Title: Raup crick analyses

Name: Tammy L. Elliott

Date: April 13, 2016

R version 3.1

Raup-Crick comparisons

# Raup-Crick comparisons

#    - Raup-Crick index is the probability that compared sampling units have non-identical species composition. 
#   - This probability can be regarded as a dissimilarity, although it is not metric: identical sampling units can 
#       have dissimilarity slightly above 0, the dissimilarity can be nearly zero over a range of shared species,
#        and sampling units with no shared species can have dissimilarity slightly below 1. 
#       Moreover, communities sharing rare species appear as more similar (lower probability of finding rare species together), 
#       than communities sharing the same number of common species.

# First do a Raup-Crick comparison for the entire presence-absence data set
#   - null = "r0"  The vegdist function implements a variant of the Raup-Crick index with equal sampling probabilities for species using exact analytic equations without simulation
#   - raupcrick(comm, null = "r0", nsimul = 999, chase = FALSE, ...)

raup.crick.pa.sp.allsp<-raupcrick(pa.sp.allsp, null="r0", nsimul=999)
# this gives a distance object with a plot-by-plot comparison

---

Raup-Crick Data Set-up

# Four cluster site.environment
#Species in cluster 1 of env.dist.4
site.env.dist.cfuz.4.cluster1<-colSums(pa.sp.allsp[site.env.dist.cfuz.4$clustering==1,])
site.env.dist.cfuz.4.cluster1[site.env.dist.cfuz.4.cluster1>0]<-1

#Species in cluster 2 of env.dist.4
site.env.dist.cfuz.4.cluster2<-colSums(pa.sp.allsp[site.env.dist.cfuz.4$clustering==2,])
site.env.dist.cfuz.4.cluster2[site.env.dist.cfuz.4.cluster2>0]<-1

#Species in cluster 3 of env.dist.4
site.env.dist.cfuz.4.cluster3<-colSums(pa.sp.allsp[site.env.dist.cfuz.4$clustering==3,])
site.env.dist.cfuz.4.cluster3[site.env.dist.cfuz.4.cluster3>0]<-1

#Species in cluster 4 of env.dist.4
site.env.dist.cfuz.4.cluster4<-colSums(pa.sp.allsp[site.env.dist.cfuz.4$clustering==4,])
site.env.dist.cfuz.4.cluster4[site.env.dist.cfuz.4.cluster4>0]<-1

#make a community of six clusters of env.dist.6
site.env.dist.cfuz.4.comm<-rbind(site.env.dist.cfuz.4.cluster1,site.env.dist.cfuz.4.cluster2,site.env.dist.cfuz.4.cluster3,
    site.env.dist.cfuz.4.cluster4)

---

Raup-Crick Environmental Distance comparisons

These are based on average comparisons between Groups, where each “Group” is treated as a separate community. Thus, each species is either present or not present in each of the “Groups” and this presence-absence is what the Raup-Crick comparison is comparing between groups.

raup.crick.site.env.dist.cfuz.4<-raupcrick(site.env.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.site.env.dist.cfuz.4.m<-as.matrix(raup.crick.site.env.dist.cfuz.4)
rownames(raup.crick.site.env.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.site.env.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.site.env.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.001  0.032  0.349
## Group2  0.001  0.000  0.006  0.571
## Group3  0.032  0.006  0.000  0.001
## Group4  0.349  0.571  0.001  0.000

---

---

Raup-crick Presence-absence RaoD

raup.crick.raoD.pa.dist.cfuz.4<-raupcrick(raoD.pa.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.raoD.pa.dist.cfuz.4.m<-as.matrix(raup.crick.raoD.pa.dist.cfuz.4)
rownames(raup.crick.raoD.pa.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.raoD.pa.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.raoD.pa.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.001  0.008  0.100
## Group2  0.001  0.000  0.001  0.001
## Group3  0.008  0.001  0.000  0.001
## Group4  0.100  0.001  0.001  0.000

---

---

Raup-crick comparison for RaoD with phylogenetic distance

raup.crick.raoD.pa.phy.dist.cfuz.4<-raupcrick(raoD.pa.phy.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.raoD.pa.phy.dist.cfuz.4.m<-as.matrix(raup.crick.raoD.pa.phy.dist.cfuz.4)
rownames(raup.crick.raoD.pa.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.raoD.pa.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.raoD.pa.phy.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.043  0.033  0.006
## Group2  0.043  0.000  0.001  0.001
## Group3  0.033  0.001  0.000  0.001
## Group4  0.006  0.001  0.001  0.000

