Title: Beta and Phylogenetic beta diverity

Comparing among community diversity to among-community diversities excluding within-community diversity

Name: Tammy L. Elliott

Date: April 20, 2016

R version 3.1

Plot four cluster presence-absence indices with Rao’s quadratic entropy (among community diversity)

#dev.new(width=6, height=8)
par(mfrow=c(3,2))
par(mar=c(5.1,4.1,4.1,2.1))
#site.env.dist.4.cmdscale
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$cluster, col="grey40", label=TRUE)
ordiellipse(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.site.env.dist<-cascadeKM((site.env.dist),2,15)
#plot(ccas.site.env.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(site.env.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")


#dkl.raoD.pa.dist.4.cmdscale
plot(dkl.raoD.pa.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(dkl.raoD.pa.dist.4.cmdscale, dkl.raoD.pa.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(dkl.raoD.pa.dist.4.cmdscale, dkl.raoD.pa.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.dkl.raoD.pa.dist<-cascadeKM((dkl.raoD.pa.dist),2,15)
#plot(ccas.dkl.raoD.pa.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(dkl.raoD.pa.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#dkl.raoD.pa.phy.dist.4.cmdscale
plot(dkl.raoD.pa.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(dkl.raoD.pa.phy.dist.4.cmdscale, dkl.raoD.pa.phy.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(dkl.raoD.pa.phy.dist.4.cmdscale, dkl.raoD.pa.phy.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.dkl.raoD.pa.phy.dist<-cascadeKM((dkl.raoD.pa.phy.dist),2,15)
#plot(ccas.dkl.raoD.pa.phy.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(dkl.raoD.pa.phy.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#textClick.bold("(a)",cex=c(size=1.5, font=2) )
#textClick.bold("(b)", cex=c(size=1.5, font=2))
#textClick.bold("(c)", cex=c(size=1.5, font=2))
#textClick.bold("(d)", cex=c(size=1.5, font=2))
#textClick.bold("(e)", cex=c(size=1.5, font=2))
#textClick.bold("(f)", cex=c(size=1.5, font=2))

Plot four cluster abundance indices with Rao’s quadratic entropy (among community diversity)

#dev.new(width=6, height=8)
par(mfrow=c(3,2))
par(mar=c(5.1,4.1,4.1,2.1))
#site.env.dist.4.cmdscale
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$cluster, col="grey40", label=TRUE)
ordiellipse(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.site.env.dist<-cascadeKM((site.env.dist),2,15)
#plot(ccas.site.env.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(site.env.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")


#dkl.raoD.abd.dist.4.cmdscale
plot(dkl.raoD.abd.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(dkl.raoD.abd.dist.4.cmdscale, dkl.raoD.abd.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(dkl.raoD.abd.dist.4.cmdscale, dkl.raoD.abd.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.dkl.raoD.abd.dist<-cascadeKM((dkl.raoD.abd.dist),2,15)
#plot(ccas.dkl.raoD.abd.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(dkl.raoD.abd.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#dkl.raoD.abd.phy.dist.4.cmdscale
plot(dkl.raoD.abd.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(dkl.raoD.abd.phy.dist.4.cmdscale, dkl.raoD.abd.phy.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(dkl.raoD.abd.phy.dist.4.cmdscale, dkl.raoD.abd.phy.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.dkl.raoD.abd.phy.dist<-cascadeKM((dkl.raoD.abd.phy.dist),2,15)
#plot(ccas.dkl.raoD.abd.phy.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(dkl.raoD.abd.phy.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#textClick.bold("(a)",cex=c(size=1.5, font=2) )
#textClick.bold("(b)", cex=c(size=1.5, font=2))
#textClick.bold("(c)", cex=c(size=1.5, font=2))
#textClick.bold("(d)", cex=c(size=1.5, font=2))
#textClick.bold("(e)", cex=c(size=1.5, font=2))
#textClick.bold("(f)", cex=c(size=1.5, font=2))

Angiosperm only analyses

Plot four cluster presence-absence indices with Rao’s quadratic entropy (Among-community diversities excluding within-community diversity)

#dev.new(width=6, height=8)
par(mfrow=c(3,2))
par(mar=c(5.1,4.1,4.1,2.1))
#site.env.dist.4.cmdscale
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$cluster, col="grey40", label=TRUE)
ordiellipse(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.site.env.dist<-cascadeKM((site.env.dist),2,15)
#plot(ccas.site.env.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(site.env.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")


