Title: Dissimilarity measure Procrustes rotations and ProTest

Name: Tammy L. Elliott

Date: October 10, 2017

R version 3.2

SiteEnv X BD; vasculars, prescence-absence vascular confidence intervals

(site.env.raoD.pa.phy.protest.left<-site.env.raoD.pa.phy.protest.ss.mean-
    site.env.raoD.pa.phy.protest.ss.E)

## [1] 0.8503095

(site.env.raoD.pa.phy.protest.right<-site.env.raoD.pa.phy.protest.ss.mean+
    site.env.raoD.pa.phy.protest.ss.E)

## [1] 0.8533531

site.env.raoD.pa.phy.protest.signif<-lapply(site.env.raoD.pa.phy.protest, function(b){
    b$signif
    })
site.env.raoD.pa.phy.protest.signif.mean<-mean(unlist(site.env.raoD.pa.phy.protest.signif))
site.env.raoD.pa.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(site.env.raoD.pa.phy.protest.signif))/
    sqrt(length(unlist(site.env.raoD.pa.phy.protest.signif)))
(site.env.raoD.pa.phy.protest.left<-site.env.raoD.pa.phy.protest.signif.mean-
    site.env.raoD.pa.phy.protest.signif.E)

## [1] 0.001

(site.env.raoD.pa.phy.protest.right<-site.env.raoD.pa.phy.protest.signif.mean+
    site.env.raoD.pa.phy.protest.signif.E)

## [1] 0.001

Procrustes test between SiteEnv and abundance-weighted, vascular BD and PhyBD

(site.env.raoD.abd.phy.protest.left<-site.env.raoD.abd.phy.protest.ss.mean-
    site.env.raoD.abd.phy.protest.ss.E)

## [1] 0.822791

(site.env.raoD.abd.phy.protest.right<-site.env.raoD.abd.phy.protest.ss.mean+
    site.env.raoD.abd.phy.protest.ss.E)

## [1] 0.8243356

site.env.raoD.abd.phy.protest.signif<-lapply(site.env.raoD.abd.phy.protest, function(b){
    b$signif
    })
site.env.raoD.abd.phy.protest.signif.mean<-mean(unlist(site.env.raoD.abd.phy.protest.signif))
site.env.raoD.abd.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(site.env.raoD.abd.phy.protest.signif))/
    sqrt(length(unlist(site.env.raoD.abd.phy.protest.signif)))
(site.env.raoD.abd.phy.protest.left<-site.env.raoD.abd.phy.protest.signif.mean-
    site.env.raoD.abd.phy.protest.signif.E)

## [1] 0.001

(site.env.raoD.abd.phy.protest.right<-site.env.raoD.abd.phy.protest.signif.mean+
    site.env.raoD.abd.phy.protest.signif.E)

## [1] 0.001

Procrustes test between presence-absence, vascular BD and PhBD

(raoD.pa.pa.phy.protest.left<-raoD.pa.pa.phy.protest.ss.mean-
    raoD.pa.pa.phy.protest.ss.E)

## [1] 0.533442

(raoD.pa.pa.phy.protest.right<-raoD.pa.pa.phy.protest.ss.mean+
    raoD.pa.pa.phy.protest.ss.E)

## [1] 0.5392768

raoD.pa.pa.phy.protest.signif<-lapply(raoD.pa.pa.phy.protest, function(b){
    b$signif
    })
raoD.pa.pa.phy.protest.signif.mean<-mean(unlist(raoD.pa.pa.phy.protest.signif))
raoD.pa.pa.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(raoD.pa.pa.phy.protest.signif))/
    sqrt(length(unlist(raoD.pa.pa.phy.protest.signif)))
(raoD.pa.pa.phy.protest.left<-raoD.pa.pa.phy.protest.signif.mean-
    raoD.pa.pa.phy.protest.signif.E)

## [1] 0.001

(raoD.pa.pa.phy.protest.right<-raoD.pa.pa.phy.protest.signif.mean+
    raoD.pa.pa.phy.protest.signif.E)

## [1] 0.001

Procrustes test between abundance-weighted, vascular BD and PhBD

(raoD.abd.abd.phy.protest.left<-raoD.abd.abd.phy.protest.ss.mean-
    raoD.abd.abd.phy.protest.ss.E)

