Schefferville - transitions; Beta diversity and phylogenetic beta diversity between sampling bands
Tammy L. Elliott
Date: February 28, 2015
R version 3.1.0
Prepare data for analysis
#Set transects that go down hill
A1<-abd.sp[grepl("A", rownames(abd.sp)),]
head(A1)## AchMil AgrMer AlnVir AmeBar AndPol AnePar AntAlp AntMon ArcAlp ArnAng
## EA1 0.00 0 0 0 0 0.0 0 0 0 0
## EA2 0.00 0 0 0 0 0.0 0 0 0 0
## EA3 0.25 0 0 0 0 0.5 0 0 0 0
## EA4 0.00 0 0 0 0 0.0 0 0 0 0
## EA5 0.00 0 0 0 0 0.0 0 0 0 0
## EA6 0.25 0 0 0 0 0.0 0 0 0 0
## BarAlp BetGla BisViv CalCan CarAqu CarBig CarBru CarCap CarCat CarDef
## EA1 0 0 0 0 0 0 0 0 0 0
## EA2 0 1 0 0 0 0 0 0 0 0
## EA3 0 7 0 0 0 0 0 0 0 0
## EA4 0 0 0 0 0 0 0 0 0 0
## EA5 0 0 0 0 0 0 0 0 0 0
## EA6 0 0 0 0 0 0 0 0 0 0
## CarDis CarGyn CarLep CarLim CarMag CarSci CarTri CarUtr CarVag CasSep
## EA1 0 0.25 0 0 0 0 0 0 6.00 0
## EA2 0 0.25 0 0 0 0 0 0 0.75 0
## EA3 0 0.25 0 0 0 0 0 0 1.00 0
## EA4 0 0.00 0 0 0 0 0 0 2.00 0
## EA5 0 0.00 0 0 0 0 0 0 0.00 0
## EA6 0 0.00 0 0 0 0 0 0 6.00 0
## CerAlp ChaAng CopTri CorCan CysMon DasFru AveFle DiaLap DipCom DryExp
## EA1 0 0 0.5 0.25 0 0 0 0 0 0
## EA2 0 0 0.0 0.25 0 0 0 0 0 0
## EA3 0 0 0.0 0.00 0 0 0 0 0 0
## EA4 0 0 0.0 0.50 0 0 0 0 0 0
## EA5 0 0 1.0 1.00 0 0 0 0 0 0
## EA6 0 0 0.0 0.25 0 0 0 0 0 0
## DryInt ElyTra EmpNig EpiHor EquArv EquSci EquSyl EquVar EriVir EurRad
## EA1 0 0 0.75 0 0 0.25 0.75 0 0 0.00
## EA2 0 0 0.00 0 0 0.25 0.00 0 0 0.00
## EA3 0 0 0.00 0 0 0.00 0.00 0 0 0.25
## EA4 0 0 0.00 0 0 0.75 0.00 0 0 0.00
## EA5 0 0 0.00 0 0 0.00 0.00 0 0 0.00
## EA6 0 0 0.00 0 0 0.25 0.00 0 0 0.00
## FraVir GauHis GeoLiv HupApr JunCom JunTri KalPol LinBor LisCor LonVil
## EA1 0 0.25 0.25 0 0 0 0.25 0.25 0 0
## EA2 0 0.00 0.00 0 0 0 0.00 1.00 0 0
## EA3 0 0.00 0.25 0 0 0 0.00 0.75 0 0
## EA4 0 0.00 0.25 0 0 0 0.00 3.00 0 0
## EA5 0 0.00 0.00 0 0 0 0.00 4.00 0 0
## EA6 8 0.00 0.00 0 0 0 0.00 20.00 0 0
## LuzPar LycAno MaiTri MinBif MitNud MoeMac MonUni MyrGal OrtSec PacAur
## EA1 0 0 0 0 0 0 0 0 0.0 0
## EA2 0 0 0 0 5 0 0 0 2.0 0
## EA3 0 0 0 0 2 0 0 0 0.5 0
## EA4 0 0 0 0 2 0 0 0 0.0 0
## EA5 0 0 0 0 0 0 0 0 0.0 0
## EA6 0 0 0 0 1 0 0 0 0.0 0
## ParKot PetFri PhyCae PoaArc PyrAsa PyrGra RhiMin RhoGro RhoLap RibGla
## EA1 0 0.00 0 0 0 0 0 1 0 0
## EA2 0 0.00 0 0 0 0 0 15 0 0
## EA3 0 0.25 0 0 0 0 0 9 0 0
## EA4 0 0.00 0 0 0 0 0 6 0 0
## EA5 0 0.00 0 0 0 0 0 10 0 0
## EA6 0 0.25 0 0 0 0 0 1 0 0
## RubArc RubCha RubIda SalArc SalArg SalGla SalHum SalPed SalPla SalUva
## EA1 0.00 0 0 0.5 0 0 0 0 0 0
## EA2 0.00 0 0 0.0 0 0 0 0 0 0
## EA3 0.00 0 0 0.0 0 0 0 0 0 0
## EA4 0.00 0 0 0.0 0 0 0 0 0 0
## EA5 0.00 0 0 0.0 0 0 0 0 0 0
## EA6 0.25 0 0 0.0 0 5 0 0 0 0
## SalVes SchPur SelSel SolMac SolMul SteBor SteLon TofPus TriAlp TriBor
## EA1 0 0 0 0.00 0 0 0 0 0 0.0
## EA2 4 0 0 0.00 0 0 0 0 0 0.0
## EA3 5 0 0 0.00 0 