Title: SCBD and indicator species values

Name: Tammy L. Elliott

Date: May 19, 2016

R version 3.1

---

Pearson’s correlation coefficients

cor.env.dist.bd.vasc<-cor(env.dist.ord,abd.vasc.ord)
cor.env.dist.ph.bd.vasc<-cor(env.dist.ord, ph.abd.vasc.ord)
cor.bd.ph.bd.vasc<-cor(abd.vasc.ord, ph.abd.vasc.ord)

# Correlation between Gower's distance and beta diversity
cor.env.dist.bd.vasc

## [1] 0.7539522

# Correlation between Gower's distance and phylogenetic beta diversity
cor.env.dist.ph.bd.vasc

## [1] 0.9273408

# Correlation between beta diversity and phylogenetic beta diversity
cor.bd.ph.bd.vasc

## [1] 0.6565143

Pearson’s correlation coefficients for angiosperms

cor.env.dist.bd.angio<-cor(env.dist.ord.angio, abd.angio.ord)
cor.env.dist.ph.bd.angio<-cor(env.dist.ord.angio, ph.abd.angio.ord)
cor.bd.ph.bd.angio<-cor(abd.angio.ord, ph.abd.angio.ord)

# Correlation between Gower's distance and beta diversity
cor.env.dist.bd.angio

## [1] 0.8822542

# Correlation between Gower's distance and phylogenetic beta diversity
cor.env.dist.ph.bd.angio

## [1] 0.8547822

# Correlation between beta diversity and phylogenetic beta diversity
cor.bd.ph.bd.angio

## [1] 0.8964106

Correlations with species frequencies across plots

# Environmental distance and frequency
(env.freq.corr<-cor(freq.sp, env.dist.ord))

## [1] -0.1658198

# Vascular abundance with SCBD
(vasc.freq.corr<-cor(freq.sp,abd.vasc.ord))

## [1] -0.1927318

# Vascular phylogenetic abundance with SCBD
(vasc.ph.freq.corr<-cor(freq.sp,ph.abd.vasc.ord))

## [1] -0.1535144

# Angiosperms with SCBD
(angio.freq.corr<-cor(angio.freq.sp,abd.angio.ord))

## [1] -0.05062588

# Angiosperms with angiosperm SCBD (phylogenetic)
(angio.ph.freq.corr<-cor(angio.freq.sp,ph.abd.angio.ord))

## [1] 0.03054706

Indicator species plots

First is for Environmental distances, 2 and 3 for vascular plants, while 4th and 5th plots are for angiosperm only analyses

#dev.new(fig.width=11.8, fig.height=11.8)
par(mfrow=c(2,3))
par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(100*env.dist.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(520,nspecies),1:nspecies,rep(520,nspecies)+(100*env.dist.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(100*env.dist.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(680,nspecies),1:nspecies,rep(680,nspecies)+(100*env.dist.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(760,nspecies),1:nspecies,rep(760,nspecies)+(100*env.dist.ord.ind.5), 1:nspecies,lwd=3, col="black")

par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(100*vasc.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(540,nspecies),1:nspecies,rep(540,nspecies)+(100*vasc.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(100*vasc.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(670,nspecies),1:nspecies,rep(670,nspecies)+(100*vasc.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(100*vasc.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")

 par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(100*vasc.ph.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(540,nspecies),1:nspecies,rep(540,nspecies)+(100*vasc.ph.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(100*vasc.ph.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(670,nspecies),1:nspecies,rep(670,nspecies)+(100*vasc.ph.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
    #segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(100*vasc.ph.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")


par(mai=c(0.05,0,0.25,0))
  plot(angio.tree.ind, x.lim=450,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(angio.tree.ind$tip.label)
    segments(rep(220,nspecies),1:nspecies,rep(220,nspecies)+(40*angio.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(265,nspecies),1:nspecies,rep(265,nspecies)+(40*angio.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(300,nspecies),1:nspecies,rep(300,nspecies)+(40*angio.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(350,nspecies),1:nspecies,rep(350,nspecies)+(40*angio.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(100*angio.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")

