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## plot.popsize.R (2004-07-4) modified by EP (2019-01-29)
## Plot population size in dependence of time
## Copyright 2004 Rainer Opgen-Rhein and Korbinian Strimmer
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
plot.popsize <-
function(x, show.median = TRUE, show.years = FALSE,
subst.rate, present.year, xlab = NULL,
ylab = "Effective population size",
log = "y", ...)
{
ylim <- range(x[, 2:5], na.rm = TRUE)
x1 <- x[, 1]
if (show.years) {
x1 <- -x1/subst.rate + present.year
if (is.null(xlab)) xlab <- "Time (years)"
} else {
if (is.null(xlab))
xlab <- "Time (past to present in units of substitutions)"
}
xlim <- range(x1, na.rm = TRUE)
j <- if (show.median) 3 else 2
plot(x1, x[, j], type = "s", xlim = xlim, ylim = ylim,
xlab = xlab, ylab = ylab, log = log, lwd = 2.5, ...)
lines(x1, x[, 4], ...)
lines(x1, x[, 5], ...)
}
lines.popsize <- function(x, show.median = TRUE, show.years = FALSE,
subst.rate, present.year, ...)
{
x1 <- x[, 1]
if (show.years) x1 <- -x1/subst.rate + present.year
j <- if (show.median) 3 else 2
lines(x1, x[, j], lwd = 2.5, ...)
lines(x1, x[, 4], ...)
lines(x1, x[, 5], ...)
}
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