0 0 0 0 0.0
## EA4 40 0 0 0.75 0 0 0 0 0 0.0
## EA5 0 0 0 0.00 0 0 0 0 0 0.5
## EA6 5 0 0 0.25 0 0 0 0 0 0.0
## TriCes TriSpi VacCes VacMyr VacOxy VacUli VacVit VibEdu VioAdu VioRen
## EA1 0 0 0.25 0 0 0 0.00 0 0 0.00
## EA2 0 0 0.00 0 0 0 2.00 0 0 2.00
## EA3 0 0 0.00 0 0 0 0.50 0 0 0.25
## EA4 0 0 0.00 0 0 0 0.25 0 0 0.25
## EA5 0 0 0.00 0 0 0 8.00 0 0 0.00
## EA6 0 0 0.00 0 0 0 0.00 2 0 0.00
## AbiBal LarLar PicGla PicMar
## EA1 0 0 0 25
## EA2 0 0 0 20
## EA3 0 0 0 7
## EA4 0 0 0 0
## EA5 0 0 0 15
## EA6 0 0 0 0B2<-abd.sp[grepl("B", rownames(abd.sp)),]
C3<-abd.sp[grepl("C", rownames(abd.sp)),]
D4<-abd.sp[grepl("D", rownames(abd.sp)),]
E5<-abd.sp[grepl("E", rownames(abd.sp)),]
F6<-abd.sp[grepl("F", rownames(abd.sp)),]
G7<-abd.sp[grepl("G", rownames(abd.sp)),]
H8<-abd.sp[grepl("H", rownames(abd.sp)),]
I9<-abd.sp[grepl("I", rownames(abd.sp)),]
J10<-abd.sp[grepl("J", rownames(abd.sp)),]
K11<-abd.sp[grepl("K", rownames(abd.sp)),]
#get phylosor values for each transect
A1.ps<-as.matrix(phylosor(A1, trans.one.tree))
B2.ps<-as.matrix(phylosor(B2, trans.one.tree))
C3.ps<-as.matrix(phylosor(C3, trans.one.tree))
D4.ps<-as.matrix(phylosor(D4, trans.one.tree))
E5.ps<-as.matrix(phylosor(E5, trans.one.tree))
F6.ps<-as.matrix(phylosor(F6, trans.one.tree))
G7.ps<-as.matrix(phylosor(G7, trans.one.tree))
H8.ps<-as.matrix(phylosor(H8, trans.one.tree))
I9.ps<-as.matrix(phylosor(I9, trans.one.tree))
J10.ps<-as.matrix(phylosor(J10, trans.one.tree))
K11.ps<-as.matrix(phylosor(K11, trans.one.tree))
A1.trans<-c(A1.ps[16,15],A1.ps[15,14],A1.ps[14,13],A1.ps[13,12],A1.ps[12,11], A1.ps[11,10],A1.ps[10,9], A1.ps[9,8], A1.ps[8,7], A1.ps[7,6], A1.ps[6,5],A1.ps[5,4],A1.ps[4,3],
A1.ps[3,2],A1.ps[2,1])
head(A1.trans)## [1] 0.8143028 0.5604423 0.4639863 0.6119204 0.6435650 0.6924640B2.trans<-c(B2.ps[16,15],B2.ps[15,14],B2.ps[14,13],B2.ps[13,12],B2.ps[12,11], B2.ps[11,10],B2.ps[10,9], B2.ps[9,8], B2.ps[8,7], B2.ps[7,6], B2.ps[6,5],B2.ps[5,4],B2.ps[4,3],
B2.ps[3,2],B2.ps[2,1])
C3.trans<-c(C3.ps[16,15],C3.ps[15,14],C3.ps[14,13],C3.ps[13,12],C3.ps[12,11], C3.ps[11,10],C3.ps[10,9], C3.ps[9,8], C3.ps[8,7], C3.ps[7,6], C3.ps[6,5],C3.ps[5,4],C3.ps[4,3],
C3.ps[3,2],C3.ps[2,1])
D4.trans<-c(D4.ps[16,15],D4.ps[15,14],D4.ps[14,13],D4.ps[13,12],D4.ps[12,11], D4.ps[11,10],D4.ps[10,9], D4.ps[9,8], D4.ps[8,7], D4.ps[7,6], D4.ps[6,5],D4.ps[5,4],D4.ps[4,3],
D4.ps[3,2],D4.ps[2,1])
E5.trans<-c(E5.ps[16,15],E5.ps[15,14],E5.ps[14,13],E5.ps[13,12],E5.ps[12,11], E5.ps[11,10],E5.ps[10,9], E5.ps[9,8], E5.ps[8,7], E5.ps[7,6], E5.ps[6,5],E5.ps[5,4],E5.ps[4,3],
E5.ps[3,2],E5.ps[2,1])
F6.trans<-c(F6.ps[16,15],F6.ps[15,14],F6.ps[14,13],F6.ps[13,12],F6.ps[12,11], F6.ps[11,10],F6.ps[10,9], F6.ps[9,8], F6.ps[8,7], F6.ps[7,6], F6.ps[6,5],F6.ps[5,4],F6.ps[4,3],
F6.ps[3,2],F6.ps[2,1])