## [1] 0.5445297

(raoD.abd.abd.phy.protest.right<-raoD.abd.abd.phy.protest.ss.mean+
    raoD.abd.abd.phy.protest.ss.E)

## [1] 0.5545486

raoD.abd.abd.phy.protest.signif<-lapply(raoD.abd.abd.phy.protest, function(b){
    b$signif
    })
raoD.abd.abd.phy.protest.signif.mean<-mean(unlist(raoD.abd.abd.phy.protest.signif))
raoD.abd.abd.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(raoD.abd.abd.phy.protest.signif))/
    sqrt(length(unlist(raoD.abd.abd.phy.protest.signif)))
(raoD.abd.abd.phy.protest.left<-raoD.abd.abd.phy.protest.signif.mean-
    raoD.abd.abd.phy.protest.signif.E)

## [1] 0.001

(raoD.abd.abd.phy.protest.right<-raoD.abd.abd.phy.protest.signif.mean+
    raoD.abd.abd.phy.protest.signif.E)

## [1] 0.001

Procrustes test between SiteEnv and presence-absence, angiosperm BD and PhyBD

(site.env.raoD.pa.angio.phy.protest.left<-site.env.raoD.pa.angio.phy.protest.ss.mean-
    site.env.raoD.pa.angio.phy.protest.ss.E)

## [1] 0.9435349

(site.env.raoD.pa.angio.phy.protest.right<-site.env.raoD.pa.angio.phy.protest.ss.mean+
    site.env.raoD.pa.angio.phy.protest.ss.E)

## [1] 0.9446531

site.env.raoD.pa.angio.phy.protest.signif<-lapply(site.env.raoD.pa.angio.phy.protest, function(b){
    b$signif
    })
site.env.raoD.pa.angio.phy.protest.signif.mean<-mean(unlist(site.env.raoD.pa.angio.phy.protest.signif))
site.env.raoD.pa.angio.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(site.env.raoD.pa.angio.phy.protest.signif))/
    sqrt(length(unlist(site.env.raoD.pa.angio.phy.protest.signif)))
(site.env.raoD.pa.angio.phy.protest.left<-site.env.raoD.pa.angio.phy.protest.signif.mean-
    site.env.raoD.pa.angio.phy.protest.signif.E)

## [1] 0.001107855

(site.env.raoD.pa.angio.phy.protest.right<-site.env.raoD.pa.angio.phy.protest.signif.mean+
    site.env.raoD.pa.angio.phy.protest.signif.E)

## [1] 0.001272145

Procrustes test between SiteEnv and abundance-weighted, angiosperm BD and PhyBD

(site.env.raoD.abd.angio.phy.protest.left<-site.env.raoD.abd.angio.phy.protest.ss.mean-
    site.env.raoD.abd.angio.phy.protest.ss.E)

## [1] 0.9322313

(site.env.raoD.abd.angio.phy.protest.right<-site.env.raoD.abd.angio.phy.protest.ss.mean+
    site.env.raoD.abd.angio.phy.protest.ss.E)

## [1] 0.9337664

site.env.raoD.abd.angio.phy.protest.signif<-lapply(site.env.raoD.abd.angio.phy.protest, function(b){
    b$signif
    })
site.env.raoD.abd.angio.phy.protest.signif.mean<-mean(unlist(site.env.raoD.abd.angio.phy.protest.signif))
site.env.raoD.abd.angio.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(site.env.raoD.abd.angio.phy.protest.signif))/
    sqrt(length(unlist(site.env.raoD.abd.angio.phy.protest.signif)))
(site.env.raoD.abd.angio.phy.protest.left<-site.env.raoD.abd.angio.phy.protest.signif.mean-
    site.env.raoD.abd.angio.phy.protest.signif.E)

## [1] 0.00102656

(site.env.raoD.abd.angio.phy.protest.right<-site.env.raoD.abd.angio.phy.protest.signif.mean+
    site.env.raoD.abd.angio.phy.protest.signif.E)

## [1] 0.00113344

Procrustes test between presence-absence, angiosperm BD and PhBD

(raoD.pa.pa.angio.phy.protest.left<-raoD.pa.pa.angio.phy.protest.ss.mean-
    raoD.pa.pa.angio.phy.protest.ss.E)

