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$set(cache=FALSE, fig.align='center')
# vascular  abundance weighted - weighted by phylogenetic distances
ph.abd.vasc.groups.7<- cbind(abd.sp.allsp, vasc.ph.abd1.cfuz.7$cluster)
colnames(ph.abd.vasc.groups.7)[which(colnames(ph.abd.vasc.groups.7) == "")] <- "Group"
Seven.clust.1.ph.abd.vasc<-subset(ph.abd.vasc.groups.7,ph.abd.vasc.groups.7[,111]=="1")
Seven.clust.2.ph.abd.vasc<-subset(ph.abd.vasc.groups.7,ph.abd.vasc.groups.7[,111]=="2")
Seven.clust.3.ph.abd.vasc<-subset(ph.abd.vasc.groups.7,ph.abd.vasc.groups.7[,111]=="3")
Seven.clust.4.ph.abd.vasc<-subset(ph.abd.vasc.groups.7,ph.abd.vasc.groups.7[,111]=="4")
Seven.clust.5.ph.abd.vasc<-subset(ph.abd.vasc.groups.7,ph.abd.vasc.groups.7[,111]=="5")
Seven.clust.6.ph.abd.vasc<-subset(ph.abd.vasc.groups.7,ph.abd.vasc.groups.7[,111]=="6")
Seven.clust.7.ph.abd.vasc<-subset(ph.abd.vasc.groups.7,ph.abd.vasc.groups.7[,111]=="7")

# Take mean across all species in a cluster
Seven.clust.1.ph.abd.vasc.mean<-colMeans(Seven.clust.1.ph.abd.vasc[,1:110])
Seven.clust.2.ph.abd.vasc.mean<-colMeans(Seven.clust.2.ph.abd.vasc[,1:110])
Seven.clust.3.ph.abd.vasc.mean<-colMeans(Seven.clust.3.ph.abd.vasc[,1:110])
Seven.clust.4.ph.abd.vasc.mean<-colMeans(Seven.clust.4.ph.abd.vasc[,1:110])
Seven.clust.5.ph.abd.vasc.mean<-colMeans(Seven.clust.5.ph.abd.vasc[,1:110])
Seven.clust.6.ph.abd.vasc.mean<-colMeans(Seven.clust.6.ph.abd.vasc[,1:110])
Seven.clust.7.ph.abd.vasc.mean<-colMeans(Seven.clust.7.ph.abd.vasc[,1:110])

Seven.clust.all.ph.abd.vasc<-rbind(Seven.clust.1.ph.abd.vasc.mean, Seven.clust.2.ph.abd.vasc.mean, Seven.clust.3.ph.abd.vasc.mean,
Seven.clust.4.ph.abd.vasc.mean,Seven.clust.5.ph.abd.vasc.mean,Seven.clust.6.ph.abd.vasc.mean,Seven.clust.7.ph.abd.vasc.mean )
rownames(Seven.clust.all.ph.abd.vasc)<-c("Cluster 1", "Cluster 2", "Cluster 3", "Cluster 4", "Cluster 5", "Cluster 6", "Cluster 7")
# Calculate contribution to beta diversity for five environmental distance clusters
ph.abd.vasc.res <- beta.div(Seven.clust.all.ph.abd.vasc, "hellinger", nperm=999)
#get species BD scores
ph.abd.vasc.clust.SCBD<-ph.abd.vasc.res$SCBD

