ape-defunct: Defunct Ape Functions

In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description

These functions have been removed from 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

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.

evolve.phylo and plot.ancestral have been deprecated by the new function rTraitCont.

chronogram, ratogram, and NPRS.criterion have ceased to be maintained: consider using chronopl.

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.