 par(mai=c(0.05,0,0.25,0))
  plot(angio.tree.ind, x.lim=450,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(angio.tree.ind$tip.label)
       segments(rep(220,nspecies),1:nspecies,rep(220,nspecies)+(40*angio.ph.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(265,nspecies),1:nspecies,rep(265,nspecies)+(40*angio.ph.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(300,nspecies),1:nspecies,rep(300,nspecies)+(40*angio.ph.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(350,nspecies),1:nspecies,rep(350,nspecies)+(40*angio.ph.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(380,nspecies),1:nspecies,rep(380,nspecies)+(40*angio.ph.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")

Plot for environmental distances with correlations for each species

#dev.new(fig.width=11.8, fig.height=11.8)
par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
     segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(110*env.dist.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(540,nspecies),1:nspecies,rep(540,nspecies)+(110*env.dist.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(640,nspecies),1:nspecies,rep(640,nspecies)+(110*env.dist.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(110*env.dist.ord.ind.4), 1:nspecies,lwd=3, col="black")

Phylogenetic signal

#Phylogenetic signal in environmental distance - vaculars
(env.dist.1.k<-Kcalc(env.dist.ord.ind.1,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01154802

(env.dist.2.k<-Kcalc(env.dist.ord.ind.2,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01202211

(env.dist.3.k<-Kcalc(env.dist.ord.ind.3,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01144663

(env.dist.4.k<-Kcalc(env.dist.ord.ind.4,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.02004414

(env.dist.1.phylosignal<-phylosignal(env.dist.ord.ind.1,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.01154802      0.003703976           0.003142162           0.72
##   PIC.variance.Z
## 1      0.5154908

(env.dist.2.phylosignal<-phylosignal(env.dist.ord.ind.2,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.01202211      0.003702836           0.003358302          0.664
##   PIC.variance.Z
## 1      0.2866219

(env.dist.3.phylosignal<-phylosignal(env.dist.ord.ind.3,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.01144663      0.004096796           0.003434879           0.71
##   PIC.variance.Z
## 1      0.3594725

(env.dist.4.phylosignal<-phylosignal(env.dist.ord.ind.4,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.02004414      0.003264312           0.004799676          0.258
##   PIC.variance.Z
## 1     -0.7304527

#Phylogenetic signal in vascular beta diversity
(vasc.abd.1.k<-Kcalc(vasc.abd1.ord.ind.1,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.04955354

(vasc.abd.2.k<-Kcalc(vasc.abd1.ord.ind.2,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01148123

(vasc.abd.3.k<-Kcalc(vasc.abd1.ord.ind.3,vasc.tree.ind,checkdata=TRUE))

##           [,1]
## [1,] 0.0124662

(vasc.abd.4.k<-Kcalc(vasc.abd1.ord.ind.4,vasc.tree.ind,checkdata=TRUE))

##             [,1]
## [1,] 0.009355493

#Phylogenetic signal in vascular phylogenetic beta diversity clusters
(vasc.ph.abd.1.k<-Kcalc(vasc.ph.abd1.ord.ind.1,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.05331261

(vasc.ph.abd.2.k<-Kcalc(vasc.ph.abd1.ord.ind.2,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01408523

(vasc.ph.abd.3.k<-Kcalc(vasc.ph.abd1.ord.ind.3,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01945341

(vasc.ph.abd.4.k<-Kcalc(vasc.ph.abd1.ord.ind.4,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01717582

#Phylogenetic signal in angiosperm beta diversity clusters
(angio.abd.1.k<-Kcalc(angio.abd1.ord.ind.1,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.02250227

(angio.abd.2.k<-Kcalc(angio.abd1.ord.ind.2,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.03262545

(angio.abd.3.k<-Kcalc(angio.abd1.ord.ind.3,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.04916715

