Nothing
autosimi <- function(comm, method="bray", binary=FALSE, log.transf=FALSE,
simi=TRUE, permutations=50){
n.samp <- nrow(comm)
spp <- ncol(comm)
size <- n.samp%/%2
sizes <- 1:size
resu.m <- matrix(NA, size, permutations)
for(i in 1:permutations){
for(j in sizes){
if(j==1){ pair<-comm[sample(1:n.samp,2), ]}
if(j>1) {
temp<-comm[sample(1:n.samp, j*2),]
temp1<-temp[1:j,]
temp2<-temp[(j+1):(j*2),]
temp1<-colSums(temp1)
temp2<-colSums(temp2)
pair<-rbind(temp1,temp2)
}
if(binary==TRUE){pair<-ifelse(pair>0,1,0)}# close if binary
if(binary==FALSE & log.transf==TRUE){pair<-log(pair+1)}
if(binary==TRUE & log.transf==TRUE){stop("You can not log-transform presence/absence data")}
if(simi==TRUE){resu.m[j,i]<-as.numeric(1-vegdist(pair, method, binary))}
if(simi==FALSE){resu.m[j,i]<-as.numeric(vegdist(pair, method, binary))}
}#close for j
}# close for i
mean.perm <- rowMeans(resu.m)
resu <- data.frame(sizes, mean.perm)
indexes <- c("manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower",
"altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao")
colnames(resu) <- c("sample.size", indexes[pmatch(method,indexes)])
return(resu)
}
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