https://github.com/cran/ape
Tip revision: eccbb978b5786096270acdf6a0db8d362652dca6 authored by Emmanuel Paradis on 19 September 2005, 00:00:00 UTC
version 1.7
version 1.7
Tip revision: eccbb97
diversi.time.Rd
\name{diversi.time}
\alias{diversi.time}
\title{Analysis of Diversification with Survival Models}
\usage{
diversi.time(x, census = NULL, censoring.codes = c(1, 0), Tc = NULL)
}
\arguments{
\item{x}{a numeric vector with the branching times.}
\item{census}{a vector of the same length than `x' used as an
indicator variable; thus, it must have only two values, one coding
for accurately known branching times, and the other for censored
branching times. This argument can be of any mode (numeric, character,
logical), or can even be a factor.}
\item{censoring.codes}{a vector of length two giving the codes used
for \code{census}: by default 1 (accurately known times) and 0 (censored
times). The mode must be the same than the one of \code{census}.}
\item{Tc}{a single numeric value specifying the break-point time to
fit Model C. If none is provided, then it is set arbitrarily to the
mean of the analysed branching times.}
}
\description{
This functions fits survival models to a set of branching times, some
of them may be known approximately (censored). Three models are
fitted, Model A assuming constant diversification, Model B assuming
that diversification follows a Weibull law, and Model C assuming that
diversification changes with a breakpoint at time `Tc'. The models are
fitted by maximum likelihood.
}
\details{
The principle of the method is to consider each branching time as an
event: if the branching time is accurately known, then it is a failure
event; if it is approximately knwon then it is a censoring event. An
analogy is thus made between the failure (or hazard) rate estimated by
the survival models and the diversification rate of the lineage. Time
is here considered from present to past.
Model B assumes a monotonically changing diversification rate. The
parameter that controls the change of this rate is called beta. If
beta is greater than one, then the diversification rate decreases
through time; if it is lesser than one, the the rate increases through
time. If beta is equal to one, then Model B reduces to Model A.
}
\value{
A NULL value is returned, the results are simply printed.
}
\references{
Paradis, E. (1997) Assessing temporal variations in diversification
rates from phylogenies: estimation and hypothesis
testing. \emph{Proceedings of the Royal Society of London. Series
B. Biological Sciences}, \bold{264}, 1141--1147.
}
\author{Emmanuel Paradis \email{paradis@isem.univ-montp2.fr}}
\seealso{
\code{\link{branching.times}}, \code{\link{diversi.gof}}
\code{\link{ltt.plot}}, \code{\link{birthdeath}},
\code{\link{bd.ext}}, \code{\link{yule}}, \code{\link{yule.cov}}
}
\keyword{models}