G7.trans<-c(G7.ps[16,15],G7.ps[15,14],G7.ps[14,13],G7.ps[13,12],G7.ps[12,11], G7.ps[11,10],G7.ps[10,9], G7.ps[9,8], G7.ps[8,7], G7.ps[7,6], G7.ps[6,5],G7.ps[5,4],G7.ps[4,3],
G7.ps[3,2],G7.ps[2,1])
H8.trans<-c(H8.ps[16,15],H8.ps[15,14],H8.ps[14,13],H8.ps[13,12],H8.ps[12,11], H8.ps[11,10],H8.ps[10,9], H8.ps[9,8], H8.ps[8,7], H8.ps[7,6], H8.ps[6,5],H8.ps[5,4],H8.ps[4,3],
H8.ps[3,2],H8.ps[2,1])
I9.trans<-c(I9.ps[16,15],I9.ps[15,14],I9.ps[14,13],I9.ps[13,12],I9.ps[12,11], I9.ps[11,10],I9.ps[10,9], I9.ps[9,8], I9.ps[8,7], I9.ps[7,6], I9.ps[6,5],I9.ps[5,4],I9.ps[4,3],
I9.ps[3,2],I9.ps[2,1])
J10.trans<-c(J10.ps[16,15],J10.ps[15,14],J10.ps[14,13],J10.ps[13,12],J10.ps[12,11], J10.ps[11,10],J10.ps[10,9], J10.ps[9,8], J10.ps[8,7], J10.ps[7,6], J10.ps[6,5],J10.ps[5,4],J10.ps[4,3],
J10.ps[3,2],J10.ps[2,1])
K11.trans<-c(K11.ps[16,15],K11.ps[15,14],K11.ps[14,13],K11.ps[13,12],K11.ps[12,11], K11.ps[11,10],K11.ps[10,9], K11.ps[9,8], K11.ps[8,7], K11.ps[7,6], K11.ps[6,5],K11.ps[5,4],K11.ps[4,3],
K11.ps[3,2],K11.ps[2,1])Plot Sorensen’s phylogenetic beta diversity showing results for all transects
#dev.new(width=11.8, height=6)
par(mar=c(5.1,5.1,5.5,2.1))
plot(A1.trans, ylim=c(0,1),type="l",axes=FALSE, col="black", lwd=2, bty="n", ylab="Phylogenetic beta diversity", cex.lab=1.25, cex.axis=1,xlab="Sampling band comparison", main="Phylogenetic beta diversity comparisons \nbetween sampling bands" )
lines(B2.trans, col="black",lwd=2)
lines(C3.trans, col="black",lwd=2)
lines(D4.trans, col="black",lwd=2)
lines(E5.trans, col="black",lwd=2)
lines(F6.trans, col="black",lwd=2)
lines(G7.trans, col="black",lwd=2)
lines(H8.trans, col="black",lwd=2)
lines(I9.trans, col="black",lwd=2)
lines(J10.trans, col="black",lwd=2)
lines(K11.trans, col="black",lwd=2)
axis(2, lwd=2)
axis(1,1:15,labels=c("800x775", "775x745", "745x710", "710x675", "675x645", "645x615", "615x600", "600x8","8x7", "7x6","6x5", "5x4", "4x3", "3x2", "2x1"))
box(bty="l", lwd=4)
***
Combine data per sampling band for further analysis
#get small dataframes for each of eight elevations in original transects
abd.600<-abd.sp[grepl("600*", rownames(abd.sp)), ]
head(abd.600)## AchMil AgrMer AlnVir AmeBar AndPol AnePar AntAlp AntMon ArcAlp
## E600A1 0 0 16 0 0 0.00 0 0 0
## E600B2 0 0 0 0 0 0.25 0 0 0
## E600C3 0 0 0 0 0 0.00 0 0 0
## E600D4 0 0 0 0 0 0.00 0 0 0
## E600E5 0 0 0 0 0 0.00 0 0 0
## E600F6 0 0 0 0 0 0.00 0 0 0
## ArnAng BarAlp BetGla BisViv CalCan CarAqu CarBig CarBru CarCap
## E600A1 0 0 0 0 0 0 0 0 0
## E600B2 0 0 0 0 0 0 0 0 0
## E600C3 0 0 8 0 0 0 0 0 0
## E600D4 0 0 0 0 0 0 0 0 0
## E600E5 0 0 35 0 0 0 0 0 0
## E600F6 0 0 0 0 0 0 0 0 0
## CarCat CarDef CarDis CarGyn CarLep CarLim CarMag CarSci CarTri
## E600A1 0 0 0 0 0 0 0 0 0
## E600B2 0 0 0 0 0 0 0 0 0
## E600C3 0 0 0 0 0 0 0 0 0
## E600D4 0 0 0 0 0 0 0 0 0
## E600E5 0 0 0 0 0 0 0 0 0
## E600F6 0 0 0 0 0 0 0 0 0
## CarUtr CarVag CasSep CerAlp ChaAng CopTri CorCan CysMon