12 \title{Defunct Ape Functions}
14 These functions have been removed from \pkg{ape} or moved to another
19 mlphylo(x, phy, model = DNAmodel(), search.tree = FALSE,
20 quiet = FALSE, value = NULL, fixed = FALSE)
21 DNAmodel(model = "K80", partition = 1,
22 ncat.isv = 1, invar = FALSE,
23 equal.isv = TRUE, equal.invar = 1)
24 sh.test(..., x, model = DNAmodel(), B = 100)
25 heterozygosity(x, variance = FALSE)
26 H(x, variance = FALSE)
27 nuc.div(x, variance = FALSE, pairwise.deletion = FALSE)
28 theta.h(x, standard.error = FALSE)
29 theta.k(x, n = NULL, k = NULL)
30 theta.s(s, n, variance = FALSE)
33 \code{klastorin} has been removed because it does not seem to be used
34 and this helped to clear some internal C code (this function may be
35 put back with a different coding).
37 \code{mlphylo}, \code{DNAmodel} and \code{sh.test} have been removed:
38 see the package \pkg{phangorn} for a much better implementation of
39 these methods (and others).
41 \code{heterozygosity}, \code{nuc.div}, \code{theta.h}, \code{theta.k}
42 and \code{theta.s} have been moved to \pkg{pegas}.