(angio.abd.4.k<-Kcalc(angio.abd1.ord.ind.4,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.02078122

#Phylogenetic signal in angiosperm phylogenetic beta diversity clusters
(angio.ph.abd.1.k<-Kcalc(angio.ph.abd1.ord.ind.1,angio.tree.ind,checkdata=TRUE))

##           [,1]
## [1,] 0.0165709

(angio.ph.abd.2.k<-Kcalc(angio.ph.abd1.ord.ind.2,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01535887

(angio.ph.abd.3.k<-Kcalc(angio.ph.abd1.ord.ind.3,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.04656126

(angio.ph.abd.4.k<-Kcalc(angio.ph.abd1.ord.ind.4,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.03119751

# Correlations between environmental distance and vascular abundance clusters
(env.vasc.cor.1<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.1))

## [1] -0.3152275

(env.vasc.cor.2<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.2))

## [1] 0.00602507

(env.vasc.cor.3<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.3))

## [1] -0.573106

(env.vasc.cor.4<-cor(env.dist.ord.ind.4, vasc.abd1.ord.ind.4))

## [1] -0.06045258

# Cross Correlations between environmental distance and vascular abundance clusters
(env.vasc.cor.1.2<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.2))

## [1] 0.1048645

(env.vasc.cor.1.3<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.3))

## [1] 0.5687968

(env.vasc.cor.1.4<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.4))

## [1] -0.4026471

(env.vasc.cor.2.3<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.3))

## [1] 0.5276995

(env.vasc.cor.2.4<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.4))

## [1] -0.2384476

(env.vasc.cor.3.4<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.4))

## [1] 0.6847883

# Correlations between environmental distance and vascular phylogenetic abundance clusters
(env.vasc.ph.cor.1<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.1))

## [1] 0.4789889

(env.vasc.ph.cor.2<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.2))

## [1] -0.307642

(env.vasc.ph.cor.3<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.3))

## [1] -0.5424174

(env.vasc.ph.cor.4<-cor(env.dist.ord.ind.4, vasc.ph.abd1.ord.ind.4))

## [1] 0.2095671

# Cross correlations between environmental distance and vascular phylogenetic abundance clusters

(env.vasc.ph.cor.1.2<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.2))

## [1] -0.4280734

(env.vasc.ph.cor.1.3<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.3))

## [1] 0.4254342

(env.vasc.ph.cor.1.4<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.4))

## [1] -0.3663671

(env.vasc.ph.cor.2.3<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.3))

## [1] 0.530381

(env.vasc.ph.cor.2.4<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.4))

## [1] -0.4398458

(env.vasc.ph.cor.3.4<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.4))

## [1] 0.53424

# Correlations between vascular abundance clusters and vascular phylogenetic abundance clusters
(vasc.vasc.ph.cor.1<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.1))

## [1] -0.1242853

(vasc.vasc.ph.cor.2<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.2))

## [1] -0.06821792

(vasc.vasc.ph.cor.3<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.3))

## [1] 0.7204712

(vasc.vasc.ph.cor.4<-cor(vasc.abd1.ord.ind.4, vasc.ph.abd1.ord.ind.4))

## [1] 0.1908305

# Cross correlatons between vascular abundance clusters and vascular phylogenetic abundance clusters
(vasc.vasc.ph.cor.1.2<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.2))

## [1] 0.3080669

(vasc.vasc.ph.cor.1.3<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.3))

## [1] -0.5005893

(vasc.vasc.ph.cor.1.4<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.4))

## [1] 0.2268724

(vasc.vasc.ph.cor.2.3<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.3))

## [1] -0.03839401

(vasc.vasc.ph.cor.2.4<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.4))

## [1] 0.06232213

(vasc.vasc.ph.cor.3.4<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.4))

## [1] -0.4109606

# Correlations between angiosperm abundance clusters and angiosperm phylogenetic abundance clusters
(angio.angio.ph.cor.1<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.1))