DasFru
## E600A1 0 0 0 0 0 0.25 0.25 0 0
## E600B2 0 1 0 0 0 0.00 0.25 0 0
## E600C3 0 0 0 0 0 0.50 2.00 0 0
## E600D4 0 0 0 0 0 0.75 0.75 0 0
## E600E5 0 0 0 0 0 0.00 0.50 0 0
## E600F6 0 0 0 0 0 0.00 2.00 0 0
## AveFle DiaLap DipCom DryExp DryInt ElyTra EmpNig EpiHor EquArv
## E600A1 0.25 0 0 0 0 0 0 0 0
## E600B2 0.00 0 0 0 0 0 0 0 0
## E600C3 0.50 0 0 0 0 0 0 0 0
## E600D4 0.50 0 0 0 0 0 0 0 0
## E600E5 0.25 0 0 0 0 0 0 0 0
## E600F6 0.25 0 0 0 0 0 0 0 0
## EquSci EquSyl EquVar EriVir EurRad FraVir GauHis GeoLiv HupApr
## E600A1 0 0 0 0 0 0 0 0 0
## E600B2 0 0 0 0 0 0 0 0 0
## E600C3 0 0 0 0 0 0 0 0 0
## E600D4 0 0 0 0 0 0 0 0 0
## E600E5 0 0 0 0 0 0 0 0 0
## E600F6 0 0 0 0 0 0 0 1 0
## JunCom JunTri KalPol LinBor LisCor LonVil LuzPar LycAno MaiTri
## E600A1 0 0 0 5 0.00 0 0 10.0 0
## E600B2 0 0 0 4 0.00 0 0 0.0 0
## E600C3 0 0 0 0 0.00 0 0 10.0 0
## E600D4 0 0 0 3 0.25 0 0 0.0 0
## E600E5 0 0 0 2 0.00 0 0 0.5 0
## E600F6 0 0 0 0 0.00 0 0 0.0 0
## MinBif MitNud MoeMac MonUni MyrGal OrtSec PacAur ParKot PetFri
## E600A1 0 0 0 0 0 0 0 0 0.00
## E600B2 0 2 0 0 0 0 0 0 0.25
## E600C3 0 0 0 0 0 0 0 0 0.00
## E600D4 0 0 0 0 0 0 0 0 0.00
## E600E5 0 0 0 0 0 0 0 0 0.00
## E600F6 0 0 0 0 0 0 0 0 0.00
## PhyCae PoaArc PyrAsa PyrGra RhiMin RhoGro RhoLap RibGla RubArc
## E600A1 0 0 0 0 0 0.0 0 0 0
## E600B2 0 0 0 0 0 0.0 0 0 0
## E600C3 0 0 0 0 0 0.0 0 0 0
## E600D4 0 0 0 0 0 0.0 0 0 0
## E600E5 0 0 0 0 0 0.5 0 0 0
## E600F6 0 0 0 0 0 1.0 0 0 0
## RubCha RubIda SalArc SalArg SalGla SalHum SalPed SalPla SalUva
## E600A1 0 0 0 0 0 0 0 0 0
## E600B2 0 0 0 0 0 0 0 10 0
## E600C3 0 0 0 0 0 0 0 0 0
## E600D4 0 0 0 0 0 0 0 0 0
## E600E5 0 0 0 0 0 0 0 0 0
## E600F6 0 0 0 0 0 0 0 0 0
## SalVes SchPur SelSel SolMac SolMul SteBor SteLon TofPus TriAlp
## E600A1 0 0 0 0.25 0 0 0 0 0
## E600B2 10 2 0 0.25 0 0 0 0 0
## E600C3 0 0 0 0.50 0 0 0 0 0
## E600D4 0 0 0 0.50 0 0 0 0 0
## E600E5 0 0 0 0.25 0 0 0 0 0
## E600F6 0 0 0 1.00 0 0 0 0 0
## TriBor TriCes TriSpi VacCes VacMyr VacOxy VacUli VacVit VibEdu
## E600A1 0.25 0 0 0 0 0 0 0.25 0
## E600B2 0.00 0 0 0 0 0 0 0.00 7
## E600C3 0.00 0 0 5 0 0 0 0.00 0
## E600D4 2.00 0 0 12 0 0 0 3.00 0
## E600E5 1.00 0 0 2 3 0 0 0.00 0
## E600F6 0.00 0 0 5 4 0 0 0.25 0
## VioAdu VioRen AbiBal LarLar PicGla PicMar
## E600A1 0 0 0 0 0 0
## E600B2 0 0 0 0 6 0
## E600C3 0 0 0 0 10 0
## E600D4 0 0 0 0 0 0
## E600E5 0 0 0 0 2 0
## E600F6 0 0 0 0 0 0abd.615<-abd.sp[grepl("615*", rownames(abd.sp)), ]
abd.645<-abd.sp[grepl("645*", rownames(abd.sp)), ]
abd.675<-abd.sp[grepl("675*", rownames(abd.sp)), ]
abd.710<-abd.sp[grepl("710*", rownames(abd.sp)), ]
abd.745<-abd.sp[grepl("745*", rownames(abd.sp)), ]
abd.775<-abd.sp[grepl("775*", rownames(abd.sp)), ]
abd.800<-abd.sp[grepl("800*", rownames(abd.sp)), ]
#get small dataframes for each of eight additional lines
abd.1<-abd.sp[grepl("1", rownames(abd.sp)), ]
