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#' Produces a dendrogram using distances between the mean
#' FA signatures of the prey types.
#'
#'
#' Performs a hierarchical cluster analysis of mean prey
#' fatty acid signatures using function \code{hclust}.
#' @export
#' @param prey.fa data frame of prey fatty acid signature
#' samples. First column must be species used to group samples. Other columns
#' are assumed to be fatty acid proportions.
#' @param method the agglomeration method to be used. This should be
#' one of the possible methods in \code{hclust} such as \code{"single"},
#' \code{"complete"} or \code{"average"}. Default is \code{"complete"}.
#' @param dist.meas distance measure to use for calculating dissimilarities:
#' 1=KL, 2=AIT or 3=CS. Default is \code{AIT}.
#' @return Plot (dendrogram)
#'
#' @examples
#'
#' ## Fatty Acids
#' data(FAset)
#' fa.set = as.vector(unlist(FAset))
#'
#' ## prey.cluster requires full prey database.
#' data(preyFAs)
#' prey.sub=(preyFAs[,4:(ncol(preyFAs))])[fa.set]
#' prey.sub=prey.sub/apply(prey.sub,1,sum)
#' group=as.vector(preyFAs$Species)
#' prey.matrix=cbind(group,prey.sub)
#'
#' prey.cluster(prey.matrix,method="average",dist.meas=3)
prey.cluster <- function(prey.fa,
method="complete",
dist.meas=2) {
mult.rep <- function(x.vec) {
no.zero <- sum(x.vec == 0)
x.vec[x.vec == 0] <- 1e-05
x.vec[x.vec > 0] <- (1 - no.zero * 1e-05) * x.vec[x.vec > 0]
return(x.vec)
}
prey.fa[,-1] <- prey.fa[,-1]/apply(prey.fa[,-1],1,sum)
sort.preytype <- order(prey.fa[,1])
prey.fa <- prey.fa[sort.preytype,]
prey.fa[,-1] <- t(apply(prey.fa[,-1],1,mult.rep))
#Calculate distances
prey.means <- MEANmeth(prey.fa)
I <- nrow(prey.means)
dist.mat <- matrix(rep(NA,I*I),nrow=I)
if (dist.meas==1) {
my.ylab <- "KL Distance"
for (i in 2:I) {
for (j in 1:(i-1)) {
dist.mat[i,j] <- KL.dist(as.vector(prey.means[i,]),as.vector(prey.means[j,]))
}
}
} else if (dist.meas==2) {
my.ylab <- "Aitchison Distance"
for (i in 2:I) {
for (j in 1:(i-1)) {
dist.mat[i,j] <- AIT.dist(as.vector(prey.means[i,]),as.vector(prey.means[j,]))
}
}
} else {
my.ylab <- "CS Distance"
for (i in 2:I) {
for (j in 1:(i-1)) {
dist.mat[i,j] <- chisq.dist(as.vector(prey.means[i,]),as.vector(prey.means[j,]),1)
}
}
}
plot(stats::hclust(stats::as.dist(dist.mat),method=method),labels=rownames(prey.means),xlab="", ylab=my.ylab, sub=NA)
}
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