---

Raup-crick comparison for RaoD with abundance data

raup.crick.raoD.abd.dist.cfuz.4<-raupcrick(raoD.abd.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.raoD.abd.dist.cfuz.4.m<-as.matrix(raup.crick.raoD.abd.dist.cfuz.4)
rownames(raup.crick.raoD.abd.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.raoD.abd.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.raoD.abd.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.001  0.003  0.001
## Group2  0.001  0.000  0.001  0.007
## Group3  0.003  0.001  0.000  0.005
## Group4  0.001  0.007  0.005  0.000

---

Raup-crick comparison for RaoD with abundance and phylogeneny

raup.crick.raoD.abd.phy.dist.cfuz.4<-raupcrick(raoD.abd.phy.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.raoD.abd.phy.dist.cfuz.4.m<-as.matrix(raup.crick.raoD.abd.phy.dist.cfuz.4)
rownames(raup.crick.raoD.abd.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.raoD.abd.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.raoD.abd.phy.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.005  0.001  0.003
## Group2  0.005  0.000  0.012  0.001
## Group3  0.001  0.012  0.000  0.004
## Group4  0.003  0.001  0.004  0.000

---

---

---

Angiosperm only analyses

Raup-Crick Environmental Distance comparisons for angiosperms only

angio.raup.crick.site.env.dist.cfuz.4<-raupcrick(angio.site.env.dist.cfuz.4.comm, null="r0", nsimul=999)
angio.raup.crick.site.env.dist.cfuz.4.m<-as.matrix(angio.raup.crick.site.env.dist.cfuz.4)
rownames(angio.raup.crick.site.env.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(angio.raup.crick.site.env.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
angio.raup.crick.site.env.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.001  0.018  0.208
## Group2  0.001  0.000  0.003  0.323
## Group3  0.018  0.003  0.000  0.001
## Group4  0.208  0.323  0.001  0.000

Raup-crick Presence-absencee RaoD for angiosperms

raup.crick.angio.raoD.pa.dist.cfuz.4<-raupcrick(angio.raoD.pa.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.angio.raoD.pa.dist.cfuz.4.m<-as.matrix(raup.crick.angio.raoD.pa.dist.cfuz.4)
rownames(raup.crick.angio.raoD.pa.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.angio.raoD.pa.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.angio.raoD.pa.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.004  0.057  0.001
## Group2  0.004  0.000  0.001  0.001
## Group3  0.057  0.001  0.000  0.001
## Group4  0.001  0.001  0.001  0.000

---

---

Raup-crick comparison for angiosperms - RaoD with phylogenetic distance

raup.crick.angio.raoD.pa.phy.dist.cfuz.4<-raupcrick(angio.raoD.pa.phy.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.angio.raoD.pa.phy.dist.cfuz.4.m<-as.matrix(raup.crick.angio.raoD.pa.phy.dist.cfuz.4)
rownames(raup.crick.angio.raoD.pa.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.angio.raoD.pa.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.angio.raoD.pa.phy.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.001  0.001  0.001
## Group2  0.001  0.000  0.010  0.001
## Group3  0.001  0.010  0.000  0.022
## Group4  0.001  0.001  0.022  0.000

---

Raup-crick comparison for RaoD with abundance data for angiosperms

raup.crick.angio.raoD.abd.dist.cfuz.4<-raupcrick(angio.raoD.abd.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.angio.raoD.abd.dist.cfuz.4.m<-as.matrix(raup.crick.angio.raoD.abd.dist.cfuz.4)
rownames(raup.crick.angio.raoD.abd.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.angio.raoD.abd.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.angio.raoD.abd.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.002  0.001  0.001
## Group2  0.002  0.000  0.001  0.005
## Group3  0.001  0.001  0.000  0.001
## Group4  0.001  0.005  0.001  0.000

---

```

Raup-crick comparison for RaoD with abundance and phylogeny for angiosperms only

raup.crick.angio.raoD.abd.phy.dist.cfuz.4<-raupcrick(angio.raoD.abd.phy.dist.cfuz.4.comm, null="r0", nsimul=999)
raup.crick.angio.raoD.abd.phy.dist.cfuz.4.m<-as.matrix(raup.crick.angio.raoD.abd.phy.dist.cfuz.4)
rownames(raup.crick.angio.raoD.abd.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
colnames(raup.crick.angio.raoD.abd.phy.dist.cfuz.4.m)<-c("Group1", "Group2", "Group3", "Group4")
raup.crick.angio.raoD.abd.phy.dist.cfuz.4.m

##        Group1 Group2 Group3 Group4
## Group1  0.000  0.009  0.088  0.001
## Group2  0.009  0.000  0.001  0.003
## Group3  0.088  0.001  0.000  0.001
## Group4  0.001  0.003  0.001  0.000