abd.1.TAM<-abd.1[c(1:11),]
abd.2<-abd.sp[grepl("2", rownames(abd.sp)), ]
abd.2.TAM<-abd.2[c(1:11),]
abd.3<-abd.sp[grepl("3", rownames(abd.sp)), ]
abd.3.TAM<-abd.3[c(1:11),]
abd.4<-abd.sp[grepl("4", rownames(abd.sp)), ]
abd.4.TAM<-abd.4[c(1:11),]
abd.5<-abd.sp[grepl("5", rownames(abd.sp)), ]
abd.5.TAM<-abd.5[c(1:11),]
abd.6<-abd.sp[grepl("6", rownames(abd.sp)), ]
abd.6.TAM<-abd.6[c(1:11),]
abd.7<-abd.sp[grepl("7", rownames(abd.sp)), ]
abd.7.TAM<-abd.7[c(1:11),]
abd.8<-abd.sp[grepl("8", rownames(abd.sp)),]
abd.8.TAM<-abd.8[c(1:11),]
#Create combined matrix
sum.600<-colMeans(abd.600, na.rm=FALSE, dims=1)
head(sum.600)## AchMil AgrMer AlnVir AmeBar AndPol AnePar
## 0.00000000 0.00000000 1.45454545 0.00000000 0.00000000 0.02272727sum.615<-colMeans(abd.615, na.rm=FALSE, dims=1)
sum.645<-colMeans(abd.645, na.rm=FALSE, dims=1)
sum.675<-colMeans(abd.675, na.rm=FALSE, dims=1)
sum.710<-colMeans(abd.710, na.rm=FALSE, dims=1)
sum.745<-colMeans(abd.745, na.rm=FALSE, dims=1)
sum.775<-colMeans(abd.775, na.rm=FALSE, dims=1)
sum.800<-colMeans(abd.800, na.rm=FALSE, dims=1)
sum.1<-colMeans(abd.1.TAM, na.rm=FALSE, dims=1)
sum.2<-colMeans(abd.2.TAM, na.rm=FALSE, dims=1)
sum.3<-colMeans(abd.3.TAM, na.rm=FALSE, dims=1)
sum.4<-colMeans(abd.4.TAM, na.rm=FALSE, dims=1)
sum.5<-colMeans(abd.5.TAM, na.rm=FALSE, dims=1)
sum.6<-colMeans(abd.6.TAM, na.rm=FALSE, dims=1)
sum.7<-colMeans(abd.7.TAM, na.rm=FALSE, dims=1)
sum.8<-colMeans(abd.8.TAM, na.rm=FALSE, dims=1)
veg.com<-rbind(sum.800,sum.775,sum.745,sum.710,sum.675,sum.645,sum.615,sum.600, sum.8, sum.7, sum.6, sum.5, sum.4, sum.3, sum.2, sum.1)
head(veg.com)## AchMil AgrMer AlnVir AmeBar AndPol AnePar AntAlp
## sum.800 0 0 0.0000000 0 0 0.00000000 0.00000000
## sum.775 0 0 0.0000000 0 0 0.02272727 0.04545455
## sum.745 0 0 3.8181818 0 0 0.00000000 0.00000000
## sum.710 0 0 0.4545455 0 0 0.00000000 0.00000000
## sum.675 0 0 1.8181818 0 0 0.00000000 0.00000000
## sum.645 0 0 7.1818182 0 0 0.00000000 0.00000000
## AntMon ArcAlp ArnAng BarAlp BetGla BisViv
## sum.800 0.00000000 0.50000000 0.00000000 0.02272727 0.3636364 0.13636364
## sum.775 0.02272727 1.90909091 0.02272727 0.02272727 1.0454545 0.06818182
## sum.745 0.00000000 0.00000000 0.00000000 0.00000000 15.6363636 0.06818182
## sum.710 0.00000000 0.09090909 0.00000000 0.00000000 20.6363636 0.02272727
## sum.675 0.00000000 0.00000000 0.00000000 0.00000000 26.5454545 0.00000000
## sum.645 0.00000000 0.00000000 0.00000000 0.00000000 5.7045455 0.00000000
## CalCan CarAqu CarBig CarBru CarCap CarCat
## sum.800 0.0000000 0 0.6363636 0.00000000 0.2500000 0.04545455
## sum.775 0.0000000 0 0.2500000 0.00000000 0.2727273 0.00000000
## sum.745 0.0000000 0 0.1818182 0.00000000 0.0000000 0.00000000
## sum.710 0.4545455 0 0.3409091 0.00000000 0.0000000 0.00000000
## sum.675 0.2727273 0 0.0000000 0.02272727 0.0000000 