new files for ape 3.0

[ape.git] / man / rlineage.Rd

diff --git a/man/rlineage.Rd b/man/rlineage.Rd
index d4412454cf78c7a056d5cd965d0eef01e1ecfae4..c37bd6d405ec21ad627d4d621bd08a5d79cfffbd 100644 (file)
--- a/man/rlineage.Rd
+++ b/man/rlineage.Rd
@@ -15,7 +15,7 @@ rlineage(birth, death, Tmax = 50, BIRTH = NULL,
          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
@@ -35,7 +35,7 @@ drop.fossil(phy, tol = 0)
   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
@@ -48,9 +48,9 @@ drop.fossil(phy, tol = 0)
   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{
@@ -60,9 +60,16 @@ drop.fossil(phy, tol = 0)
 \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}