plot.geohisse.states {hisse}

Plotting function geohisse.states objects

Description

A plotting function for visualizing changes in states and rates over a phylogeny

Usage

## S3 method for class 'geohisse.states'
plot(x, rate.param = "net.div", type = "fan",
show.tip.label = TRUE, fsize = 1.0, legend = TRUE, ...)

Arguments

x

a hisse.states object or a list of such objects.

rate.param

indicates the type of rates to plot. Options include: “turnover”, “net.div”, “speciation”, “extinction”, “extinction.fraction”.

type

a character string specifying the type of phylogeny to be drawn. Options are "fan" (default) or "phylogram".

show.tip.label

a logical indicating whether tip names should be included. Default is TRUE

fsize

sets the font size for the tip labels.

legend

indicates if the legend is to be plotted. TRUE or FALSE.

...

Additional parameters to control the plot. See “Details”.

Details

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 state 1 (endemic area '0'), state 2 (endemic area '1') and state 0 (widespread area '01'). Always 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.

Author(s)

Brian O'Meara and Daniel Caetano

References

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.