Nothing
`orglellipse` <-
function(object, groups, display = "sites", w = weights(object, display),
kind = c("sd", "se", "ehull"), conf, choices = 1:3, alpha = 0.3,
col = "red", ...)
{
weights.default <- function(object, ...) NULL
kind <- match.arg(kind)
x <- scores(object, display = display, choices = choices, ...)
groups <- as.factor(groups)
## evaluate weights
w <- eval(w)
if (is.null(w) || length(w) == 1)
w <- rep(1, nrow(x))
## covariance and centres as lists
Cov <- list()
for (g in levels(groups))
if (kind == "ehull") {
Cov[[g]] <- ellipsoidhull(x[groups == g,, drop = FALSE])
Cov[[g]]$n.obs <- sum(groups == g)
}
else
Cov[[g]] <- cov.wt(x[groups == g,, drop = FALSE],
wt = w[groups == g])
if (kind == "se")
for(i in seq_len(length(Cov)))
Cov[[i]]$cov <- Cov[[i]]$cov * sum(Cov[[i]]$wt^2)
## recycle colours
if (is.factor(col))
col <- as.numeric(col)
col <- rep(col, length = length(Cov))
## rgl::ellipse3d defaults to confidence envelopes, but we want to
## default to sd/se and only use confidence ellipses if conf is
## given
if (missing(conf))
t <- 1
else
t <- sqrt(qchisq(conf, 3))
## graph
for(i in seq_len(length(Cov)))
if (Cov[[i]]$n.obs > 3)
if (kind == "ehull")
plot3d(ellipse3d(Cov[[i]]$cov, centre = Cov[[i]]$loc,
t = sqrt(Cov[[i]]$d2)),
add = TRUE, alpha = alpha, col = col[i], ...)
else
plot3d(ellipse3d(Cov[[i]]$cov, centre = Cov[[i]]$center, t = t),
add = TRUE, alpha = alpha, col = col[i], ...)
}
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