#angio.dkl.raoD.pa.dist.4.cmdscale
plot(angio.dkl.raoD.pa.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.dkl.raoD.pa.dist.4.cmdscale, angio.dkl.raoD.pa.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(angio.dkl.raoD.pa.dist.4.cmdscale, angio.dkl.raoD.pa.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.angio.dkl.raoD.pa.dist<-cascadeKM((angio.dkl.raoD.pa.dist),2,15)
#plot(ccas.angio.dkl.raoD.pa.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(angio.dkl.raoD.pa.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#angio.dkl.raoD.pa.phy.dist.4.cmdscale
plot(angio.dkl.raoD.pa.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.dkl.raoD.pa.phy.dist.4.cmdscale, angio.dkl.raoD.pa.phy.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(angio.dkl.raoD.pa.phy.dist.4.cmdscale, angio.dkl.raoD.pa.phy.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.angio.dkl.raoD.pa.phy.dist<-cascadeKM((angio.dkl.raoD.pa.phy.dist),2,15)
#plot(ccas.angio.dkl.raoD.pa.phy.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(angio.dkl.raoD.pa.phy.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#textClick.bold("(a)",cex=c(size=1.5, font=2) )
#textClick.bold("(b)", cex=c(size=1.5, font=2))
#textClick.bold("(c)", cex=c(size=1.5, font=2))
#textClick.bold("(d)", cex=c(size=1.5, font=2))
#textClick.bold("(e)", cex=c(size=1.5, font=2))
#textClick.bold("(f)", cex=c(size=1.5, font=2))

Plot four cluster abundance indices with Rao’s quadratic entropy (Among-community diversities excluding within-community diversity)

#dev.new(width=6, height=8)
par(mfrow=c(3,2))
par(mar=c(5.1,4.1,4.1,2.1))
#site.env.dist.4.cmdscale
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$cluster, col="grey40", label=TRUE)
ordiellipse(site.env.dist.4.cmdscale, site.env.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.site.env.dist<-cascadeKM((site.env.dist),2,15)
#plot(ccas.site.env.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(site.env.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")


#angio.dkl.raoD.abd.dist.4.cmdscale
plot(angio.dkl.raoD.abd.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.dkl.raoD.abd.dist.4.cmdscale, angio.dkl.raoD.abd.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(angio.dkl.raoD.abd.dist.4.cmdscale, angio.dkl.raoD.abd.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.angio.dkl.raoD.abd.dist<-cascadeKM((angio.dkl.raoD.abd.dist),2,15)
#plot(ccas.angio.dkl.raoD.abd.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(angio.dkl.raoD.abd.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#angio.dkl.raoD.abd.phy.dist.4.cmdscale
plot(angio.dkl.raoD.abd.phy.dist.4.cmdscale, type="n", xlab="", ylab="", main="", cex=1, pch=16, col="black", xaxt='n', yaxt="n")
ordispider(angio.dkl.raoD.abd.phy.dist.4.cmdscale, angio.dkl.raoD.abd.phy.dist.cfuz.4$cluster, col="grey40", label=TRUE)
ordiellipse(angio.dkl.raoD.abd.phy.dist.4.cmdscale, angio.dkl.raoD.abd.phy.dist.cfuz.4$cluster, col="grey70")
box(lwd=1)

#ccas.angio.dkl.raoD.abd.phy.dist<-cascadeKM((angio.dkl.raoD.abd.phy.dist),2,15)
#plot(ccas.angio.dkl.raoD.abd.phy.dist,sortq=TRUE)

cols <- myColorRamp(c("black", "white", "grey60", "grey30"), as.numeric(angio.dkl.raoD.abd.phy.dist.cfuz.4$cluster))
colfunc <- colorRampPalette(c("black", "white", "grey60", "grey30"))
#par(mar=c(5.1,4.1,4.1,2.1))
plot(site.coord$Latitude..WGS.84.datum., site.coord$Longitude..WGS.84.datum., xlab="Latitude", ylab="Longitude",
bg=cols, pch=21, col="black",cex=1.75, cex.lab=1.5, cex.axis=1, main="", cex.main=1.25)
#xl <- 1
#yb <- -2.3
#xr <- 1.5
#yt <- 2.7
legend("bottomleft", c("Group 1","Group 2"), pch=21,
    pt.bg=c("black", "white"),col="black",  cex=0.85,  bty="n")
legend("bottomright", c("Group 3", "Group 4"), pch=21,
    pt.bg=c("gray60", "grey30"), col="black",  cex=0.85,  bty="n")

#textClick.bold("(a)",cex=c(size=1.5, font=2) )
#textClick.bold("(b)", cex=c(size=1.5, font=2))
#textClick.bold("(c)", cex=c(size=1.5, font=2))
#textClick.bold("(d)", cex=c(size=1.5, font=2))
#textClick.bold("(e)", cex=c(size=1.5, font=2))
#textClick.bold("(f)", cex=c(size=1.5, font=2))