abd.vasc.clust.SCBD<-abd.vasc.res$SCBD

vasc.tree.tip.order<-c("AbiBal","LarLar","PicGla","PicMar","JunCom","AchMil","EurRad","SolMac","SolMul","AntAlp","PacAur","PetFri","ArnAng","LinBor","LonVil","VibEdu","BarAlp",
"RhiMin","CasSep","AndPol","GauHis","VacCes","VacMyr","VacOxy","VacUli","VacVit","EmpNig","KalPol","RhoGro","RhoLap","MonUni","OrtSec","PyrAsa","PyrGra",
"ArcAlp","DiaLap","TriBor","CorCan","CerAlp","SteBor","MinBif","BisViv","GeoLiv","AlnVir","BetGla","MyrGal","AmeBar","DasFru","FraVir","RubArc",
"RubIda","RubCha","DryInt","SalArc","SalPla","SalGla","SalPed","SalArg","SalVes","SalUva","SalHum","VioAdu","VioRen","ChaAng","EpiHor","MitNud","RibGla",
"AnePar","CopTri","AgrMer","CalCan","TriSpi","AntMon","AveFle","PoaArc","ElyTra","SchPur","CarAqu","CarBig","CarLim","CarMag","CarUtr","CarCap","CarDef","CarVag",
"CarSci","CarBru","CarTri","CarGyn","CarDis","CarCat","CarLep","EriVir","TriAlp","TriCes","JunTri","LuzPar","LisCor","MaiTri","TofPus","CysMon","DryExp","EquArv",
"EquSyl","EquSci","EquVar","DipCom","LycAno","HupApr","SelSel")

env.dist.match <- match(vasc.tree.tip.order, names(env.clust.SCBD)) 
env.dist.ord<- env.clust.SCBD[env.dist.match] 

abd.vasc.match <- match(vasc.tree.tip.order, names(abd.vasc.clust.SCBD)) 
abd.vasc.ord<- abd.vasc.clust.SCBD[abd.vasc.match] 

ph.abd.vasc.match <- match(vasc.tree.tip.order, names(ph.abd.vasc.clust.SCBD)) 
ph.abd.vasc.ord<- ph.abd.vasc.clust.SCBD[ph.abd.vasc.match]

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

# Pearson's correlation coefficients of SCBD values

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] 0.8777063
# Correlation between Gower's distance and phylogenetic beta diversity
cor.env.dist.ph.bd.vasc
## [1] 0.9195063
# Correlation between beta diversity and phylogenetic beta diversity
cor.bd.ph.bd.vasc
## [1] 0.9283242
#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; SCBD values
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] 0.8556148
# Correlation between Gower's distance and phylogenetic beta diversity
cor.env.dist.ph.bd.angio
## [1] 0.8250279
# Correlation between beta diversity and phylogenetic beta diversity
cor.bd.ph.bd.angio
## [1] 0.9603419
cor.bd.ph.bd.angio
## [1] 0.9603419

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

#dev.new(width=11.8, 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(290,nspecies),1:nspecies,rep(290,nspecies)+(180*ph.abd.angio.ord), 1:nspecies,lwd=4, col="grey50")

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

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<-(colSums(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] -0.1697375
# Vascular abundance with SCBD
(vasc.freq.corr<-cor(freq.sp,abd.vasc.ord))
## [1] -0.1144554
# Vascular phylogenetic abundance with SCBD
(vasc.ph.freq.corr<-cor(freq.sp,ph.abd.vasc.ord))
## [1] -0.1247391
# Angiosperms with SCBD
(angio.freq.corr<-cor(angio.freq.sp,abd.angio.ord))
## [1] 0.03323914
# Angiosperms with angiosperm SCBD (phylogenetic)
(angio.ph.freq.corr<-cor(angio.freq.sp,ph.abd.angio.ord))
## [1] 0.03934478

Indicator species analysis - correlations of species with different habitats

Order for the following plots is top - vasculars; bottom -angiosperms


1 - environmental distance; 2 - vasc.BD; 3 - vasc.phBD; 4 - angioBD; 5 -angioPh.BD

#dev.new(width=11.8, height=8)
par(mfrow=c(2,3))
par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=1000,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(90*env.dist.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(540,nspecies),1:nspecies,rep(540,nspecies)+(90*env.dist.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(640,nspecies),1:nspecies,rep(640,nspecies)+(90*env.dist.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(730,nspecies),1:nspecies,rep(730,nspecies)+(90*env.dist.ord.ind.4), 1:nspecies,lwd=3, col="black")
    segments(rep(820,nspecies),1:nspecies,rep(820,nspecies)+(90*env.dist.ord.ind.5), 1:nspecies,lwd=3, col="black")
     segments(rep(910,nspecies),1:nspecies,rep(910,nspecies)+(90*env.dist.ord.ind.6), 1:nspecies,lwd=3, col="black")
     segments(rep(1000,nspecies),1:nspecies,rep(1000,nspecies)+(90*env.dist.ord.ind.7), 1:nspecies,lwd=3, col="black")