## [1] 0.5678262

(raoD.pa.pa.angio.phy.protest.right<-raoD.pa.pa.angio.phy.protest.ss.mean+
    raoD.pa.pa.angio.phy.protest.ss.E)

## [1] 0.5747502

raoD.pa.pa.angio.phy.protest.signif<-lapply(raoD.pa.pa.angio.phy.protest, function(b){
    b$signif
    })
raoD.pa.pa.angio.phy.protest.signif.mean<-mean(unlist(raoD.pa.pa.angio.phy.protest.signif))
raoD.pa.pa.angio.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(raoD.pa.pa.angio.phy.protest.signif))/
    sqrt(length(unlist(raoD.pa.pa.angio.phy.protest.signif)))
(raoD.pa.pa.angio.phy.protest.left<-raoD.pa.pa.angio.phy.protest.signif.mean-
    raoD.pa.pa.angio.phy.protest.signif.E)

## [1] 0.001

(raoD.pa.pa.angio.phy.protest.right<-raoD.pa.pa.angio.phy.protest.signif.mean+
    raoD.pa.pa.angio.phy.protest.signif.E)

## [1] 0.001

Procrustes test between abundance-weighted, angiosperm BD and PhBD

(raoD.abd.abd.angio.phy.protest.left<-raoD.abd.abd.angio.phy.protest.ss.mean-
    raoD.abd.abd.angio.phy.protest.ss.E)

## [1] 0.4904214

(raoD.abd.abd.angio.phy.protest.right<-raoD.abd.abd.angio.phy.protest.ss.mean+
    raoD.abd.abd.angio.phy.protest.ss.E)

## [1] 0.5002275

raoD.abd.abd.angio.phy.protest.signif<-lapply(raoD.abd.abd.angio.phy.protest, function(i){
    i$signif
    })
raoD.abd.abd.angio.phy.protest.signif.mean<-mean(unlist(raoD.abd.abd.angio.phy.protest.signif))
raoD.abd.abd.angio.phy.protest.signif.E<-qnorm(0.975)*sd(unlist(raoD.abd.abd.angio.phy.protest.signif))/
    sqrt(length(unlist(raoD.abd.abd.angio.phy.protest.signif)))
(raoD.abd.abd.angio.phy.protest.left<-raoD.abd.abd.angio.phy.protest.signif.mean-
    raoD.abd.abd.angio.phy.protest.signif.E)

## [1] 0.001

(raoD.abd.abd.angio.phy.protest.right<-raoD.abd.abd.angio.phy.protest.signif.mean+
    raoD.abd.abd.angio.phy.protest.signif.E)

## [1] 0.001

Tables comparing values

Presence-absence table for supporting

write.table(protest.pa.table)

## "m12" "P-value" "m12" "P-value"
## "SiteEnvxBD" 0.7 0.001 0.74 0.001
## "SiteEnvxPhBD" 0.85 0.001 0.94 0.00119
## "BDxPhBD" 0.54 0.001 0.57 0.001

Tables comparing values

Abundance-weighted table for main manuscript

write.table(protest.abd.table)

## "m12" "P-value" "m12" "P-value"
## "SiteEnvxBD" 0.81 0.001 0.84 0.001
## "SiteEnvxPhBD" 0.82 0.001 0.93 0.00108
## "BDxPhBD" 0.55 0.001 0.5 0.001

Maximum clade credibility analyses

Table for presence absence values (maximum clade credibility)

write.table(protest.pa.table.one.tree)

## "m12" "P-value" "m12" "P-value"
## "SiteEnvxBD" 0.7 0.001 0.74 0.001
## "SiteEnvxPhBD" 0.85 0.001 0.95 0.001
## "BDxPhBD" 0.54 0.001 0.57 0.001

Table for abundance-weighted values (maximum clade credibility)

write.table(protest.abd.table.one.tree.abd)

## "m12" "P-value" "m12" "P-value"
## "SiteEnvxBD" 0.81 0.001 0.84 0.001
## "SiteEnvxPhBD" 0.82 0.001 0.93 0.001
## "BDxPhBD" 0.55 0.001 0.5 0.001