\name{ape-defunct}
+\alias{ape-defunct}
\alias{klastorin}
\alias{mlphylo}
\alias{DNAmodel}
\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
}
\usage{
klastorin(phy)
-mlphylo(x, phy, model = DNAmodel(), search.tree = FALSE,
- quiet = FALSE, value = NULL, fixed = FALSE)
-DNAmodel(model = "K80", partition = 1,
- ncat.isv = 1, invar = FALSE,
- equal.isv = TRUE, equal.invar = 1)
-sh.test(..., x, model = DNAmodel(), B = 100)
+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
\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}