0.00000000
## sum.645 0.0000000 0 0.0000000 0.00000000 0.0000000 0.00000000
## CarDef CarDis CarGyn CarLep CarLim CarMag CarSci CarTri
## sum.800 0.00000000 0 0 0 0 0 2.8863636 0
## sum.775 0.00000000 0 0 0 0 0 1.8636364 0
## sum.745 0.00000000 0 0 0 0 0 0.2954545 0
## sum.710 0.02272727 0 0 0 0 0 0.1136364 0
## sum.675 0.00000000 0 0 0 0 0 0.0000000 0
## sum.645 0.04545455 0 0 0 0 0 0.1136364 0
## CarUtr CarVag CasSep CerAlp ChaAng CopTri
## sum.800 0 0.09090909 0 0.00000000 0.00000000 0.00000000
## sum.775 0 0.13636364 0 0.00000000 0.00000000 0.02272727
## sum.745 0 0.18181818 0 0.02272727 0.00000000 0.00000000
## sum.710 0 0.38636364 0 0.00000000 0.06818182 0.09090909
## sum.675 0 0.00000000 0 0.00000000 0.00000000 0.02272727
## sum.645 0 0.56818182 0 0.00000000 0.36363636 0.22727273
## CorCan CysMon DasFru AveFle DiaLap DipCom
## sum.800 0.00000000 0 0 0.00000000 0.72727273 0.00000000
## sum.775 0.00000000 0 0 0.00000000 0.04545455 0.00000000
## sum.745 0.00000000 0 0 0.00000000 0.00000000 0.00000000
## sum.710 0.09090909 0 0 0.04545455 0.00000000 0.22727273
## sum.675 1.63636364 0 0 0.00000000 0.00000000 0.09090909
## sum.645 0.52272727 0 0 0.25000000 0.00000000 0.00000000
## DryExp DryInt ElyTra EmpNig EpiHor EquArv EquSci
## sum.800 0.00000000 0.9090909 0.00000000 1.45454545 0 0 0
## sum.775 0.00000000 0.7954545 0.00000000 2.47727273 0 0 0
## sum.745 0.00000000 0.0000000 0.36363636 0.09090909 0 0 0
## sum.710 0.00000000 0.0000000 0.02272727 0.04545455 0 0 0
## sum.675 0.02272727 0.0000000 0.00000000 0.00000000 0 0 0
## sum.645 0.00000000 0.0000000 0.00000000 0.09090909 0 0 0
## EquSyl EquVar EriVir EurRad FraVir GauHis GeoLiv HupApr
## sum.800 0 0 0 0 0 0 0.0000000 0.02272727
## sum.775 0 0 0 0 0 0 0.0000000 0.02272727
## sum.745 0 0 0 0 0 0 0.0000000 0.00000000
## sum.710 0 0 0 0 0 0 0.0000000 0.00000000
## sum.675 0 0 0 0 0 0 0.0000000 0.00000000
## sum.645 0 0 0 0 0 0 0.1818182 0.00000000
## JunCom JunTri KalPol LinBor LisCor LonVil LuzPar
## sum.800 0.0000000 0.00000000 0 0.06818182 0 0 0
## sum.775 0.2727273 0.06818182 0 0.00000000 0 0 0
## sum.745 0.2727273 0.02272727 0 0.04545455 0 0 0
## sum.710 0.0000000 0.00000000 0 0.27272727 0 0 0
## sum.675 0.0000000 0.00000000 0 2.56818182 0 0 0
## sum.645 1.8181818 0.00000000 0 0.18181818 0 0 0
## LycAno MaiTri MinBif MitNud MoeMac MonUni MyrGal
## sum.800 0.09090909 0 0.00000000 0.00000000 0 0 0
## sum.775 0.00000000 0 0.00000000 0.00000000 0 0 0
## sum.745 0.00000000 0 0.02272727 0.04545455 0 0 0
## sum.710 5.84090909 0 0.00000000 0.00000000 0 0 0
## sum.675 0.81818182 0 0.00000000 0.00000000 0 0 0
## sum.645 3.47727273 0 0.00000000 0.18181818 0 0 0
## OrtSec PacAur ParKot PetFri PhyCae PoaArc PyrAsa
## sum.800 0 0 0 0.00000000 0 0.00000000 0
## sum.775 0 0 0 0.00000000 0 0.02272727 0
## sum.745 0 0 0 0.00000000 0 0.00000000 0