par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=1000,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(90*vasc.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(550,nspecies),1:nspecies,rep(550,nspecies)+(90*vasc.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(90*vasc.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
    segments(rep(670,nspecies),1:nspecies,rep(670,nspecies)+(90*vasc.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
    segments(rep(775,nspecies),1:nspecies,rep(775,nspecies)+(90*vasc.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")
    segments(rep(880,nspecies),1:nspecies,rep(880,nspecies)+(90*vasc.abd1.ord.ind.6), 1:nspecies,lwd=3, col="black")
    segments(rep(975,nspecies),1:nspecies,rep(975,nspecies)+(90*vasc.abd1.ord.ind.7), 1:nspecies,lwd=3, col="black")

 par(mai=c(0.05,0,0.25,0))
  plot(vasc.tree.ind, x.lim=1000,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(vasc.tree.ind$tip.label)
    segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(90*vasc.ph.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(550,nspecies),1:nspecies,rep(550,nspecies)+(90*vasc.ph.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(600,nspecies),1:nspecies,rep(600,nspecies)+(90*vasc.ph.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
    segments(rep(670,nspecies),1:nspecies,rep(670,nspecies)+(90*vasc.ph.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
    segments(rep(735,nspecies),1:nspecies,rep(735,nspecies)+(90*vasc.ph.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")
    segments(rep(830,nspecies),1:nspecies,rep(830,nspecies)+(90*vasc.ph.abd1.ord.ind.6), 1:nspecies,lwd=3, col="black")
    segments(rep(925,nspecies),1:nspecies,rep(925,nspecies)+(90*vasc.ph.abd1.ord.ind.7), 1:nspecies,lwd=3, col="black")

par(mai=c(0.05,0,0.25,0))
  plot(angio.tree.ind, x.lim=500,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(angio.tree.ind$tip.label)
    segments(rep(220,nspecies),1:nspecies,rep(220,nspecies)+(35*angio.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(265,nspecies),1:nspecies,rep(265,nspecies)+(35*angio.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(300,nspecies),1:nspecies,rep(300,nspecies)+(35*angio.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
      segments(rep(350,nspecies),1:nspecies,rep(350,nspecies)+(35*angio.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
      segments(rep(400,nspecies),1:nspecies,rep(400,nspecies)+(35*angio.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")
      segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(35*angio.abd1.ord.ind.6), 1:nspecies,lwd=3, col="black")
      segments(rep(500,nspecies),1:nspecies,rep(500,nspecies)+(35*angio.abd1.ord.ind.7), 1:nspecies,lwd=3, col="black")
 
