fix a bug in as.hclust.phylo + a few typos in man pages

[ape.git] / man / ape-defunct.Rd

diff --git a/man/ape-defunct.Rd b/man/ape-defunct.Rd
index 6549d5925477e6196799f621b084a23dcb7bf95f..95dc2ec684cfbd02230537e878e4d89c4756a449 100644 (file)
--- a/man/ape-defunct.Rd
+++ b/man/ape-defunct.Rd
@@ -1,11 +1,20 @@
 \name{ape-defunct}
+\alias{ape-defunct}
 \alias{klastorin}
+\alias{mlphylo}
+\alias{DNAmodel}
+\alias{sh.test}
 \alias{heterozygosity}
 \alias{H}
 \alias{nuc.div}
 \alias{theta.h}
 \alias{theta.k}
 \alias{theta.s}
+\alias{evolve.phylo}
+\alias{plot.ancestral}
+\alias{chronogram}
+\alias{ratogram}
+\alias{NPRS.criterion}
 \title{Defunct Ape Functions}
 \description{
   These functions have been removed from \pkg{ape} or moved to another
@@ -13,19 +22,37 @@
 }
 \usage{
 klastorin(phy)
+mlphylo(...)
+DNAmodel(...)
+sh.test(...)
 heterozygosity(x, variance = FALSE)
 H(x, variance = FALSE)
 nuc.div(x, variance = FALSE, pairwise.deletion = FALSE)
 theta.h(x, standard.error = FALSE)
 theta.k(x, n = NULL, k = NULL)
 theta.s(s, n, variance = FALSE)
+evolve.phylo(phy, value, var)
+plot.ancestral(...)
+chronogram(...)
+ratogram(...)
+NPRS.criterion(...)
 }
 \details{
   \code{klastorin} has been removed because it does not seem to be used
   and this helped to clear some internal C code (this function may be
   put back with a different coding).
 
+  \code{mlphylo}, \code{DNAmodel} and \code{sh.test} have been removed:
+  see the package \pkg{phangorn} for a much better implementation of
+  these methods (and others).
+
   \code{heterozygosity}, \code{nuc.div}, \code{theta.h}, \code{theta.k}
   and \code{theta.s} have been moved to \pkg{pegas}.
+
+  \code{evolve.phylo} and \code{plot.ancestral} have been deprecated by
+  the new function \code{\link{rTraitCont}}.
+
+  \code{chronogram}, \code{ratogram}, and \code{NPRS.criterion} have
+  ceased to be maintained: consider using \code{\link{chronopl}}.
 }
 \keyword{internal}