## sum.710 0 0 0 0.02272727 0 0.00000000 0
## sum.675 0 0 0 0.00000000 0 0.00000000 0
## sum.645 0 0 0 0.00000000 0 0.00000000 0
## PyrGra RhiMin RhoGro RhoLap RibGla RubArc RubCha
## sum.800 0.02272727 0 1.363636 0.4772727 0.0000000 0.00000000 0
## sum.775 0.02272727 0 0.000000 0.6363636 0.0000000 0.00000000 0
## sum.745 0.02272727 0 0.000000 0.0000000 0.0000000 0.09090909 0
## sum.710 0.00000000 0 4.181818 0.0000000 0.0000000 0.04545455 0
## sum.675 0.00000000 0 2.545455 0.0000000 3.3181818 0.00000000 0
## sum.645 0.00000000 0 2.772727 0.0000000 0.2727273 0.00000000 0
## RubIda SalArc SalArg SalGla SalHum SalPed SalPla SalUva
## sum.800 0.00000000 0 0 0.000000 0.0000000 0 0 1.045455
## sum.775 0.00000000 0 0 0.000000 0.0000000 0 0 0.000000
## sum.745 0.02272727 0 0 1.181818 0.0000000 0 0 0.000000
## sum.710 0.27272727 0 0 0.000000 0.0000000 0 0 0.000000
## sum.675 1.13636364 0 0 0.000000 0.2727273 0 0 0.000000
## sum.645 0.00000000 0 0 0.000000 0.0000000 0 0 0.000000
## SalVes SchPur SelSel SolMac SolMul SteBor SteLon
## sum.800 5.8181818 0 0 0.0000000 0.06818182 0.00000000 0
## sum.775 4.6363636 0 0 0.0000000 0.09090909 0.00000000 0
## sum.745 8.8181818 0 0 0.7500000 0.11363636 0.02272727 0
## sum.710 2.0909091 0 0 3.0909091 0.00000000 0.00000000 0
## sum.675 0.0000000 0 0 3.4545455 0.00000000 0.00000000 0
## sum.645 0.6363636 0 0 0.7045455 0.00000000 0.00000000 0
## TofPus TriAlp TriBor TriCes TriSpi VacCes
## sum.800 0.13636364 0 0.0000000 1.2045455 0.00000000 0.0000000
## sum.775 0.04545455 0 0.0000000 0.3636364 0.00000000 0.0000000
## sum.745 0.27272727 0 0.0000000 0.0000000 0.04545455 0.0000000
## sum.710 0.00000000 0 0.1590909 0.0000000 0.00000000 0.5454545
## sum.675 0.00000000 0 1.1136364 0.0000000 0.00000000 0.3636364
## sum.645 0.00000000 0 0.4545455 0.0000000 0.00000000 1.1818182
## VacMyr VacOxy VacUli VacVit VibEdu VioAdu
## sum.800 0.00000000 0 6.2272727 0.2272727 0.0000000 0.04545455
## sum.775 0.00000000 0 8.5000000 0.3181818 0.0000000 0.02272727
## sum.745 0.00000000 0 7.8181818 0.5000000 0.0000000 0.00000000
## sum.710 0.00000000 0 8.8181818 0.2272727 0.6363636 0.00000000
## sum.675 0.09090909 0 0.9772727 0.2045455 0.0000000 0.00000000
## sum.645 3.77272727 0 9.2727273 0.2500000 0.0000000 0.18181818
## VioRen AbiBal LarLar PicGla PicMar
## sum.800 0.00000000 0 0 0.0000000 0.000000
## sum.775 0.02272727 0 0 0.0000000 0.000000
## sum.745 0.20454545 0 0 0.3636364 0.000000
## sum.710 0.02272727 0 0 0.4090909 0.000000
## sum.675 0.00000000 0 0 2.4545455 0.000000
## sum.645 0.00000000 0 0 1.4545455 1.181818## Sorensen's beta diversity and Sorensen's beta diversity calculations#sorensen comparison
veg.beta<-betadiver(veg.com, "sor")
#phylosor comparison
veg.ps<-as.matrix(phylosor(veg.com, trans.one.tree))
veg.com.ps<-c(veg.ps[16,15],veg.ps[15,14],veg.ps[14,13],veg.ps[13,12],veg.ps[12,11], veg.ps[11,10],veg.ps[10,9], veg.ps[9,8], veg.ps[8,7], veg.ps[7,6],
