various fixes in C files

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

diff --git a/man/ape-defunct.Rd b/man/ape-defunct.Rd
deleted file mode 100644 (file)
index 95dc2ec..0000000
--- a/man/ape-defunct.Rd
+++ /dev/null
@@ -1,58 +0,0 @@
-\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
-  package.
-}
-\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}