Nothing
beta.temp <- function(x, y, index.family="sorensen"){
# test for a valid index
index.family <- match.arg(index.family, c('jaccard','sorensen'))
# test for pre-existing betapart objects - validates data in x if not
if (! inherits(x, "betapart")){
x <- betapart.core(x)
}
# test for pre-existing betapart objects - validates data in x if not
if (! inherits(y, "betapart")){
y <- betapart.core(y)
}
# check x and y match
if(! identical(dim(x$data), dim(y$data)))
stop('The two data matrices do not have the same dimensions.')
if(! identical(rownames(x$data), rownames(y$data)))
stop('The two data matrices do not have the same site names.')
if(! identical(colnames(x$data), colnames(y$data)))
stop('The two data matrices do not have the same species names .')
# get differences between groups
ai<-apply(x$data & y$data, 1, sum)
bi<-apply(x$data & ! y$data, 1, sum)
ci<-apply(! x$data & y$data, 1, sum)
switch(index.family,
sorensen = {
beta.sor<- (bi+ci) / (2*ai+bi+ci)
beta.sim<- pmin(bi,ci)/(ai+pmin(bi,ci))
beta.sne<- beta.sor - beta.sim
result<-data.frame(beta.sim, beta.sne, beta.sor)},
jaccard = {
beta.jac<- (bi+ci) / (ai+bi+ci)
beta.jtu<- 2*pmin(bi,ci)/(ai+(2*pmin(bi,ci)))
beta.jne<- beta.jac - beta.jtu
result<-data.frame(beta.jtu, beta.jne, beta.jac)})
return(result)
}
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