https://github.com/cran/ape
Tip revision: fa2a72e2814d26112792cf4676f6737abb7f7e0d authored by Emmanuel Paradis on 01 December 2016, 16:40:32 UTC
version 4.0
version 4.0
Tip revision: fa2a72e
rlineage.Rd
\name{rlineage}
\alias{rlineage}
\alias{rbdtree}
\alias{rphylo}
\alias{drop.fossil}
\title{Tree Simulation Under the Time-Dependent Birth--Death Models}
\description{
These three functions simulate phylogenies under any time-dependent
birth--death model: \code{rlineage} generates a complete tree including
the species going extinct before present; \code{rbdtree} generates a
tree with only the species living at present (thus the tree is
ultrametric); \code{rphylo} generates a tree with a fixed number of
species at present time. \code{drop.fossil} is a utility function to
remove the extinct species.
}
\usage{
rlineage(birth, death, Tmax = 50, BIRTH = NULL,
DEATH = NULL, eps = 1e-6)
rbdtree(birth, death, Tmax = 50, BIRTH = NULL,
DEATH = NULL, eps = 1e-6)
rphylo(n, birth, death, BIRTH = NULL, DEATH = NULL,
T0 = 50, fossils = FALSE, eps = 1e-06)
drop.fossil(phy, tol = 1e-8)
}
\arguments{
\item{birth, death}{a numeric value or a (vectorized) function
specifying how speciation and extinction rates vary through time.}
\item{Tmax}{a numeric value giving the length of the simulation.}
\item{BIRTH, DEATH}{a (vectorized) function which is the primitive
of \code{birth} or \code{death}. This can be used to speed-up the
computation. By default, a numerical integration is done.}
\item{eps}{a numeric value giving the time resolution of the
simulation; this may be increased (e.g., 0.001) to shorten
computation times.}
\item{n}{the number of species living at present time.}
\item{T0}{the time at present (for the backward-in-time algorithm).}
\item{fossils}{a logical value specifying whether to output the
lineages going extinct.}
\item{phy}{an object of class \code{"phylo"}.}
\item{tol}{a numeric value giving the tolerance to consider a species
as extinct.}
}
\details{
These three functions use continuous-time algorithms: \code{rlineage}
and \code{rbdtree} use the forward-in-time algorithms described in
Paradis (2011), whereas \code{rphylo} uses a backward-in-time
algorithm from Stadler (2011). The models are time-dependent
birth--death models as described in Kendall (1948). Speciation
(birth) and extinction (death) rates may be constant or vary through
time according to an \R function specified by the user. In the latter
case, \code{BIRTH} and/or \code{DEATH} may be used if the primitives
of \code{birth} and \code{death} are known. In these functions time is
the formal argument and must be named \code{t}.
Note that \code{rphylo} simulates trees in a way similar to what
the package \pkg{TreeSim} does, the difference is in the
parameterization of the time-dependent models which is here the same
than used in the two other functions. In this parameterization scheme,
time is measured from past to present (see details in Paradis 2015
which includes a comparison of these algorithms).
The difference between \code{rphylo} and \code{rphylo(... fossils
= TRUE)} is the same than between \code{rbdtree} and \code{rlineage}.
}
\value{
An object of class \code{"phylo"}.
}
\references{
Kendall, D. G. (1948) On the generalized ``birth-and-death''
process. \emph{Annals of Mathematical Statistics}, \bold{19}, 1--15.
Paradis, E. (2011) Time-dependent speciation and extinction from
phylogenies: a least squares approach. \emph{Evolution}, \bold{65},
661--672.
Paradis, E. (2015) Random phylogenies and the distribution of
branching times. Manuscript.
Stadler, T. (2011) Simulating trees with a fixed number of extant
species. \emph{Systematic Biology}, \bold{60}, 676--684.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{yule}}, \code{\link{yule.time}}, \code{\link{birthdeath}},
\code{\link{rtree}}, \code{\link{stree}}
}
\examples{
set.seed(10)
plot(rlineage(0.1, 0)) # Yule process with lambda = 0.1
plot(rlineage(0.1, 0.05)) # simple birth-death process
b <- function(t) 1/(1 + exp(0.2*t - 1)) # logistic
layout(matrix(0:3, 2, byrow = TRUE))
curve(b, 0, 50, xlab = "Time", ylab = "")
mu <- 0.07
segments(0, mu, 50, mu, lty = 2)
legend("topright", c(expression(lambda), expression(mu)),
lty = 1:2, bty = "n")
plot(rlineage(b, mu), show.tip.label = FALSE)
title("Simulated with 'rlineage'")
plot(rbdtree(b, mu), show.tip.label = FALSE)
title("Simulated with 'rbdtree'")
}
\keyword{datagen}