plotTHETA: Plot THETA From coalescentMCMC Output

In coalescentMCMC: MCMC Algorithms for the Coalescent

Plot THETA From coalescentMCMC Output

Description

This function plots the values of THETA predicted from model fitted with coalescentMCMC.

Usage

plotTHETA(x, phy, add = FALSE, rightwards = TRUE, col = "blue",
          transparency = 50/length(phy), xlab = "Time",
          ylab = expression(Theta), ylim = NULL, x.scale = 1,
          y.scale = 1, show.present = TRUE, ...)

Arguments

x	an output from.
phy	an object of class "phylo" or "multiPhylo".
add	a logical value: whether to add the curves on an existing plot?
rightwards	a logical value: whether to draw the time (horizontal) axis rightwards (the default).
col	the base colour of the curves.
transparency	the degree of transparency of the curves.
xlab, ylab	character strings giving the labels for the x- and y-axes.
ylim	a numeric vector with two values giving the limits of the y-axis (useful if several curves are drawn).
x.scale	the scaling factor for the x-axis; typically, the inverse of the mutation rate.
y.scale	the scaling factor for the y-axis; typically, the inverse of twice the mutation rate.
show.present	a logical value: whether to indicate the present in italics (near the zero coordinate on the x-axis).
...	further arguments passed to plot.

Value

NULL

Author(s)

Emmanuel Paradis

See Also

coalescentMCMC

coalescentMCMC documentation built on April 22, 2022, 5:05 p.m.