ltt95: Creates a (1-\(\alpha\))% CI for a set of LTTs

Description

This function computes LTT plots for a set of trees & plots a (1-\(\alpha\))% CI by various methods. (See ltt for more details.)

ltt95(trees, alpha=0.05, log=FALSE, method=c("lineages","times"),
   mode=c("median","mean"), ...)
# S3 method for 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-\(\alpha\))% 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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.