Nothing
Optimal.Similarity <-
function(Distance, CheckArguments = TRUE)
{
if (CheckArguments)
CheckentropartArguments()
# Distance must be either a matrix or a dist object (ade4)
if (is.matrix(Distance)) {
if (nrow(Distance) != ncol(Distance)) {
stop("Distance must be a square matrix")
}
if (any(diag(Distance) != 0)) {
stop("The diagonal of Distance must contain zeros only")
}
} else {
if (!inherits(Distance, "dist")) {
stop("Distance must be a matrix or a dist object")
}
}
#' Optimize u
Distances <- as.numeric(Distance/max(Distance))
u <- 1
Optim <- stats::optim(u, function(u) stats::var(exp(-u*Distances)), lower=0, upper=1000, method="L-BFGS-B", control=list(fnscale=-1))
Result <- list(u=Optim$par, Matrix=exp(-u*as.matrix(Distance)/max(Distances)))
return (Result)
}
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