DEATH = NULL, eps = 1e-6)
rbdtree(birth, death, Tmax = 50, BIRTH = NULL,
DEATH = NULL, eps = 1e-6)
-drop.fossil(phy, tol = 0)
+drop.fossil(phy, tol = 1e-8)
}
\arguments{
\item{birth, death}{a numeric value or a (vectorized) function
Both functions use continuous-time algorithms described in the
references. 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
+ 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 of the primitives of \code{birth} and
\code{death} are known. In these functions time is the formal argument
Kendall, D. G. (1948) On the generalized ``birth-and-death''
process. \emph{Annals of Mathematical Statistics}, \bold{19}, 1--15.
- Paradis, E. (2010) Time-dependent speciation and extinction from
- phylogenies: a least squares approach. (under revision)
- %\emph{Evolution}, \bold{59}, 1--12.
+ Paradis, E. (2011) Time-dependent speciation and extinction from
+ phylogenies: a least squares approach. \emph{Evolution}, \bold{65},
+ 661--672.
}
\author{Emmanuel Paradis}
\seealso{
\examples{
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(0.1*t - 2)) # logistic
-layout(matrix(1:2, 1))
-plot(rlineage(b, 0.01))
-plot(rbdtree(b, 0.01))
+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}