Nothing
"mpd" <-
function(x, method="simpson", all=FALSE)
{
## preparations
METHODS <- c("simpson", "sorensen", "nestedness")
method <- pmatch(method, METHODS)
## transform to presence/absence matrix
df <- as.matrix(x > 0)
## calculate b: species occurring only on one of any two compared plots
b <- df %*% (1 - t(df))
## calculate c: species occurring only on the other of any two compared plots
c <- (1 - df) %*% t(df)
## Summing up 'min(bi,bj)' for all possible pairings
smin <- sum(pmin(b[row(b) > col(b)], c[row(c) > col(c)]))
## Summing up 'max(bi,bj)' for all possible pairings
smax <- sum(pmax(b[row(b) > col(b)], c[row(c) > col(c)]))
## the number of species shared by at least two sites, with
## sum(df) = sum of total species occurrences within data matrix,
## 2nd term: total number of species including a check for empty species
nss <- sum(df) - sum(colSums(df>0) != 0)
## calculating multi plot dissimilarity indices
sim <- smin / (nss + smin)
sor <- (smin + smax) / (2*nss + smin + smax)
nes <- sor-sim
res <- c(sim, sor, nes)
names(res) <- c("Simpson based mpd", "Sorensen based mpd", "Nestedness mpd")
if(!all){
res <- res[method]
}
res
}
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