 par(mai=c(0.05,0,0.25,0))
  plot(angio.tree.ind, x.lim=500,show.tip.label = FALSE,edge.width=2)
    nspecies <- length(angio.tree.ind$tip.label)
       segments(rep(220,nspecies),1:nspecies,rep(220,nspecies)+(35*angio.ph.abd1.ord.ind.1), 1:nspecies,lwd=3, col="black")
     segments(rep(265,nspecies),1:nspecies,rep(265,nspecies)+(35*angio.ph.abd1.ord.ind.2), 1:nspecies,lwd=3, col="black")
     segments(rep(300,nspecies),1:nspecies,rep(300,nspecies)+(35*angio.ph.abd1.ord.ind.3), 1:nspecies,lwd=3, col="black")
     segments(rep(350,nspecies),1:nspecies,rep(350,nspecies)+(35*angio.ph.abd1.ord.ind.4), 1:nspecies,lwd=3, col="black")
     segments(rep(400,nspecies),1:nspecies,rep(400,nspecies)+(35*angio.ph.abd1.ord.ind.5), 1:nspecies,lwd=3, col="black")
     segments(rep(450,nspecies),1:nspecies,rep(450,nspecies)+(35*angio.ph.abd1.ord.ind.6), 1:nspecies,lwd=3, col="black")
    segments(rep(500,nspecies),1:nspecies,rep(500,nspecies)+(35*angio.ph.abd1.ord.ind.7), 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,] 0.01544149
(env.dist.2.k<-Kcalc(env.dist.ord.ind.2,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01726992
(env.dist.3.k<-Kcalc(env.dist.ord.ind.3,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02554687
(env.dist.4.k<-Kcalc(env.dist.ord.ind.4,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01500557
(env.dist.5.k<-Kcalc(env.dist.ord.ind.5,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01840924
(env.dist.6.k<-Kcalc(env.dist.ord.ind.6,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02972459
(env.dist.7.k<-Kcalc(env.dist.ord.ind.7,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01464341
#Phylogenetic signal in vascular beta diversity
(vasc.abd.1.k<-Kcalc(vasc.abd1.ord.ind.1,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02247142
(vasc.abd.2.k<-Kcalc(vasc.abd1.ord.ind.2,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01880492
(vasc.abd.3.k<-Kcalc(vasc.abd1.ord.ind.3,vasc.tree.ind,checkdata=TRUE))
##           [,1]
## [1,] 0.0128595
(vasc.abd.4.k<-Kcalc(vasc.abd1.ord.ind.4,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02131859
(vasc.abd.5.k<-Kcalc(vasc.abd1.ord.ind.5,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.00457153
(vasc.abd.6.k<-Kcalc(vasc.abd1.ord.ind.6,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01069588
(vasc.abd.7.k<-Kcalc(vasc.abd1.ord.ind.7,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01600371
#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,] 0.04469123
(vasc.ph.abd.2.k<-Kcalc(vasc.ph.abd1.ord.ind.2,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01053975
(vasc.ph.abd.3.k<-Kcalc(vasc.ph.abd1.ord.ind.3,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01661019
(vasc.ph.abd.4.k<-Kcalc(vasc.ph.abd1.ord.ind.4,vasc.tree.ind,checkdata=TRUE))
##             [,1]
## [1,] 0.005846679
(vasc.ph.abd.5.k<-Kcalc(vasc.ph.abd1.ord.ind.5,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01743579
(vasc.ph.abd.6.k<-Kcalc(vasc.ph.abd1.ord.ind.6,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02232636
(vasc.ph.abd.7.k<-Kcalc(vasc.ph.abd1.ord.ind.7,vasc.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.01704068
#Phylogenetic signal in angiosperm beta diversity clusters
(angio.abd.1.k<-Kcalc(angio.abd1.ord.ind.1,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02201821
(angio.abd.2.k<-Kcalc(angio.abd1.ord.ind.2,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.03155374
(angio.abd.3.k<-Kcalc(angio.abd1.ord.ind.3,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.04720777
(angio.abd.4.k<-Kcalc(angio.abd1.ord.ind.4,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.04866125
(angio.abd.5.k<-Kcalc(angio.abd1.ord.ind.5,angio.tree.ind,checkdata=TRUE))
##             [,1]
## [1,] 0.008400953
(angio.abd.6.k<-Kcalc(angio.abd1.ord.ind.6,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02483113
(angio.abd.7.k<-Kcalc(angio.abd1.ord.ind.7,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02126447
#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,] 0.03257588
(angio.ph.abd.2.k<-Kcalc(angio.ph.abd1.ord.ind.2,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02017966
(angio.ph.abd.3.k<-Kcalc(angio.ph.abd1.ord.ind.3,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.06590139
(angio.ph.abd.4.k<-Kcalc(angio.ph.abd1.ord.ind.4,angio.tree.ind,checkdata=TRUE))
##             [,1]
## [1,] 0.008681027
(angio.ph.abd.5.k<-Kcalc(angio.ph.abd1.ord.ind.5,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.07263425
(angio.ph.abd.6.k<-Kcalc(angio.ph.abd1.ord.ind.6,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02274282
(angio.ph.abd.7.k<-Kcalc(angio.ph.abd1.ord.ind.7,angio.tree.ind,checkdata=TRUE))
##            [,1]
## [1,] 0.02610468

