A plotting function for visualizing changes in states and rates over a phylogeny
# S3 method for muhisse.states
plot(x, rate.param = "net.div", type = "fan",
show.tip.label = TRUE, fsize = 1.0, legend = TRUE, ...)a muhisse.states object or a list of such objects.
indicates the type of rates to plot. Options include: “turnover”, “net.div”, “speciation”, “extinction”, “extinction.fraction”.
a character string specifying the type of phylogeny to be drawn. Options are "fan" (default) or "phylogram".
a logical indicating whether tip names should be included. Default is TRUE
sets the font size for the tip labels.
indicates if the legend is to be plotted. TRUE or FALSE.
Additional parameters to control the plot. See “Details”.
Brian O'Meara and Daniel Caetano
Additional parameters can be defined using “...”:
“do.observed.only” is a logical indicating whether just the
states should be plotted; for now, only TRUE
works.
“rate.colors” are user specified colors to be used for
coloring rates.
“state.colors” are user specified colors to be
used for coloring states. A vector with the color for states 00, 01, 10, and 11 (in this order).
“edge.width” is the width of the
branches of the phylogeny.
“width.factor” is the factor
multiplying the “edge.width” to get the width of the branch
for the states tree. Needs to be a numeric value between 0 and 1.
“rate.range” is an optional two element
vector. If present, specifies the range of rate values to use for
plotting.
“lims.percentage.correction” deals with cases where
the limits are slightly smaller than the values due to imprecision
issues.
“legend.position” are the coordinates for placing the
legend.
“legend.cex” is the text size inside the
legend.
“legend.kernel” lets you specify the way the density
plot or histogram is made for rates. A value of “auto” chooses
what we think is the best option given your data, “hist” makes
a histogram, “rectangular”, “gaussian”, and others make
a density plot. See ?density for all non-“hist”
options.
“legend.bg” sets the color for the legend
background.
“mar” sets the margins for the plot. See more
information in 'help(par)'.
“outline” is whether to plot an
outline on the branches of the tree. Choose the color of the outline
using the parameter outline.color.
“outline.color” is the color
for the outline. Defaults to "black".
“swap.underscore” sets
whether to substitute all "_" with " " on the labels for the tips.
This function is very similar to the hisse::plot.hisse.states
function. See more details in help page for hisse::plot.hisse.states function.
Beaulieu, J.M, and B.C. O'Meara. 2016. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst. Biol. 65:583-601.