paleotree (version 2.5)

kanto: Example Species Abundances Tables

Description

A totally fictional example of species abundance data, for testing functions that require a site-by-taxon table of community ecology data.

format

A table of type integer, representing terrestrial fauna and flora abundance counts.

source

Pokemon And All Respective Names are Trademark and Copyright of Nintendo 1996-2015.

Details

A classic dataset of ecological data collected by Satoshi and Okido, consisting of individual counts for 54 terrestrial faunal and floral species, fron 23 sites across the mainland Kanto region. Different ontogenetic stages were compounded and recorded by the common name for the first ontogenetic stage, with some inconsistency for species whose earliest stage have only been recently recognized. When separate names are commonly applied to sexual dimorphic forms, these were also combined and a single common name was used. Note: This data is a totally made-up, satirical homage to a well-known video game series (thus constituting fair-use).

Examples

data(kanto)

#visualize site abundances as barplots
barplotAbund<-function(x){
	x<-x[,colSums(x)>0]
	layout(1:(nrow(x)+1))
	xpar<-par(mar=c(0,7,2,0))
	for(i in 1:(nrow(x)-1)){
		barplot(x[i,],ylab=rownames(x)[i],
			names.arg="")
		}
	barplot(x[nrow(x),],
		ylab=rownames(x)[nrow(x)],las=3)
	par(xpar)
	layout(1)
	mtext("Abundances",side=2,line=3,adj=0.8)
	}

#first five sites
kanto5<-kanto[1:5,]
barplotAbund(kanto5)

#get pairwise Spearman rho coefficients
rhoCoeff<-pairwiseSpearmanRho(kanto,dropAbsent="bothAbsent")

#what are the nearest-neighbor rhos (largest rho correlations)?
diag(rhoCoeff)<-NA
rhoNearest<-apply(rhoCoeff,1,max,na.rm=TRUE)
rhoNearest

# We can see the power plant sample is extremely different from the rest

# measure evenness: Hurlbert's PIE

kantoPIE<-HurlbertPIE(kanto)

# compare to dominance (relative abundance of most abundant taxon)

dominance<-apply(kanto,1,function(x) max(x)/sum(x) )

plot(kantoPIE,dominance)

# relatively strong relationship!


#get bray-curtis distances
library(vegan)
bcDist <- vegdist(kanto,method="bray")

#do a PCO on the bray-curtis distances
pcoRes <- pcoa(bcDist,correction="lingoes")
scores <- pcoRes$vectors
#plot the PCO
plot(scores,type="n")
text(labels=rownames(kanto),scores[,1],scores[,2],cex=0.5)

#the way the power plant the the pokemon tower converge
	# is very suspicious: may be distortion due to a long gradient

#do a DCA instead with vegan's decorana
dcaRes<-decorana(kanto)
#plot using native vegan functions
	#will show species scores in red
plot(dcaRes,cex=0.5)
#kind of messy

#show just the sites scores
plot(dcaRes,cex=0.5,display="sites")

#show just the species scores
plot(dcaRes,cex=0.5,display="species")

#well, that's pretty cool


#get the nearest neighbor for each site based on pair-wise rho coefficients
rhoNeighbor<-apply(rhoCoeff,1,function(x)
	rownames(kanto)[tail(order(x,na.last=NA),1)])

#let's plot the nearest neighbor connections with igraph
NNtable<-cbind(rownames(kanto),rhoNeighbor)

# now plot with igraph
library(igraph)
NNlist <- graph.data.frame(NNtable)
plot(NNlist)

#arrows point at the nearest neighbor of each sample
	# based on maximum Spearman rho correlation

#testing for differences between groups of sites

#is there a difference between routes and non-routes
groups<-rep(0,nrow(kanto))
groups[grep(rownames(kanto),pattern="Route")]<-1

#anosim (in vegan)
	#are distances within groups smaller than distances between?
#we could also use adonis from vegan instead
library(vegan)

anosim(dat=kanto,grouping=groups)
adonis(kanto~factor(groups))
#both are very significant

#alternative: using multivariate GLMs in mvabund

library(mvabund)

ft <- manyglm(formula=kanto~factor(groups))
anova(ft)
#also highly significant!