veg.ps[6,5], veg.ps[5,4], veg.ps[4,3],veg.ps[3,2],veg.ps[2,1])
veg.com.ps## [1] 0.8992636 0.8883212 0.8315074 0.8271996 0.8246314 0.8861623 0.8446367
## [8] 0.7549164 0.8177719 0.8154755 0.7841937 0.8178856 0.6463608 0.6868661
## [15] 0.7966121Sorensen’s phylogenetic beta diversity comparisons between adjacent sampling bands
#dev.new(width=5.9, height=4)
par(mar=c(5.1,5.1,5.5,2.1))
plot(veg.com.ps, ylim=c(0.6,1),type="l",axes=FALSE, col="black", lwd=3, bty="n", ylab="Phylogenetic beta diversity", cex.lab=1, cex.main=1.25,xlab="Comparison between sampling bands",
main="Phylogenetic beta diversity comparisons \nbetween sampling bands" )
axis(2, lwd=2)
axis(1,1:15,labels=c("800x775", "775x745", "745x710", "710x675", "675x645", "645x615", "615x600", "600x8","8x7", "7x6","6x5", "5x4", "4x3", "3x2", "2x1"))
box(bty="l", lwd=4)
Sorensen’s beta diversity comparisons between adjacent sampling bands
#look at beta diversity
#sorensen comparison
veg.beta<-as.matrix(betadiver(veg.com, "sor"))
elev.trans<-c(veg.beta[16,15],veg.beta[15,14],veg.beta[14,13],veg.beta[13,12],veg.beta[12,11], veg.beta[11,10],veg.beta[10,9], veg.beta[9,8], veg.beta[8,7], veg.beta[7,6],
veg.beta[6,5],veg.beta[5,4],veg.beta[4,3],veg.beta[3,2],veg.beta[2,1])
elev.trans## [1] 0.7899160 0.7706422 0.7032967 0.7317073 0.7692308 0.7948718 0.7407407
## [8] 0.5714286 0.7169811 0.7547170 0.6250000 0.6153846 0.5762712 0.5172414
## [15] 0.7500000Plots comparing Sorensen’s beta diversity and Sorensen’s phylogenetic beta diversity
#dev.new(width=11.8, height=6)
plot(veg.com.ps, ylim=c(0.5,1),type="l",axes=FALSE, col="black", lwd=2, bty="n", ylab="Beta diversity", cex.lab=1.25, xlab="Comparison between sampling bands",
main="Comparison between beta diversity and phylogenetic beta diversity \nbetweem sampling bands" , cex.main=1.5)
lines(elev.trans, lwd=2, col="grey70")
axis(2, lwd=2)
axis(1,1:15,labels=c("800x775", "775x745", "745x710", "710x675", "675x645", "645x615", "615x600", "600x8","8x7", "7x6","6x5", "5x4", "4x3", "3x2", "2x1"))
box(bty="l", lwd=4)
legend("topright", c("Sorensen's beta diversity", "Sorensen's phylogenetic beta diversity"), col = c("black","grey70" ), cex=1.1,
lty = c(1, 1), pch = c(NA, NA), lwd=3 , bg = "white", bty="n")
beta.diff<-veg.com.ps-elev.trans
#dev.new(width=5.9, height=4)
plot(beta.diff, ylim=c(0,0.25),type="l",axes=FALSE, col="black", lwd=2, bty="n", ylab="Difference in beta diversity", cex.lab=1, xlab="Comparison between sampling bands",
main="Exceedance of beta diversity over phylogenetic \nbeta diversity between sampling bands" , cex.main=1.25)
axis(2, lwd=2)
axis(1,1:15,labels=c("800x775", "775x745", "745x710", "710x675", "675x645", "645x615", "615x600", "600x8","8x7", "7x6","6x5", "5x4", "4x3", "3x2", "2x1"))
box(bty="l", lwd=4)