Cluster comparisons

Vascular cluster comparisons

Values closer to 1.00 show that groupings (clusterings) have higher resemblance.

dkl - means among community groupings, clustering methods without dkl are calculated from $H values (among community diversities excluding within community diversities)

compPart.5.crand

##                   Env.dist Vasc.BD Vasc.PhBD Vasc.BD.abd Vasc.PhBD.abd
## Env.dist              1.00    0.38      0.35        0.33          0.42
## Vasc.BD               0.38    1.00      0.39        0.35          0.36
## Vasc.PhBD             0.35    0.39      1.00        0.32          0.42
## Vasc.BD.abd           0.33    0.35      0.32        1.00          0.36
## Vasc.PhBD.abd         0.42    0.36      0.42        0.36          1.00
## Vasc.BD.dkl           0.27    0.31      0.39        0.28          0.30
## Vasc.PhBD.dkl         0.35    0.35      0.43        0.26          0.35
## Vasc.BD.abd.dkl       0.34    0.37      0.36        0.35          0.40
## Vasc.PhBD.abd.dkl     0.45    0.36      0.39        0.33          0.77
##                   Vasc.BD.dkl Vasc.PhBD.dkl Vasc.BD.abd.dkl
## Env.dist                 0.27          0.35            0.34
## Vasc.BD                  0.31          0.35            0.37
## Vasc.PhBD                0.39          0.43            0.36
## Vasc.BD.abd              0.28          0.26            0.35
## Vasc.PhBD.abd            0.30          0.35            0.40
## Vasc.BD.dkl              1.00          0.28            0.32
## Vasc.PhBD.dkl            0.28          1.00            0.36
## Vasc.BD.abd.dkl          0.32          0.36            1.00
## Vasc.PhBD.abd.dkl        0.30          0.40            0.39
##                   Vasc.PhBD.abd.dkl
## Env.dist                       0.45
## Vasc.BD                        0.36
## Vasc.PhBD                      0.39
## Vasc.BD.abd                    0.33
## Vasc.PhBD.abd                  0.77
## Vasc.BD.dkl                    0.30
## Vasc.PhBD.dkl                  0.40
## Vasc.BD.abd.dkl                0.39
## Vasc.PhBD.abd.dkl              1.00

Angiosperm cluster comparisons

Values closer to 1.00 show that groupings (clusterings) have higher resemblance.

dkl - means among community groupings, clustering methods without dkl are calculated from $H values (among community diversities excluding within community diversities)

angio.compPart.5.crand

##                          Env.dist Angio.BD Angio.PhBD Angio.BD.abd
## Env.dist                     1.00     0.36       0.31         0.26
## Angio.BD                     0.36     1.00       0.38         0.33
## Angio.PhBD                   0.31     0.38       1.00         0.27
## Angio.BD.abd                 0.26     0.33       0.27         1.00
## Angio.PhBD.abd               0.34     0.37       0.47         0.47
## Angio.BD.dkl                 0.38     0.38       0.46         0.27
## Angio.PhBD.dkl               0.31     0.32       0.72         0.24
## Angio.BD.abd.dkl             0.34     0.32       0.35         0.41
## Angio.PhBD.abd.angio.dkl     0.35     0.34       0.47         0.38
##                          Angio.PhBD.abd Angio.BD.dkl Angio.PhBD.dkl
## Env.dist                           0.34         0.38           0.31
## Angio.BD                           0.37         0.38           0.32
## Angio.PhBD                         0.47         0.46           0.72
## Angio.BD.abd                       0.47         0.27           0.24
## Angio.PhBD.abd                     1.00         0.45           0.45
## Angio.BD.dkl                       0.45         1.00           0.52
## Angio.PhBD.dkl                     0.45         0.52           1.00
## Angio.BD.abd.dkl                   0.45         0.42           0.35
## Angio.PhBD.abd.angio.dkl           0.65         0.44           0.46
##                          Angio.BD.abd.dkl Angio.PhBD.abd.angio.dkl
## Env.dist                             0.34                     0.35
## Angio.BD                             0.32                     0.34
## Angio.PhBD                           0.35                     0.47
## Angio.BD.abd                         0.41                     0.38
## Angio.PhBD.abd                       0.45                     0.65
## Angio.BD.dkl                         0.42                     0.44
## Angio.PhBD.dkl                       0.35                     0.46
## Angio.BD.abd.dkl                     1.00                     0.51
## Angio.PhBD.abd.angio.dkl             0.51                     1.00