Package: apTreeshape 1.5-0.1

Michael Blum

apTreeshape: Analyses of Phylogenetic Treeshape

Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005) <doi:10.1093/bioinformatics/bti798> and Maliet et al. (2017) <doi:10.1101/224295>.

Authors:Nicolas Bortolussi, Michael Blum, Eric Durand, Olivier Francois, Odile Maliet

apTreeshape_1.5-0.1.tar.gz
apTreeshape_1.5-0.1.zip(r-4.7)apTreeshape_1.5-0.1.zip(r-4.6)apTreeshape_1.5-0.1.zip(r-4.5)
apTreeshape_1.5-0.1.tgz(r-4.6-any)apTreeshape_1.5-0.1.tgz(r-4.5-any)
apTreeshape_1.5-0.1.tar.gz(r-4.7-any)apTreeshape_1.5-0.1.tar.gz(r-4.6-any)
apTreeshape_1.5-0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
apTreeshape/json (API)

# Install 'apTreeshape' in R:
install.packages('apTreeshape', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.89 score 154 scripts 120 downloads 15 mentions 41 exports 14 dependencies

Last updated from:7232c230cc. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE187
source / vignettesOK158
linux-release-x86_64NOTE187
macos-release-arm64NOTE98
macos-oldrel-arm64NOTE82
windows-develNOTE97
windows-releaseNOTE110
windows-oldrelNOTE95
wasm-releaseOK92

Exports:aldous.testall.equal.treeshapeancestoras.phylo.treeshapeas.treeshapeas.treeshape.phyloas.treeshape.treebalancecladesizecollesscolless.testcutreeshapeDeltaget_PD_sampleget_tree_betais.binary.phylolikelihood.testlogratiomaxlik.betasplitmcmc_alphamcmc_etaplot.treeshaperaldousrbiasedrpdartreeshaperyulesackinsackin.testshape.statisticshift.testsimulate_kingmansimulate_treesimulate_yulesmaller.clade.spectrumsmaller.clade.spectrum2spectrum.treeshapesubtree.testsummary.treeshapetipsubtreetreebalancetreeshape

Dependencies:apecodacubaturedigestlatticeMASSMatrixMatrixModelsnlmepbapplyquantregRcppSparseMsurvival

Readme and manuals

Help Manual

Help pageTopics
Computes a_na_N
Visualizing balance via scatter diagramsaldous.test
Compare two objects of class treeshapeall.equal.treeshape
Conversion among tree objectsas.phylo.treeshape
Conversion among tree objectsas.treeshape as.treeshape.phylo
Probability of the sampled node positionaux_lik
Binds two tree togetherbind.trees
Internal BetaAlphaEta functionbuild_tree
Phylogeny of carnivores.carnivora.treeshape
Internal functionchange_int
Internal functionchange_int_eta
Compute the number of children of a randomly chosen nodecladesize
Compute the Colless' shape statistic on tree datacolless
Cut objects of class "treeshape"cutreeshape
Phylogeny of the cytochrome C family.cytochromc
Gets the node depths of the treedepth
Internal functionenhance
Internal functionenhance_eta
Gives the tips of the phylogeny in their extinction orderget_extinction_list
Computes the proportion of conserved PDget_PD_sample
Beta parameter as a function of the proportion of remaining tipsget_tree_beta
Phylogenetic Tree of 193 HIV-1 Sequenceshivtree.treeshape
Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statisticcolless.test sackin.test
Insert an element in a vectorinsert
Computation of lambda_epsilonlambda_N
Computes lambda_epsilonlambda.epsilon
Test the Yule model vs PDA (uniform) model.likelihood.test
Maximum likelihood of beta in the Beta-splitting modelmaxlik.betasplit
Inference of the alpha parametermcmc_alpha
Inference of the alpha and eta parametersmcmc_eta
Gets the node depths of the treenodes_depths_ordonnes
Plot phylogenetic treeshapes.plot.treeshape
Phylogeny of the primates.primates
Proposal for the mcmc functionsrbactrian
Phylogeny of rhodopsin proteins.rhodopsin
Generate a list of random binary trees according to a given modelrtreeshape
Compute the Sackin's index of a treesackin
Computes the log of the likelihood ratio (yule/pda)shape.statistic
Testing diversification rate variation in phylogenetic treesshift.test
Ranked topology with Kingman's coalescent depthssimulate_kingman
Simulates ranked topologysimulate_tree
Ranked topology with Birth-death process depthssimulate_yule
Simulate R knowing K=ksimulate.R
Simulate (R,K)simulate.R.K
Simulate (Tau, X_Tau-)simulate.Tau.X
Simulates the random variables Y_isimulate.Yi
Compute the smaller clade spectrum of a tree.smaller.clade.spectrum
Compute the spectrum of a treespectrum.treeshape
Computes the splits at each node of a treesplit
Test the Yule or PDA hypothesissubtree.test
Print a summary of an object of class "treeshape"summary.treeshape
Extract a subtree that contains pre-specified tip names or labelstipsubtree
Internal functiontransform
Internal functiontransform_eta
Builds an object of class treeshapetreeshape
Universal phylogenetic tree of lifeuniversal.treeshape
Internal BetaAlphaEta functionyule_lengths