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] 0.1149759
(env.vasc.cor.2<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.2))
## [1] -0.1071011
(env.vasc.cor.3<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.3))
## [1] 0.09082502
(env.vasc.cor.4<-cor(env.dist.ord.ind.4, vasc.abd1.ord.ind.4))
## [1] 0.09644649
(env.vasc.cor.5<-cor(env.dist.ord.ind.5, vasc.abd1.ord.ind.5))
## [1] -0.2263778
(env.vasc.cor.6<-cor(env.dist.ord.ind.6, vasc.abd1.ord.ind.6))
## [1] 0.6444065
(env.vasc.cor.7<-cor(env.dist.ord.ind.7, vasc.abd1.ord.ind.7))
## [1] -0.2928288
# 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] 0.06385534
(env.vasc.cor.1.3<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.3))
## [1] 0.5784403
(env.vasc.cor.1.4<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.4))
## [1] -0.29635
(env.vasc.cor.1.5<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.5))
## [1] -0.1135239
(env.vasc.cor.1.6<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.6))
## [1] -0.366108
(env.vasc.cor.1.7<-cor(env.dist.ord.ind.1, vasc.abd1.ord.ind.7))
## [1] 0.1560864
(env.vasc.cor.2.3<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.3))
## [1] 0.3536335
(env.vasc.cor.2.4<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.4))
## [1] -0.2478085
(env.vasc.cor.2.5<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.5))
## [1] 0.176534
(env.vasc.cor.2.6<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.6))
## [1] -0.4237109
(env.vasc.cor.2.7<-cor(env.dist.ord.ind.2, vasc.abd1.ord.ind.7))
## [1] 0.07338939
(env.vasc.cor.3.4<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.4))
## [1] -0.2340247
(env.vasc.cor.3.5<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.5))
## [1] -0.004987125
(env.vasc.cor.3.6<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.6))
## [1] -0.2983485
(env.vasc.cor.3.7<-cor(env.dist.ord.ind.3, vasc.abd1.ord.ind.7))
## [1] 0.3662713
(env.vasc.cor.4.5<-cor(env.dist.ord.ind.4, vasc.abd1.ord.ind.5))
## [1] -0.4212047
(env.vasc.cor.4.6<-cor(env.dist.ord.ind.4, vasc.abd1.ord.ind.6))
## [1] 0.1213187
(env.vasc.cor.4.7<-cor(env.dist.ord.ind.4, vasc.abd1.ord.ind.7))
## [1] 0.3592117
(env.vasc.cor.5.6<-cor(env.dist.ord.ind.5, vasc.abd1.ord.ind.6))
## [1] -0.005214133
(env.vasc.cor.5.7<-cor(env.dist.ord.ind.5, vasc.abd1.ord.ind.7))
## [1] -0.1279543
(env.vasc.cor.6.7<-cor(env.dist.ord.ind.6, vasc.abd1.ord.ind.7))
## [1] -0.4053868
# 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] -0.08838228
(env.vasc.ph.cor.2<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.2))
## [1] 0.598388
(env.vasc.ph.cor.3<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.3))
## [1] -0.4257033
(env.vasc.ph.cor.4<-cor(env.dist.ord.ind.4, vasc.ph.abd1.ord.ind.4))
## [1] -0.1618167
(env.vasc.ph.cor.5<-cor(env.dist.ord.ind.5, vasc.ph.abd1.ord.ind.5))
## [1] -0.1477845
(env.vasc.ph.cor.6<-cor(env.dist.ord.ind.6, vasc.ph.abd1.ord.ind.6))
## [1] 0.408036
(env.vasc.ph.cor.7<-cor(env.dist.ord.ind.7, vasc.ph.abd1.ord.ind.7))
## [1] -0.0748238
# Cross correlations between environmental distance and vascular phylogenetic abundance clusters
(env.vasc.cor.1.2<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.2))
## [1] 0.4267052
(env.vasc.cor.1.3<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.3))
## [1] -0.128093
(env.vasc.cor.1.4<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.4))
## [1] 0.5908637
(env.vasc.cor.1.5<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.5))
