Nothing
## Plots probability of Analogue based on
## Bayes factors
plot.bayesF <- function(x, group = "all",
xlab = NULL,
ylab = "Pr (A+ | d)",
col = "red",
abline.col = "lightgrey",
abline.lty = "dashed",
...) {
pfun <- function(x, xlab, ylab, col, abline.col, main, ...) {
prob.pos <- x$posterior.odds$pos / (1 + x$posterior.odds$pos)
prob.pos[is.nan(prob.pos)] <- 1
plot(rev(x$roc.points), prob.pos, type = "n",
ylab = "", xlab = "", axes = FALSE, main = main)
abline(v = x$optimal, lty = abline.lty, col = abline.col)
lines(rev(x$roc.points), prob.pos, col = col)
axis(1)
axis(2)
box()
}
if(!inherits(x, "bayesF"))
stop("Plot method only for objects of class \"bayesF\".")
if(is.null(xlab))
xlab <- paste("Dissimilarity (", attr(x, "method"), ")",
sep = "")
## need to check 'group'; can be "all", "Combined" or one of the
## group names in list
if(length(group) > 1) {
group <- group[1]
warning("More than 1 'group' specified. Using only the first\nDid you mean to use '\"all'\"")
}
comp.want <- length(x) - 2
GROUP <- c("all", names(x[seq_len(comp.want)]))
group <- match.arg(group, GROUP)
## only split region if "all" plotting
if(group == "all") {
n.plot <- comp.want
xy.nums <- n2mfrow(n.plot)
layout(matrix(seq_len(prod(xy.nums)), nrow = xy.nums[1],
ncol = xy.nums[2]))
op <- par(mar = c(2,2,3,1) + 0.1, oma = c(2,2,2,0),
no.readonly = TRUE)
on.exit({par(op)
layout(1)})
} else {
n.plot <- 1
xy.nums <- rep(1, 2)
}
g.names <- names(x[seq_len(comp.want)])
for(i in seq_len(comp.want)) {
if(group != "all" && group != g.names[i])
next
pfun(x[[i]], col = col, abline.col = abline.col,
main = g.names[i], ...)
}
if(n.plot > 1) {
title(xlab = xlab, outer = TRUE, line = 0.5, cex.lab = 1.3)
title(ylab = ylab, outer = TRUE, line = 0.5, cex.lab = 1.3)
title(main = "Posterior probability of analogue",
outer = TRUE, line = 0.5, cex.main = 1.3)
} else {
title(xlab = xlab, ylab = ylab,
sub = "Posterior probability of analogue")
}
invisible()
}
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