klastorin

tree.build

f.cherry.yule

f.cherry.uniform

sortIndex

nsca

perm.rowscols

mant.zstat

lower.triang

clado.build

getDurations

getEdgeLengths

getExternalParams

getNEdges

getNFreeParams

getRates

objFuncLogScale

optimTree

phylogram

prepareTree

setTree

nEdges

nNodes

phylogram.plot

cladogram.plot

circular.plot

unrooted.plot

unrooted.xy

node.height

node.height.clado

birth.step

death.step

ht.move

loglik.pop

pos.move

BOTHlabels

chronopl.cv

prepareDNA

floating.pie.asp

checkLabel

getMRCA

plotCophylo2

plotPhyloCoor

internal

ape-internal

ape provides functions for reading, writing, plotting, and
        manipulating phylogenetic trees, analyses of comparative data
        in a phylogenetic framework, analyses of diversification and
        macroevolution, computing distances from allelic and nucleotide
        data, reading nucleotide sequences, and several tools such as
        Mantel's test, computation of minimum spanning tree, the
        population parameter theta based on various approaches,
        nucleotide diversity, generalized skyline plots, estimation of
        absolute evolutionary rates and clock-like trees using mean
        path lengths, non-parametric rate smoothing and penalized
        likelihood. Phylogeny estimation can be done with the NJ,
        BIONJ, and ME methods.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

ape-internal function

Internal Ape Functions

ape-internal: Internal Ape Functions

Description

Arguments