ape (version 2.5-1)

ape-defunct: Defunct Ape Functions

Description

These functions have been removed from ape or moved to another package.

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)
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)

Details

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).

mlphylo, DNAmodel and sh.test have been removed: see the package phangorn for a much better implementation of these methods (and others).

heterozygosity, nuc.div, theta.h, theta.k and theta.s have been moved to pegas.