Nothing
AlphaEntropy <-
function(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE, Z = NULL, CheckArguments = TRUE)
{
if (CheckArguments)
CheckentropartArguments()
# Communities
if (!is.null(Tree)) {
Method <- "HCDT"
# Preprocess the tree before apply
ppTree <- Preprocess.Tree(Tree)
# Get the entropy of communities.
DetailedCommunities <- apply(MC$Nsi, 2, bcPhyloEntropy, q=q, Tree=ppTree, Normalize=Normalize, Correction=Correction, CheckArguments=FALSE)
# Get $Total in each community's list
Communities <- unlist(lapply(DetailedCommunities, function(x) x$Total))
} else {
if (!is.null(Z)) {
Method <- "Similarity-based"
Communities <- apply(MC$Nsi, 2, bcHqz, q=q, Correction=Correction, Z=Z, CheckArguments=FALSE)
} else {
Method <- "Neutral"
Communities <- apply(MC$Nsi, 2, bcTsallis, q=q, Correction=Correction, CheckArguments=FALSE)
}
}
# Weighted sum of Communities
Total <- sum(Communities*MC$Wi)
Entropy <- list(
MetaCommunity = ArgumentOriginalName(MC),
Method = Method,
Type = "alpha",
Order = q,
Correction = Correction,
Normalized = Normalize,
Weights = MC$Wi,
Communities = Communities,
Total=Total
)
if(!is.null(Tree))
Entropy$Tree <- ArgumentOriginalName(Tree)
if(!is.null(Z))
Entropy$Z <- ArgumentOriginalName(Z)
class(Entropy) <- "MCentropy"
return(Entropy)
}
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