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simprof
2011 May 17
1
simprof test using jaccard distance
...function by bypassing the input of a raw community matrix (sites x species) by inputing instead a distance matrix already calculated with vegdist (vegan package) (Jaccard distance is available in vegdist, but not in the function dist used in simprof...)
I therefore modified the function as follow:
simprof2=function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average",
alpha = 0.05, sample.orientation = "row", const = 0, silent = TRUE,
increment = 100)
{ hclust.results <- hclust(data, method = method.cluster)
pMatrix <- cbind(hclust.result...