14 \alias{plot.ancestral}
17 \alias{NPRS.criterion}
18 \title{Defunct Ape Functions}
20 These functions have been removed from \pkg{ape} or moved to another
28 heterozygosity(x, variance = FALSE)
29 H(x, variance = FALSE)
30 nuc.div(x, variance = FALSE, pairwise.deletion = FALSE)
31 theta.h(x, standard.error = FALSE)
32 theta.k(x, n = NULL, k = NULL)
33 theta.s(s, n, variance = FALSE)
34 evolve.phylo(phy, value, var)
41 \code{klastorin} has been removed because it does not seem to be used
42 and this helped to clear some internal C code (this function may be
43 put back with a different coding).
45 \code{mlphylo}, \code{DNAmodel} and \code{sh.test} have been removed:
46 see the package \pkg{phangorn} for a much better implementation of
47 these methods (and others).
49 \code{heterozygosity}, \code{nuc.div}, \code{theta.h}, \code{theta.k}
50 and \code{theta.s} have been moved to \pkg{pegas}.
52 \code{evolve.phylo} and \code{plot.ancestral} have been deprecated by
53 the new function \code{\link{rTraitCont}}.
55 \code{chronogram}, \code{ratogram}, and \code{NPRS.criterion} have
56 ceased to be maintained: consider using \code{\link{chronopl}}.