This function computes LTT plots for a set of trees & plots a (1-\(\alpha\))-percent CI by various methods.
ltt95(trees, alpha=0.05, log=FALSE, method=c("lineages","times"),
mode=c("median","mean"), ...)
# S3 method for ltt95
plot(x, ...)is an object of class "multiPhylo" containing a list of phylogenetic trees.
confidence level. Defaults to alpha=0.05. alpha=0 will mean that the interval around all trees in the set will be plotted.
logical value indicating whether or not to plot on the semi-log scale.
plot the CI on the number of lineages given time ("lineages"); or on times given a number of lineages ("times").
plot the median or mean LTT.
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-\(\alpha\))-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.