(raoD.abd.angio.1,2), round(raoD.abd.angio.2,2))
raoD.abd.angio.phy.row<-cbind(round(raoD.abd.angio.phy.r2.mean,2), 
    round(raoD.abd.angio.phy.1.mean,2), round(raoD.abd.angio.phy.2.mean,2))
pseudo.r2.abd<-rbind(site.env,raoD.abd.row, raoD.abd.phy.row, raoD.abd.angio.row,
    raoD.abd.angio.phy.row)
colnames(pseudo.r2.abd)<-c("pseudo r2", "PCoA 1", "PCoA 2")
rownames(pseudo.r2.abd)<-c("SiteEnv", "BD - vasculars", "PhBD - vasculars", "BD - angiosperms", "PhBD - angiosperms")

Table showing pseudo-r2 and variation explained by first two PCoA axes (abundance data)

write.table(pseudo.r2.abd)

## "pseudo r2" "PCoA 1" "PCoA 2"
## "SiteEnv" 0.95 0.8 0.15
## "BD - vasculars" 0.66 0.47 0.19
## "PhBD - vasculars" 0.82 0.61 0.22
## "BD - angiosperms" 0.65 0.43 0.22
## "PhBD - angiosperms" 0.8 0.57 0.23

pseudo-r2 and variance explained by first two PCoA axes: Maximum Clade Credibility Tree

Presence-abscence vascular plant data

(raoD.pa.phy.one.tree.r2<-(raoD.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[1]+
    raoD.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[2])/sum(raoD.pa.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.7757932

(raoD.pa.phy.one.tree.1<-raoD.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[1]/sum(raoD.pa.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.4191003

(raoD.pa.phy.one.tree.2<-raoD.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[2]/sum(raoD.pa.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.3566929

Abundance-weighted vascular plant data

(raoD.abd.phy.one.tree.r2<-(raoD.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[1]+
    raoD.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[2])/sum(raoD.abd.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.8259019

(raoD.abd.phy.one.tree.1<-raoD.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[1]/sum(raoD.abd.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.6107117

(raoD.abd.phy.one.tree.2<-raoD.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[2]/sum(raoD.abd.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.2151902

Presence-abscence angiosperm plant data

(raoD.angio.pa.phy.one.tree.r2<-(raoD.angio.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[1]+
    raoD.angio.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[2])/sum(raoD.angio.pa.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.9032063

(raoD.angio.pa.phy.one.tree.1<-raoD.angio.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[1]/sum(raoD.angio.pa.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.5848345

(raoD.angio.pa.phy.one.tree.2<-raoD.angio.pa.phy.one.tree.dist.4.cmdscale.eigen$eig[2]/sum(raoD.angio.pa.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.3183718

Abundance-weighted angiosperm plant data

(raoD.angio.abd.phy.one.tree.r2<-(raoD.angio.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[1]+
    raoD.angio.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[2])/sum(raoD.angio.abd.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.7995024

(raoD.angio.abd.phy.one.tree.1<-raoD.angio.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[1]/sum(raoD.angio.abd.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.569785

(raoD.angio.abd.phy.one.tree.2<-raoD.angio.abd.phy.one.tree.dist.4.cmdscale.eigen$eig[2]/sum(raoD.angio.abd.phy.one.tree.dist.4.cmdscale.eigen$eig))

## [1] 0.2297174