Nothing
`caprescale` <-
function (x, verbose = FALSE)
{
if (is.null(x$CCA)) {
nr <- nrow(x$CA$u)
nunpeiv <- x$CA$rank
neiv <- npeiv <- length(x$CA$eig)
sumpeiv <- sum(x$CA$eig[1:nunpeiv])
sumeiv <- sum(x$CA$eig)
}
else {
nr <- nrow(x$CCA$u)
nceiv <- length(x$CCA$eig)
nunpeiv <- x$CA$rank
nuneiv <- length(x$CA$length)
npeiv <- nceiv + nunpeiv
neiv <- nceiv + nuneiv
sumpeiv <- sum(x$CA$eig[1:nunpeiv]) + sum(x$CCA$eig)
sumeiv <- sum(x$CA$eig) + sum(x$CCA$eig)
}
const <- attributes(scores(x))$const
if (is.null(x$CCA) == F) {
x$CCA$v <- x$CCA$v * const
x$CCA$wa <- x$CCA$wa * const
x$CCA$u <- x$CCA$u * const
x$CCA$biplot <- x$CCA$biplot * const
x$CCA$centroids <- x$CCA$centroids * const
}
x$CA$v <- x$CA$v * const
x$CA$u <- x$CA$u * const
if (verbose == T) {
distmat <- as.matrix(vegdist(summary(x, axes = npeiv,
scaling = 1)$sites, method = "euc"))
ssdist <- sum((distmat)^2)/(2 * nrow(distmat))
if (substr(x$inertia, 1, 4) == "mean") {
sstot <- sumpeiv * (nr - 1)
sumeiv <- sumeiv * (nr - 1)
}else {
sstot <- sumpeiv
ssdist <- ssdist / (nr-1)
}
cat("SSTot obtained from sum of all eigenvalues:", sumeiv, "\n")
cat("SSTot obtained from sum of all positive eigenvalues:", sstot, "\n")
cat("SSTot reflected by distances among site scores on all axes:",
ssdist, "\n")
if (is.null(x$CCA) == F) {
distmat <- as.matrix(vegdist(summary(x, axes = nceiv,
scaling = 1)$constraints, method = "euc"))
ssdistcf <- sum((distmat)^2)/(2 * nrow(distmat))
distmat <- as.matrix(vegdist(summary(x, axes = nceiv,
scaling = 1)$sites, method = "euc"))
ssdistcs <- sum((distmat)^2)/(2 * nrow(distmat))
distmat <- as.matrix(vegdist(summary(x, axes = npeiv,
scaling = 1)$sites[, ((nceiv + 1):npeiv)], method = "euc"))
ssdistus <- sum((distmat)^2)/(2 * nrow(distmat))
if (substr(x$inertia, 1, 4) == "mean") {
sstotc <- sum(x$CCA$eig) * (nr - 1)
sstotu <- sum(x$CA$eig[1:nunpeiv]) * (nr - 1)
}
else {
sstotc <- sum(x$CCA$eig)
ssdistcs <- ssdistcs / (nr-1)
ssdistcf <- ssdistcf / (nr-1)
sstotu <- sum(x$CA$eig[1:nunpeiv])
ssdistus <- ssdistus / (nr-1)
}
cat("SSExpl obtained from eigenvalues of constrained axes:",
sstotc, "\n")
cat("SSExpl reflected by distances among site scores on constrained axes (scaling 1):",
ssdistcs, "\n")
cat("SSExpl reflected by distances among fitted site scores on constrained axes (scaling 1):",
ssdistcf, "\n")
cat("SSRes obtained from eigenvalues of positive unconstrained axes:",
sstotu, "\n")
cat("SSRes reflected by distances among site scores on positive unconstrained axes (scaling 1):",
ssdistus, "\n")
}
}
return(x)
}
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