phytools: ltt95 – R documentation

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ltt95

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. Defaults to `alpha=0.05`. `alpha=0` will mean that the interval around all trees in the set will be plotted.
`log`	logical value indicating whether or not to plot on the semi-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; `lend` determines the line end type (as in `par`); `shaded` determines whether to plot the (1-α)-percent CI using dotted lines (if `FALSE`) or shading (if `TRUE`); and `bg` is the background color for shading if `shaded=TRUE`.

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.