1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
|
\name{ltt95}
\alias{ltt95}
\alias{plot.ltt95}
\title{Creates a (1-\eqn{\alpha})-percent CI for a set of LTTs}
\usage{
ltt95(trees, alpha=0.05, log=FALSE, method=c("lineages","times"),
mode=c("median","mean"), ...)
\method{plot}{ltt95}(x, ...)
}
\arguments{
\item{trees}{is an object of class \code{"multiPhylo"} containing a list of phylogenetic trees.}
\item{alpha}{confidence level.}
\item{log}{logical value indicating whether or not to plot on the log-scale.}
\item{method}{plot the CI on the number of lineages given time (\code{"lineages"}); or on times given a number of lineages (\code{"times"}).}
\item{mode}{plot the median or mean LTT.}
\item{x}{object of class \code{"ltt95"} for plotting method.}
\item{...}{optional arguments to be used by \code{ltt95} or the plotting method. So far, \code{res} gives the number of time-steps (defaults to \code{res=100}. \code{xaxis} (\code{"standard"}, \code{"negative"}, or \code{"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.}
}
\description{
This function computes LTT plots for a set of trees & plots a (1-\eqn{\alpha})-percent CI by various methods.
}
\details{
This function creates a plot and invisibly returns an object of class \code{"ltt95"}.
}
\references{
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
\code{\link{ltt}}
}
\keyword{phylogenetics}
\keyword{plotting}
\keyword{diversification analysis}
|
