Title: Vector fitting on ordinations
Name: Tammy L. Elliott
Date: April 10, 2016
R version 3.1
Vector fitting with each of the PCoA ordinations
4 Abundance-weighted
### 1. site.env, 2. VascBD, 3. VascPhBD, 4. AngioBD, 5. AngioPhBD
#dev.new(width=8, height=6)
par(mfrow=c(2,3), mar=c(1,2,3,1))
site.env.dist.envfit<-envfit(site.env.dist.4.cmdscale, site.dist, permutations=999)
plot(site.env.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey70")
plot(site.env.dist.envfit, col="black")
box(lwd=1)
raoD.abd.dist.4.envfit<-envfit(raoD.abd.dist.4.cmdscale, site.dist, permutations=999)
plot(raoD.abd.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(raoD.abd.dist.4.cmdscale, raoD.abd.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(raoD.abd.dist.4.cmdscale, raoD.abd.dist.cfuz.4$cluster, col="grey70")
plot(raoD.abd.dist.4.envfit, col="black")
box(lwd=1)
raoD.abd.phy.dist.4.envfit<-envfit(raoD.abd.phy.dist.4.cmdscale, site.dist, permutations=999)
plot(raoD.abd.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(raoD.abd.phy.dist.4.cmdscale, raoD.abd.phy.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(raoD.abd.phy.dist.4.cmdscale, raoD.abd.phy.dist.cfuz.4$cluster, col="grey70")
plot(raoD.abd.phy.dist.4.envfit, col="black")
box(lwd=1)
angio.raoD.abd.dist.4.envfit<-envfit(angio.raoD.abd.dist.4.cmdscale, site.dist, permutations=999)
plot(angio.raoD.abd.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.raoD.abd.dist.4.cmdscale, angio.raoD.abd.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(angio.raoD.abd.dist.4.cmdscale, angio.raoD.abd.dist.cfuz.4$cluster, col="grey70")
plot(angio.raoD.abd.dist.4.envfit, col="black")
box(lwd=1)
angio.raoD.abd.phy.dist.4.envfit<-envfit(angio.raoD.abd.phy.dist.4.cmdscale, site.dist, permutations=999)
plot(angio.raoD.abd.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.raoD.abd.phy.dist.4.cmdscale, angio.raoD.abd.phy.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(angio.raoD.abd.phy.dist.4.cmdscale, angio.raoD.abd.phy.dist.cfuz.4$cluster, col="grey70")
plot(angio.raoD.abd.phy.dist.4.envfit, col="black")
box(lwd=1)
#textClick.bold("(a)", cex=1.75)
#textClick.bold("(b)", cex=1.75)
#textClick.bold("(c)", cex=1.75)
#textClick.bold("(d)", cex=1.75)
#textClick.bold("(e)", cex=1.75)
4 Presence-absence analyses
### 1. site.env, 2. VascBD, 3. VascPhBD, 4. AngioBD, 5. AngioPhBD
#dev.new(width=8, height=6)
par(mfrow=c(2,3), mar=c(1,2,3,1))
site.env.dist.envfit<-envfit(site.env.dist.4.cmdscale, site.dist, permutations=999)
plot(site.env.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey70")
plot(site.env.dist.envfit, col="black")
box(lwd=1)
raoD.pa.dist.4.envfit<-envfit(raoD.pa.dist.4.cmdscale, site.dist, permutations=999)
plot(raoD.pa.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(raoD.pa.dist.4.cmdscale, raoD.pa.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(raoD.pa.dist.4.cmdscale, raoD.pa.dist.cfuz.4$cluster, col="grey70")
plot(raoD.pa.dist.4.envfit, col="black")
box(lwd=1)
raoD.pa.phy.dist.4.envfit<-envfit(raoD.pa.phy.dist.4.cmdscale, site.dist, permutations=999)
plot(raoD.pa.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(raoD.pa.phy.dist.4.cmdscale, raoD.pa.phy.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(raoD.pa.phy.dist.4.cmdscale, raoD.pa.phy.dist.cfuz.4$cluster, col="grey70")
plot(raoD.pa.phy.dist.4.envfit, col="black")
box(lwd=1)
angio.raoD.pa.dist.4.envfit<-envfit(angio.raoD.pa.dist.4.cmdscale, site.dist, permutations=999)
plot(angio.raoD.pa.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.raoD.pa.dist.4.cmdscale, angio.raoD.pa.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(angio.raoD.pa.dist.4.cmdscale, angio.raoD.pa.dist.cfuz.4$cluster, col="grey70")
plot(angio.raoD.pa.dist.4.envfit, col="black")
box(lwd=1)
angio.raoD.pa.phy.dist.4.envfit<-envfit(angio.raoD.pa.phy.dist.4.cmdscale, site.dist, permutations=999)
plot(angio.raoD.pa.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.raoD.pa.phy.dist.4.cmdscale, angio.raoD.pa.phy.dist.cfuz.4$cluster, col="grey75", label=TRUE)
ordiellipse(angio.raoD.pa.phy.dist.4.cmdscale, angio.raoD.pa.phy.dist.cfuz.4$cluster, col="grey70")
plot(angio.raoD.pa.phy.dist.4.envfit, col="black")
box(lwd=1)
#textClick.bold("(a)", cex=1.75)
#textClick.bold("(b)", cex=1.75)
#textClick.bold("(c)", cex=1.75)
#textClick.bold("(d)", cex=1.75)
#textClick.bold("(e)", cex=1.75)