removing NPRS + change bind.tree.Rd to avoid crash during R CMD check ape

[ape.git] / man / ratogram.Rd

diff --git a/man/ratogram.Rd b/man/ratogram.Rd
deleted file mode 100644 (file)
index 42feb2c..0000000
--- a/man/ratogram.Rd
+++ /dev/null
@@ -1,56 +0,0 @@
-\name{ratogram}
-\alias{ratogram}
-
-\title{Ratogram Computed by Nonparametric Rate Smoothing}
-\usage{
-ratogram(phy, scale = 1, expo = 2, minEdgeLength = 1e-06)
-}
-\arguments{
-  \item{phy}{A phylogenetic tree (i.e. an object of class \code{"phylo"}), where
-    the branch lengths are measured in substitutions.}
-
-  \item{scale}{Age of the root in the chronogram corresponding to the inferred ratogram(default value: 0). }
-
-  \item{expo}{Exponent in the objective function (default value: 2)}
-  \item{minEdgeLength}{Minimum edge length in the phylogram (default value: 1e-06). If any branch lengths are
-    smaller then they will be set to this value. }
-}
-\description{
-
- \code{ratogram} computes a ratogram from a phylogram by applying the NPRS
- (nonparametric rate smoothing) algorithm described in Sanderson (1997).
-}
-\details{
-  Please refer to Sanderson (1997) for mathematical details
-}
-\value{
-\code{chronogram} returns an object of class \code{"phylo"}. The branch lengths of this
-tree will be the absolute rates estimated for each branch.
-}
-\author{Gangolf Jobb (\url{http://www.treefinder.de}) and
-Korbinian Strimmer (\url{http://www.stat.uni-muenchen.de/~strimmer/})
-}
-\seealso{
-\code{\link{chronogram}}, \code{\link{NPRS.criterion}}.
-}
-\references{
-  Sanderson, M. J. (1997) A nonparametric approach to estimating
-  divergence times in the absence of rate constancy. \emph{Molecular
-    Biology and Evolution}, \bold{14}, 1218--1231.
-}
-\examples{
-# get tree
-data("landplants.newick") # example tree in NH format
-tree.landplants <- read.tree(text = landplants.newick)
-
-# plot tree
-tree.landplants
-plot(tree.landplants, label.offset = 0.001)
-
-# estimate ratogram
-rato.plants <- ratogram(tree.landplants)
-
-# plot
-plot(rato.plants, label.offset = 0.001)
-}
-\keyword{manip}