R: Creates a (1-alpha)-percent CI for a set of LTTs

ltt95 {phytools}

R Documentation

Creates a (1-α)-percent CI for a set of LTTs

This function computes LTT plots for a set of trees & plots a (1-α)-percent CI by various methods.

ltt95(trees, alpha=0.05, log=FALSE, method=c("lineages","times"),
	mode=c("median","mean"), ...)
## S3 method for class 'ltt95'
plot(x, ...)

`trees`	is an object of class `"multiPhylo"` containing a list of phylogenetic trees.
`alpha`	confidence level.
`log`	logical value indicating whether or not to plot on the log-scale.
`method`	plot the CI on the number of lineages given time (`"lineages"`); or on times given a number of lineages (`"times"`).
`mode`	plot the median or mean LTT.
`x`	object of class `"ltt95"` for plotting method.
`...`	optional arguments to be used by `ltt95` or the plotting method. So far, `res` gives the number of time-steps (defaults to `res=100`. `xaxis` (`"standard"`, `"negative"`, or `"flipped"`) determines the scale (time from the root, time back from the present, or time from the present) of the x-axis of the plot.

This function creates a plot and invisibly returns an object of class "ltt95".

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.