plot.history: Plot Character History

In diversitree: Comparative 'Phylogenetic' Analyses of Diversification

Plot Character History

Description

Both stochastic character mapping and simulation may create character histories. This function plots these histories

Usage

## S3 method for class 'history'
plot(x, phy, cols=seq_along(states),
             states=x$states,
             xlim=NULL, ylim=NULL, show.tip.label=TRUE,
             show.node.label=FALSE, show.tip.state=TRUE,
             show.node.state=TRUE, no.margin=FALSE, cex=1, font=3,
             srt=0, adj=0, label.offset=NA, lwd=1, ...)

Arguments

x	An object of class history.discrete containing a discrete character history. This could be made by history.from.sim.discrete.
phy	The phylogeny used to generate the history. Few checks are made to make sure that this is really correct, and all manner of terrible things might happen if these are not compatible. This may change in future.
cols	A vector of colours.
states	The different state types. Probably best to leave alone.
xlim	Plot x-limits (optional).
ylim	Plot y-limits (optional).
show.tip.label	Logical: show the species tip labels?
show.node.label	Logical: show the species node labels?
show.tip.state	Logical: draw a symbol at the tips to indicate tip state?
show.node.state	Logical: draw a symbol at the nodes to indicate node state?
no.margin	Supress drawing of margins around the plot
cex	Font and symbol scaling factor.
font	Font used for tip and node labels (see par).
srt	String rotation for tip and node labels.
adj	Label adjustment (see par).
label.offset	Horizontal offset of tip and node labels, in branch length units.
lwd	Line width
...	Additional arguments (currently ignored)

Details

This attempts to be as compatible with ape's plotting functions as possible, but currently implements only right-facing cladegrams.

Author(s)

Richard G. FitzJohn

Examples

## Due to a change in sample() behaviour in newer R it is necessary to
## use an older algorithm to replicate the previous examples
if (getRversion() >= "3.6.0") {
  RNGkind(sample.kind = "Rounding")
}

## Simulate a tree, but retain extinct species.
pars <- c(.1, .2, .03, .04, 0.05, 0.1) # BiSSE pars
set.seed(2)
phy <- tree.bisse(pars, 20, x0=0, include.extinct=TRUE)

## Create a 'history' from the information produced by the simulation
## and plot this
h <- history.from.sim.discrete(phy, 0:1)
plot(h, phy, cex=.7)

## Prune the extinct taxa.
phy2 <- prune(phy)

## The history must be recreated for this pruned tree:
h2 <- history.from.sim.discrete(phy2, 0:1)
plot(h2, phy2, cex=.7)

diversitree documentation built on Oct. 2, 2024, 9:13 a.m.