Schefferville - transitions; Indicator value analysis

Tammy L. Elliott

Date: May 8, 2015

R version 3.1.0

In all analyzes MoeMac, SteLon, PhyCae, and ParKot dropped because of very low frequency affecting SCBD and indval analyzes

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

Correlations between SCBD for beta diversity and phylogenetic beta diversity in five environmental distance clusters

# 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] 0.7201603

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

## [1] 0.8553047

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

## [1] 0.8659517

#drop values for env.dist.ord to get angiosperms only
env.dist.ord.angio<-env.dist.ord[-match(c("LycAno", "HupApr", "DipCom", "SelSel", "CysMon", "DryExp", "EquSyl", "EquArv", "EquSci", "EquVar",
 "JunCom", "PicMar", "PicGla", "AbiBal", "LarLar"), names(env.dist.ord))]



# 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] 0.485916

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

## [1] 0.7135971

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

## [1] 0.8563642

SCBD ploted onto vascular(left) and angiosperm trees (right)

#dev.new(fig.width=11.8, fig.height=8)
par(mfrow=c(1,2))
par(mai=c(0.05,0,0.35,0))
 #Botany 2014 tree

  plot(trans.one.tree.short,x.lim=620,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(trans.one.tree.short$tip.label)
    segments(rep(430,nspecies),1:nspecies,rep(430,nspecies)+(400*env.dist.ord), 1:nspecies,lwd=4, col="grey15")
    segments(rep(490,nspecies),1:nspecies,rep(490,nspecies)+(400*abd.vasc.ord), 1:nspecies,lwd=4, col="grey65")
    segments(rep(575,nspecies),1:nspecies,rep(575,nspecies)+(400*ph.abd.vasc.ord), 1:nspecies,lwd=4, col="grey30")


par(mai=c(0.05,0,0.35,0.05))
  plot(angio.one.tree,x.lim=330,show.tip.label = FALSE,edge.width=2)

#angiosperms
    nspecies <- length(angio.one.tree$tip.label)
    segments(rep(210,nspecies),1:nspecies,rep(210,nspecies)+(180*env.dist.ord.angio), 1:nspecies,lwd=4, col="grey15")
    segments(rep(240,nspecies),1:nspecies,rep(240,nspecies)+(180*abd.angio.ord), 1:nspecies,lwd=4, col="grey80")
    segments(rep(300,nspecies),1:nspecies,rep(300,nspecies)+(180*ph.abd.angio.ord), 1:nspecies,lwd=4, col="grey50")

   ### Correlations with species frequencies across plots

    #Calculate number of occurrences per species
abd.sp.allsp.pa<-abd.sp.allsp
abd.sp.allsp.pa[abd.sp.allsp.pa > 0] <- 1 
freq.sp<-(rowSums(abd.sp.allsp.pa))

angio.sp.abd.pa<-angio.sp.abd
angio.sp.abd.pa[angio.sp.abd.pa > 0] <- 1 
angio.freq.sp<-(colSums(angio.sp.abd.pa))

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

## [1] -0.1658407

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

## [1] -0.08587918

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

## [1] -0.1299427

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

## [1] 0.07334939

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

## [1] 0.08223505

Indicator species analysis - correlations of species with different habitats

#dev.new(width=11.8, 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(540,nspecies),1:nspecies,rep(540,nspecies)+(100*env.dist.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(640,nspecies),1:nspecies,rep(640,nspecies)+(100*env.dist.ord.ind.3), 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(560,nspecies),1:nspecies,rep(560,nspecies)+(100*vasc.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(680,nspecies),1:nspecies,rep(680,nspecies)+(100*vasc.abd1.ord.ind.3), 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(560,nspecies),1:nspecies,rep(560,nspecies)+(100*vasc.ph.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(680,nspecies),1:nspecies,rep(680,nspecies)+(100*vasc.ph.abd1.ord.ind.3), 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")
 
 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")

Phylogenetic signal for each five cluster grouping

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

##            [,1]
## [1,] 0.01894965

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

##            [,1]
## [1,] 0.01320449

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

##            [,1]
## [1,] 0.01998485

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

##            [,1]
## [1,] 0.01417455

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

##            [,1]
## [1,] 0.01134952

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

##            [,1]
## [1,] 0.01626578

#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,] 0.02737991

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

##            [,1]
## [1,] 0.01700435

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

##            [,1]
## [1,] 0.01879321

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

##            [,1]
## [1,] 0.01514493

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

##            [,1]
## [1,] 0.01182563

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

##           [,1]
## [1,] 0.0272152

#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,] 0.02334658

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

##            [,1]
## [1,] 0.04212502

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

##           [,1]
## [1,] 0.0329172

Pearson’s correlation coefficients within and among same number clusters

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

## [1] 0.656703

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

## [1] -0.3607291

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

## [1] 0.1720055

# 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] -0.04991576

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

## [1] -0.6549457

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

## [1] 0.5988971

# 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] 0.5762924

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

## [1] -0.3437969

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

## [1] 0.2485699

# 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] 0.01432886

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

## [1] -0.6103926

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

## [1] 0.4560971

# 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] 0.783941

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

## [1] 0.7738621

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

## [1] 0.7693461

# 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] -0.5413719

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

## [1] -0.1964945

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

## [1] -0.495216

# 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] -0.1772756

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

## [1] -0.5322955

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

## [1] 0.8010058

# 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] 0.6547644

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

## [1] -0.4415199

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

## [1] -0.3068363