## [1] -0.0916221
(env.vasc.cor.1.6<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.6))
## [1] -0.2859728
(env.vasc.cor.1.7<-cor(env.dist.ord.ind.1, vasc.ph.abd1.ord.ind.7))
## [1] -0.3631767
(env.vasc.cor.2.3<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.3))
## [1] -0.2318916
(env.vasc.cor.2.4<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.4))
## [1] 0.3442483
(env.vasc.cor.2.5<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.5))
## [1] -0.01665331
(env.vasc.cor.2.6<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.6))
## [1] -0.4696675
(env.vasc.cor.2.7<-cor(env.dist.ord.ind.2, vasc.ph.abd1.ord.ind.7))
## [1] -0.3366515
(env.vasc.cor.3.4<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.4))
## [1] 0.08397413
(env.vasc.cor.3.5<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.5))
## [1] 0.6625281
(env.vasc.cor.3.6<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.6))
## [1] -0.2109846
(env.vasc.cor.3.7<-cor(env.dist.ord.ind.3, vasc.ph.abd1.ord.ind.7))
## [1] -0.3391508
(env.vasc.cor.4.5<-cor(env.dist.ord.ind.4, vasc.ph.abd1.ord.ind.5))
## [1] 0.2959771
(env.vasc.cor.4.6<-cor(env.dist.ord.ind.4, vasc.ph.abd1.ord.ind.6))
## [1] 0.5825083
(env.vasc.cor.4.7<-cor(env.dist.ord.ind.4, vasc.ph.abd1.ord.ind.7))
## [1] 0.1162141
(env.vasc.cor.5.6<-cor(env.dist.ord.ind.5, vasc.ph.abd1.ord.ind.6))
## [1] 0.1733007
(env.vasc.cor.5.7<-cor(env.dist.ord.ind.5, vasc.ph.abd1.ord.ind.7))
## [1] 0.8335282
(env.vasc.cor.6.7<-cor(env.dist.ord.ind.6, vasc.ph.abd1.ord.ind.7))
## [1] 0.2909692
# 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] 0.6732019
(vasc.vasc.ph.cor.2<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.2))
## [1] 0.2045106
(vasc.vasc.ph.cor.3<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.3))
## [1] -0.2519662
(vasc.vasc.ph.cor.4<-cor(vasc.abd1.ord.ind.4, vasc.ph.abd1.ord.ind.4))
## [1] -0.1351901
(vasc.vasc.ph.cor.5<-cor(vasc.abd1.ord.ind.5, vasc.ph.abd1.ord.ind.5))
## [1] -0.3974845
(vasc.vasc.ph.cor.6<-cor(vasc.abd1.ord.ind.6, vasc.ph.abd1.ord.ind.6))
## [1] 0.7073811
(vasc.vasc.ph.cor.7<-cor(vasc.abd1.ord.ind.7, vasc.ph.abd1.ord.ind.7))
## [1] -0.2102613
# Cross correlatons between vascular abundance clusters and vascular phylogenetic abundance cluster
(vasc.vasc.ph.cor.1.2<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.2))
## [1] -0.1097822
(vasc.vasc.ph.cor.1.3<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.3))
## [1] -0.4089772
(vasc.vasc.ph.cor.1.4<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.4))
## [1] 0.147999
(vasc.vasc.ph.cor.1.5<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.5))
## [1] 0.7038536
(vasc.vasc.ph.cor.1.6<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.6))
## [1] -0.2227658
(vasc.vasc.ph.cor.1.7<-cor(vasc.abd1.ord.ind.1, vasc.ph.abd1.ord.ind.7))
## [1] -0.3855439
(vasc.vasc.ph.cor.2.3<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.3))
## [1] 0.04108092
(vasc.vasc.ph.cor.2.4<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.4))
## [1] -0.2454858
(vasc.vasc.ph.cor.2.5<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.5))
## [1] -0.2408045
(vasc.vasc.ph.cor.2.6<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.6))
## [1] 0.06917386
(vasc.vasc.ph.cor.2.7<-cor(vasc.abd1.ord.ind.2, vasc.ph.abd1.ord.ind.7))
## [1] 0.1399444
(vasc.vasc.ph.cor.3.4<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.4))
