R/betabas.R In marcog77/divalt:

Defines functions betabas

```#' Function for calculating beta diversity between altitudinal bands following the
#' methods of Baselga et al. (2010)
#'
#' @ indat = matrix containing community data
#' @ alt = character vector indicating column name for altitude values
#' @ group =character vector indicating column name for site IDs (if there is more than one site )
#'
betabas<- function(indat=NULL,alt=NULL,group=NULL) {
results <- NULL
if(is.null(group)){
alt.l<-sort(unique(indat[,alt]))
for (y in 1:(length(alt.l)- 1)){
d1<-indat[indat[,alt] %in% alt.l[y],]
d2<-indat[indat[,alt] %in% alt.l[y+ 1],]
Btotal <- NULL
Brepl <- NULL
Bnest <- NULL
for (z in 1:dim(d1)[1]) {
d1<-d1[,!names(d1) %in% alt]
d2<-d2[,!names(d2) %in% alt]
d1[d1 > 1] <- 1
d2[d2 > 1] <- 1
rownames(d1)<-c("1")
rownames(d2)<-c("1")
betaValues<- beta.temp(d1, d2, index.family="jaccard")
betaValues[is.na(betaValues)]<-0
Btotal[z] <- betaValues[3][,1]
Bnest[z] <- betaValues[2][,1]
Brepl[z] <- betaValues[1][,1]
}
res <- data.frame(Btotal = mean(Btotal), Brepl = mean(Brepl),Bnest = mean(Bnest), Altitude=paste(alt.l[y],alt.l[y+1],sep="-"),Altitude.midpoint=((alt.l[y]+alt.l[y+1])/2))
results <- rbind(res, results)
}
results.l<-melt(results,id.vars=c("Altitude","Altitude.midpoint"))
plot.results<-ggplot(results.l,aes(x=Altitude.midpoint,y=value,colour=variable))+
geom_line(size=0.5)+geom_point(size=1.5)+theme_bw()+ylab("Beta Diversity")+
xlab("Altitude")+theme(legend.title=element_blank())+theme(strip.text.x = element_text(size=9, face="bold"),strip.text.y = element_text(size=9, face="bold"))
results1<-list(results,plot.results)
} else {
results <- NULL
site.l<-unique(indat[,group])
for (i in 1:length(site.l)){
indat1<-indat[indat[,group] %in% site.l[i],]
colsdel<-c(alt,group)
indat.tmp<-indat1[, !colnames(indat1) %in% colsdel]
totalsp <- colSums(indat.tmp)
cols <- names(totalsp[totalsp > 0])
cols1 <- c(alt,group,cols)
indat2 <- indat1[, cols1]
alt.l<-sort(unique(indat2[,alt]))
for (y in 1:(length(alt.l)- 1)){
d1<-indat2[indat2[,alt] %in% alt.l[y],]
d2<-indat2[indat2[,alt] %in% alt.l[y+ 1],]
Btotal <- NULL
Brepl <- NULL
Bnest <- NULL
for (z in 1:dim(d1)[1]) {
d1<-d1[,!names(d1) %in% alt]
d2<-d2[,!names(d2) %in% alt]
d1[d1 > 1] <- 1
d2[d2 > 1] <- 1
rownames(d1)<-c("1")
rownames(d2)<-c("1")
betaValues<- beta.temp(d1, d2, index.family="jaccard")
betaValues[is.na(betaValues)]<-0
Btotal[z] <- betaValues[3][,1]
Bnest[z] <- betaValues[2][,1]
Brepl[z] <- betaValues[1][,1]
}
res <- data.frame(Btotal = mean(Btotal), Brepl = mean(Brepl),Bnest = mean(Bnest), Altitude=paste(alt.l[y],alt.l[y+1],sep="-"),Altitude.midpoint=((alt.l[y]+alt.l[y+1])/2))
results <- rbind(res, results)
}
}
results.l<-melt(results,id.vars=c(group,"Altitude","Altitude.midpoint"))
plot.results<-ggplot(results.l,aes(x=Altitude.midpoint,y=value,colour=variable))+
geom_line(size=0.5)+geom_point(size=1.5)+theme_bw()+ylab("Beta Diversity")+
xlab("Altitude")+theme(legend.title=element_blank())+theme(strip.text.x = element_text(size=9, face="bold"),strip.text.y = element_text(size=9, face="bold"))+facet_wrap(~site)
results1<-list(results,plot.results)
}
return(results1)
}
```
marcog77/divalt documentation built on Nov. 22, 2018, 6:25 p.m.