f.cherry.yule

f.cherry.uniform

sortIndex

nsca

perm.rowscols

mant.zstat

lower.triang

phylogram.plot

cladogram.plot

circular.plot

unrooted.plot

unrooted.xy

birth.step

death.step

ht.move

loglik.pop

pos.move

BOTHlabels

chronopl.cv

floating.pie.asp

checkLabel

plotCophylo2

plotPhyloCoor

integrateTrapeze

CDF.birth.death

postprocess.prop.part

ONEwise

BaseProportion

C_additive

C_bionj

C_bionjs

C_ewLasso

C_mvr

C_mvrs

C_nj

C_njs

C_pic

C_rTraitCont

C_treePop

C_triangMtd

C_triangMtds

C_ultrametric

C_where

GlobalDeletionDNA

DNAbin2indelblock

SegSites

bipartition

delta_plot

dist_dna

dist_nodes

mat_expo

me_b

me_o

neworder_phylo

neworder_pruningwise

node_depth

node_depth_edgelength

node_height

node_height_clado

_ape_bipartition2

_ape_prop_part2

_ape_reorderRcpp

bipartition2

prop_part2

reorderRcpp

rawStreamToDNAbin

seq_root2tip

treeBuild

treeBuildWithTokens

cladoBuild

cladoBuildWithTokens

polar2rect

rect2polar

CountBipartitionsFromTrees

bitsplits_multiPhylo

bitsplits_phylo

racine

renumeroteArbre

calculeC

calculeC_ABM

calculeC_OU

glsABM

glsBM

glsOUv1

glsOUv2

getSumSquare

getMLHessian

getREMLHessian

trans_DNA2AA

writeFastaDNAbin

charVectorToDNAbinVector

rawStreamToDNAorAAbin

writeAAbinToFASTA

writeDNAbinToFASTA

<p>Internal <span class="pkg">ape</span> functions. Do not call these from other packages.</p>

internal

ape-internal

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

Simon Blomberg

Ben Bolker

Joseph Brown

Julien Claude

Hoa Sien Cuong

Richard Desper

Gilles Didier

Benoit Durand

Julien Dutheil

RJ Ewing

Olivier Gascuel

Thomas Guillerme

Christoph Heibl

Anthony Ives

Bradley Jones

Franz Krah

Daniel Lawson

Vincent Lefort

Pierre Legendre

Jim Lemon

Rosemary McCloskey

Johan Nylander

Rainer Opgen-Rhein

Andrei-Alin Popescu

Manuela Royer-Carenzi

Klaus Schliep

Korbinian Strimmer

Damien de Vienne

ape-internal function

Internal Ape Functions — ape-internal

Internal Ape Functions

ape-internal: Internal Ape Functions

Description

Arguments