## [1] 0.3192203

(angio.angio.ph.cor.2<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.2))

## [1] 0.5966589

(angio.angio.ph.cor.3<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.3))

## [1] -0.2042222

(angio.angio.ph.cor.4<-cor(angio.abd1.ord.ind.4, angio.ph.abd1.ord.ind.4))

## [1] 0.2657396

# Cross correlatons between angiosperm abundance clusters and angiosperm phylogenetic abundance clusters
(angio.angio.ph.cor.1.2<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.2))

## [1] -0.151293

(angio.angio.ph.cor.1.3<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.3))

## [1] 0.1117277

(angio.angio.ph.cor.1.4<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.4))

## [1] -0.363996

(angio.angio.ph.cor.2.3<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.3))

## [1] 0.01454866

(angio.angio.ph.cor.2.4<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.4))

## [1] -0.640978

(angio.angio.ph.cor.3.4<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.4))

## [1] 0.8121781

Presence-absence analyses

Presence-absence indicator species plots

First is for Environmental distances, 2 and 3 for vascular plants, while 4th and 5th plots are for angiosperm only analyses

#dev.new(fig.width=11.8, fig.height=11.8)
par(mfrow=c(2,3))
par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(100*env.dist.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(520,nspecies),1:nspecies,rep(520,nspecies)+(100*env.dist.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(100*env.dist.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(680,nspecies),1:nspecies,rep(680,nspecies)+(100*env.dist.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(760,nspecies),1:nspecies,rep(760,nspecies)+(100*env.dist.ord.ind.5), 1:nspecies,lwd=3, col="black")

par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(100*vasc.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(540,nspecies),1:nspecies,rep(540,nspecies)+(100*vasc.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(100*vasc.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(670,nspecies),1:nspecies,rep(670,nspecies)+(100*vasc.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(100*vasc.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")

 par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(100*vasc.ph.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(540,nspecies),1:nspecies,rep(540,nspecies)+(100*vasc.ph.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(100*vasc.ph.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(670,nspecies),1:nspecies,rep(670,nspecies)+(100*vasc.ph.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(100*vasc.ph.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")


par(mai=c(0.05,0,0.25,0))
  plot(angio.tree.ind, x.lim=450,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(angio.tree.ind$tip.label)
    segments(rep(220,nspecies),1:nspecies,rep(220,nspecies)+(40*angio.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(265,nspecies),1:nspecies,rep(265,nspecies)+(40*angio.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(300,nspecies),1:nspecies,rep(300,nspecies)+(40*angio.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(350,nspecies),1:nspecies,rep(350,nspecies)+(40*angio.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(100*angio.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")

 par(mai=c(0.05,0,0.25,0))
  plot(angio.tree.ind, x.lim=450,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(angio.tree.ind$tip.label)
       segments(rep(220,nspecies),1:nspecies,rep(220,nspecies)+(40*angio.ph.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(265,nspecies),1:nspecies,rep(265,nspecies)+(40*angio.ph.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(300,nspecies),1:nspecies,rep(300,nspecies)+(40*angio.ph.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(350,nspecies),1:nspecies,rep(350,nspecies)+(40*angio.ph.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     #segments(rep(380,nspecies),1:nspecies,rep(380,nspecies)+(40*angio.ph.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")

Presence-absence correlations for environmental distances

#dev.new(fig.width=11.8, fig.height=11.8)
par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=800,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(110*env.dist.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(540,nspecies),1:nspecies,rep(540,nspecies)+(110*env.dist.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(640,nspecies),1:nspecies,rep(640,nspecies)+(110*env.dist.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(740,nspecies),1:nspecies,rep(740,nspecies)+(110*env.dist.ord.ind.4), 1:nspecies,lwd=3, col="black")

     #segments(rep(760,nspecies),1:nspecies,rep(760,nspecies)+(100*env.dist.ord.ind.5), 1:nspecies,lwd=3, col="black")

