Nothing
plot.mcarlo <-
function (x, which = c(1:2), alpha = 0.05,
caption = c("Distribution of dissimilarities",
expression(paste("Simulated probability Pr (Dissim < ", alpha,
")"))),
col.poly = "lightgrey", border.poly = "lightgrey",
ask = prod(par("mfcol")) < length(which) && dev.interactive(),
...)
{
if (!inherits(x, "mcarlo"))
stop("\"x\" must be or inherit from class \"mcarlo\".")
if (!is.numeric(which) || any(which < 1) || any(which > 2))
stop("'which' must be in 1:2")
show <- rep(FALSE, 2)
show[which] <- TRUE
one.fig <- as.integer(prod(par("mfcol"))) == 1L
if (ask) {
op <- par(ask = TRUE)
on.exit(par(op))
}
xlabel <- paste("Dissimilarity (", attr(x, "method"), ")",
sep = "")
evalDists <- switch(attr(x, "method"),
SQchord = seq(from = 0, to = 2, by = 0.01),
chord = seq(from = 0, to = sqrt(2), by = 0.01),
seq(from = 0, to = max(x, na.rm = TRUE), by = 0.01))
if (show[1]) {
range.dists <- max(evalDists)
h <- hist(x, plot = FALSE)
d <- density(x, adjust = 2, from = 0, to = range.dists)
y.lim <- range(0, h$density, d$y)
hist(x, freq = FALSE, ylim = y.lim, xlim = c(0, range.dists),
main = "", xlab = "", ylab = "", ann = FALSE, col = col.poly,
border = border.poly)
box()
title(main = caption[1], ylab = "Density", xlab = xlabel)
lines(d)
}
if (show[2]) {
num.dists <- length(x)
cumfreq <- sapply(evalDists,
function(x, y) length(y[y <= x]), x,
USE.NAMES = FALSE) / num.dists
cummu <- data.frame(distances = evalDists, cumfreq = cumfreq)
suppressWarnings(critical <- approx(cummu$cumfreq, cummu$distances,
alpha))
tlen <- length(critical$x)
sigx <- cummu$distances <= (max(critical$y, na.rm = TRUE))
sigx <- cummu[sigx, ]
plot(cumfreq ~ distances, data = cummu, type = "n", ann = FALSE)
title(main = caption[2], ylab = "Probability", xlab = xlabel)
polygon(c(0, sigx[, 1], sigx[nrow(sigx), 1]),
c(0, sigx[, 2], 0), col = col.poly, border = border.poly)
lines(cumfreq ~ distances, data = cummu)
}
if(show[2])
invisible(critical)
else
invisible()
}
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