Nothing
bestref <- function(x, optim.crit = c("WCC", "RMS"),
trwdth=20, wghts = NULL, smooth.param = 0)
{
optim.crit <- match.arg(optim.crit)
if (inherits(x, "array") & length(dim(x)) == 3) {
nsamp <- dim(x)[1]
xl <- vector("list", nsamp)
for (i in 1:nsamp) {
if (smooth.param > 0) {
xl[[i]] <- apply(x[i,,], 2, difsm, smooth.param)
} else {
xl[[i]] <- x[i,,]
}
}
xl <- lapply(xl, t)
best <- numeric()
best.mat <- matrix(NA, nrow = dim(x)[3], ncol = nsamp)
for (i in 1:length(xl)) {
calc <- bestref(xl[[i]], optim.crit=optim.crit, trwdth=trwdth,
wghts=wghts, smooth.param=smooth.param)
best[i] <- calc[[1]]
best.mat[,i] <- calc[[2]]
}
list(best.ref = best, crit.values = best.mat)
} else {
if (optim.crit == "RMS") {
if (smooth.param > 0)
x <- t(apply(x, 1, difsm, smooth.param))
x.dist <- as.matrix(dist(x))
dimnames(x.dist) <- NULL
list(best.ref = which.min(colSums(x.dist^2)),
crit.values = colSums(x.dist^2))
} else {
if (is.null(wghts))
wghts <- 1 - (0:trwdth)/trwdth
nx <- nrow(x)
x.wcc <- rep(0, nx * (nx - 1) / 2)
counter <- 0
for (i in 1:(nx - 1)) {
for (j in (i+1):nx) {
counter <- counter + 1
x.wcc[counter] <- wcc(x[i,], x[j,], trwdth, wghts)
}
}
attr(x.wcc, "Size") <- nx
class(x.wcc) <- "dist"
x.wcc <- as.matrix(x.wcc)
dimnames(x.wcc) <- NULL
x.wcc <- x.wcc + t(x.wcc)
list(best.ref = which.max(colSums(x.wcc)),
crit.values = colSums(x.wcc))
}
}
}
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