Phylogenetic signal with presence absence data

#Phylogenetic signal in environmental distance - vaculars
(env.dist.1.k<-Kcalc(env.dist.ord.ind.1,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01154802

(env.dist.2.k<-Kcalc(env.dist.ord.ind.2,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01202211

(env.dist.3.k<-Kcalc(env.dist.ord.ind.3,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01144663

(env.dist.4.k<-Kcalc(env.dist.ord.ind.4,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.02004414

(env.dist.1.phylosignal<-phylosignal(env.dist.ord.ind.1,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.01154802      0.003703976           0.003141092          0.741
##   PIC.variance.Z
## 1      0.4962177

(env.dist.2.phylosignal<-phylosignal(env.dist.ord.ind.2,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.01202211      0.003702836           0.003419992           0.64
##   PIC.variance.Z
## 1      0.2284798

(env.dist.3.phylosignal<-phylosignal(env.dist.ord.ind.3,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.01144663      0.004096796           0.003506376          0.699
##   PIC.variance.Z
## 1      0.3073321

(env.dist.4.phylosignal<-phylosignal(env.dist.ord.ind.4,vasc.tree.ind))

##            K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P
## 1 0.02004414      0.003264312           0.004669687          0.251
##   PIC.variance.Z
## 1      -0.713421

#Phylogenetic signal in vascular beta diversity
(vasc.pa.1.k<-Kcalc(vasc.abd1.ord.ind.1,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.04955354

(vasc.pa.2.k<-Kcalc(vasc.abd1.ord.ind.2,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01148123

(vasc.pa.3.k<-Kcalc(vasc.abd1.ord.ind.3,vasc.tree.ind,checkdata=TRUE))

##           [,1]
## [1,] 0.0124662

(vasc.pa.4.k<-Kcalc(vasc.abd1.ord.ind.4,vasc.tree.ind,checkdata=TRUE))

##             [,1]
## [1,] 0.009355493

#Phylogenetic signal in vascular phylogenetic beta diversity clusters
(vasc.ph.pa.1.k<-Kcalc(vasc.ph.abd1.ord.ind.1,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.05331261

(vasc.ph.pa.2.k<-Kcalc(vasc.ph.abd1.ord.ind.2,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01408523

(vasc.ph.pa.3.k<-Kcalc(vasc.ph.abd1.ord.ind.3,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01945341

(vasc.ph.pa.4.k<-Kcalc(vasc.ph.abd1.ord.ind.4,vasc.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01717582

#Phylogenetic signal in angiosperm beta diversity clusters
(angio.pa.1.k<-Kcalc(angio.abd1.ord.ind.1,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.02250227

(angio.pa.2.k<-Kcalc(angio.abd1.ord.ind.2,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.03262545

(angio.pa.3.k<-Kcalc(angio.abd1.ord.ind.3,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.04916715

(angio.pa.4.k<-Kcalc(angio.abd1.ord.ind.4,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.02078122

#Phylogenetic signal in angiosperm phylogenetic beta diversity clusters
(angio.ph.pa.1.k<-Kcalc(angio.ph.abd1.ord.ind.1,angio.tree.ind,checkdata=TRUE))

##           [,1]
## [1,] 0.0165709

(angio.ph.pa.2.k<-Kcalc(angio.ph.abd1.ord.ind.2,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.01535887

(angio.ph.pa.3.k<-Kcalc(angio.ph.abd1.ord.ind.3,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.04656126

(angio.ph.pa.4.k<-Kcalc(angio.ph.abd1.ord.ind.4,angio.tree.ind,checkdata=TRUE))

##            [,1]
## [1,] 0.03119751

Correlations for presence absence data

# Correlations between environmental distance and vascular abundance clusters
(env.vasc.cor.1<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.1))

## [1] -0.3152275

(env.vasc.cor.2<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.2))

## [1] 0.00602507

(env.vasc.cor.3<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.3))