## [1] 0.7529133
(vasc.vasc.ph.cor.3.5<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.5))
## [1] 0.2507026
(vasc.vasc.ph.cor.3.6<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.6))
## [1] -0.08411931
(vasc.vasc.ph.cor.3.7<-cor(vasc.abd1.ord.ind.3, vasc.ph.abd1.ord.ind.7))
## [1] -0.3617645
(vasc.vasc.ph.cor.4.5<-cor(vasc.abd1.ord.ind.4, vasc.ph.abd1.ord.ind.5))
## [1] -0.1647397
(vasc.vasc.ph.cor.4.6<-cor(vasc.abd1.ord.ind.4, vasc.ph.abd1.ord.ind.6))
## [1] 0.0468029
(vasc.vasc.ph.cor.4.7<-cor(vasc.abd1.ord.ind.4, vasc.ph.abd1.ord.ind.7))
## [1] 0.8058188
(vasc.vasc.ph.cor.5.6<-cor(vasc.abd1.ord.ind.5, vasc.ph.abd1.ord.ind.6))
## [1] -0.4215794
(vasc.vasc.ph.cor.5.7<-cor(vasc.abd1.ord.ind.5, vasc.ph.abd1.ord.ind.7))
## [1] -0.1458774
(vasc.vasc.ph.cor.6.7<-cor(vasc.abd1.ord.ind.6, vasc.ph.abd1.ord.ind.7))
## [1] -0.00254899
# 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] -0.08198223
(angio.angio.ph.cor.2<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.2))
## [1] -0.1603121
(angio.angio.ph.cor.3<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.3))
## [1] 0.3736046
(angio.angio.ph.cor.4<-cor(angio.abd1.ord.ind.4, angio.ph.abd1.ord.ind.4))
## [1] -0.1623956
(angio.angio.ph.cor.5<-cor(angio.abd1.ord.ind.5, angio.ph.abd1.ord.ind.5))
## [1] -0.361842
(angio.angio.ph.cor.6<-cor(angio.abd1.ord.ind.6, angio.ph.abd1.ord.ind.6))
## [1] 0.607431
(angio.angio.ph.cor.7<-cor(angio.abd1.ord.ind.7, angio.ph.abd1.ord.ind.7))
## [1] -0.1241695
# 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] 0.6557186
(angio.angio.ph.cor.1.3<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.3))
## [1] 0.275655
(angio.angio.ph.cor.1.4<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.4))
## [1] -0.1667193
(angio.angio.ph.cor.1.5<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.5))
## [1] -0.2153561
(angio.angio.ph.cor.1.6<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.6))
## [1] 0.1211153
(angio.angio.ph.cor.1.7<-cor(angio.abd1.ord.ind.1, angio.ph.abd1.ord.ind.7))
## [1] -0.3853187
(angio.angio.ph.cor.2.3<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.3))
## [1] -0.1275841
(angio.angio.ph.cor.2.4<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.4))
## [1] -0.1628338
(angio.angio.ph.cor.2.5<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.5))
## [1] -0.2529564
(angio.angio.ph.cor.2.6<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.6))
## [1] -0.2797077
(angio.angio.ph.cor.2.7<-cor(angio.abd1.ord.ind.2, angio.ph.abd1.ord.ind.7))
## [1] 0.2260766
(angio.angio.ph.cor.3.4<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.4))
## [1] -0.2707599
(angio.angio.ph.cor.3.5<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.5))
## [1] 0.2488969
(angio.angio.ph.cor.3.6<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.6))
## [1] 0.3748796
(angio.angio.ph.cor.3.7<-cor(angio.abd1.ord.ind.3, angio.ph.abd1.ord.ind.7))
## [1] -0.1778793
(angio.angio.ph.cor.4.5<-cor(angio.abd1.ord.ind.4, angio.ph.abd1.ord.ind.5))
## [1] 0.6605797
(angio.angio.ph.cor.4.6<-cor(angio.abd1.ord.ind.4, angio.ph.abd1.ord.ind.6))
## [1] -0.1664746
(angio.angio.ph.cor.4.7<-cor(angio.abd1.ord.ind.4, angio.ph.abd1.ord.ind.7))
## [1] 0.7251939
(angio.angio.ph.cor.5.6<-cor(angio.abd1.ord.ind.5, angio.ph.abd1.ord.ind.6))
## [1] -0.4764965
(angio.angio.ph.cor.5.7<-cor(angio.abd1.ord.ind.5, angio.ph.abd1.ord.ind.7))
## [1] -0.237013
(angio.angio.ph.cor.6.7<-cor(angio.abd1.ord.ind.6, angio.ph.abd1.ord.ind.7))
## [1] -0.1407931