Nothing
transformRateMatrix <- function(rateData, rate=NULL) {
V <- rateData$Vmat
if(is.null(rate)) { rate <- c(rep(1,length(rateData$Vmat))) } else { rate <- rate }
nV <- length(rate)
if(length(rate) != length(rateData$Vmat)){stop("The number of rates defined differs from the number of rate matrices")}
v1 <- V[[1]]
rateMats <- vector(mode="list", length = nV)
retMat <- matrix(0, nrow = dim(v1)[1], ncol = dim(v1)[2])
for(i in 1:nV) {
rateMats[[i]] <- rate[i] * V[[i]]
retMat <- retMat + rateMats[[i]]
}
return(retMat)}
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