## [1] -0.573106

(env.vasc.cor.4<-cor(env.dist.ord.ind.4, vasc.abd1.ord.ind.4))

## [1] -0.06045258

# Cross Correlations between environmental distance and vascular abundance clusters
(env.vasc.cor.1.2<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.2))

## [1] 0.1048645

(env.vasc.cor.1.3<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.3))

## [1] 0.5687968

(env.vasc.cor.1.4<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.4))

## [1] -0.4026471

(env.vasc.cor.2.3<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.3))

## [1] 0.5276995

(env.vasc.cor.2.4<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.4))

## [1] -0.2384476

(env.vasc.cor.3.4<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.4))

## [1] 0.6847883

# Correlations between environmental distance and vascular phylogenetic abundance clusters
(env.vasc.ph.cor.1<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.1))

## [1] 0.4789889

(env.vasc.ph.cor.2<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.2))

## [1] -0.307642

(env.vasc.ph.cor.3<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.3))

## [1] -0.5424174

(env.vasc.ph.cor.4<-cor(env.dist.ord.ind.4, vasc.ph.abd1.ord.ind.4))

## [1] 0.2095671

# Cross correlations between environmental distance and vascular phylogenetic abundance clusters

(env.vasc.ph.cor.1.2<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.2))

## [1] -0.4280734

(env.vasc.ph.cor.1.3<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.3))

## [1] 0.4254342

(env.vasc.ph.cor.1.4<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.4))

## [1] -0.3663671

(env.vasc.ph.cor.2.3<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.3))

## [1] 0.530381

(env.vasc.ph.cor.2.4<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.4))

## [1] -0.4398458

(env.vasc.ph.cor.3.4<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.4))

## [1] 0.53424

# Correlations between vascular abundance clusters and vascular phylogenetic abundance clusters
(vasc.vasc.ph.cor.1<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.1))

## [1] -0.1242853

(vasc.vasc.ph.cor.2<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.2))

## [1] -0.06821792

(vasc.vasc.ph.cor.3<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.3))

## [1] 0.7204712

(vasc.vasc.ph.cor.4<-cor(vasc.abd1.ord.ind.4, vasc.ph.abd1.ord.ind.4))

## [1] 0.1908305

# Cross correlatons between vascular abundance clusters and vascular phylogenetic abundance clusters
(vasc.vasc.ph.cor.1.2<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.2))

## [1] 0.3080669

(vasc.vasc.ph.cor.1.3<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.3))

## [1] -0.5005893

(vasc.vasc.ph.cor.1.4<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.4))

## [1] 0.2268724

(vasc.vasc.ph.cor.2.3<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.3))

## [1] -0.03839401

(vasc.vasc.ph.cor.2.4<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.4))

## [1] 0.06232213

(vasc.vasc.ph.cor.3.4<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.4))

## [1] -0.4109606

# Correlations between angiosperm abundance clusters and angiosperm phylogenetic abundance clusters
(angio.angio.ph.cor.1<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.1))

## [1] 0.3192203

(angio.angio.ph.cor.2<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.2))

## [1] 0.5966589

(angio.angio.ph.cor.3<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.3))

## [1] -0.2042222

(angio.angio.ph.cor.4<-cor(angio.abd1.ord.ind.4, angio.ph.abd1.ord.ind.4))

## [1] 0.2657396

# Cross correlatons between angiosperm abundance clusters and angiosperm phylogenetic abundance clusters
(angio.angio.ph.cor.1.2<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.2))

## [1] -0.151293

(angio.angio.ph.cor.1.3<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.3))

## [1] 0.1117277

(angio.angio.ph.cor.1.4<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.4))

## [1] -0.363996

(angio.angio.ph.cor.2.3<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.3))

## [1] 0.01454866

(angio.angio.ph.cor.2.4<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.4))

## [1] -0.640978

(angio.angio.ph.cor.3.4<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.4))

## [1] 0.8121781