X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Frlineage.Rd;h=e01a810ec06178b5b6315c7167556b9c890802f3;hb=c488b74490ee3d9d200de0e471881f002a18fe4f;hp=b2b1aed354c2fb780689216142543d5ef444dc22;hpb=a8d86ed3981c64b6d20316d54d3ed4d02c2b887e;p=ape.git

diff --git a/man/rlineage.Rd b/man/rlineage.Rd
index b2b1aed..e01a810 100644
--- a/man/rlineage.Rd
+++ b/man/rlineage.Rd
@@ -15,11 +15,11 @@ 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
-    specifying how speciation and extinction through time.}
+    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
@@ -35,9 +35,9 @@ 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} 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}.
 }
@@ -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. \emph{Evolution} (in press)
-  %, \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{