Package: geiger 2.0.12

Luke Harmon

geiger: Analysis of Evolutionary Diversification

Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.

Authors:Luke Harmon [aut, cre], Matthew Pennell [aut], Chad Brock [aut], Joseph Brown [aut], Wendell Challenger [aut], Jon Eastman [aut], Rich FitzJohn [aut], Rich Glor [aut], Gene Hunt [aut], Liam Revell [aut], Graham Slater [aut], Josef Uyeda [aut], Jason Weir [aut], CRAN team [ctb]

geiger_2.0.12.tar.gz
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geiger_2.0.12.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
geiger/json (API)

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

Bug tracker:https://github.com/mwpennell/geiger-v2/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

openblascpp

11.51 score 26 stars 30 packages 2.9k scripts 9.4k downloads 179 mentions 101 exports 40 dependencies

Last updated from:969d3212a8. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK157
linux-devel-x86_64OK231
source / vignettesOK238
linux-release-arm64OK161
linux-release-x86_64OK176
macos-release-arm64OK201
macos-release-x86_64OK236
macos-oldrel-arm64OK207
macos-oldrel-x86_64OK255
windows-devel-arm64OK385
windows-devel-x86_64OK171
windows-release-arm64OK360
windows-release-x86_64OK137
windows-oldrel-x86_64OK128
wasm-releaseOK122

Exports:aicmaicwaov.phyloargnargn<-as.Qmatrix.gfitbd.kmbd.msBDsimbfbirthdeath.treebm.likcalibrate.meccacalibrate.rjmcmccherriescongruify.phylocrown.limitscrown.pdcountdeltaTreedisparitydlunifdrop.extinctdrop.randomdtpoisdttedgelabels.auteuredges.phyloessex.jumpsimulatorex.ratesimulatorex.traitgramexemplar.phyloexponentialchangeTreefitContinuousfitContinuousMCMCfitDiscretegbcontaingbresolvegetAncStatesglomogram.phylohash.nodehashes.phylohashes.rjmcmchdrheightshmeic.sigmais.constrainedis.extinctis.phylois.rootkappaTreelambdaTreelinearchangeTreeLinnaeanload.rjmcmclookup.phylomake.bm.relaxedmake.gbmmeccamedusamkn.likname.checknh.testnode.leavesnodelabel.phyloouTreePATHd8.phylophylo.cladesphylo.lookuppp.mcmcprune.extinct.taxaprune.random.taxar8s.phylorate.estimateratematrixrcrescaleTreerjmcmc.bmsemsim.bdsim.bdtreesim.charsim.meccaspan.phylospeciationalTreestartingpt.meccastem.limitsstem.ptip.disparitytipsto.auteurto.codatreedatatworateTreeuniqueMultiPhylowhite.mknwrite.pathd8write.r8swrite.treePL

Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dsubplexvctrs

Readme and manuals

Help Manual

Help pageTopics
GEIGERgeiger-package geiger
Akaike's Information Criterion for MCMC samples (AICM)aicm
determining Akaike weightsaicw
phylogenetic ANOVA and MANOVAaov.phylo
estimate net diversification ratebd.km bd.ms crown.limits crown.p stem.limits stem.p
calibrating MECCAcalibrate.mecca
initialize proposal widthcalibrate.rjmcmc
ultrametricization of trees from a supplied timetreecongruify.phylo
prior densities for truncated discrete random variabledcount
prune specified taxa from a phylogenetic treedrop.extinct drop.random is.extinct
disparity-through-timedisparity dtt
Model fitting for continuous comparative datafitContinuous
Fit models of continuous trait evolution to comparative data using MCMCfitContinuousMCMC
Model fitting for discrete comparative dataas.Qmatrix.gfit fitDiscrete
NCBI taxonomygbcontain gbresolve gbresolve.phylo
example datasetsamphibia caniformia carnivores caudata chelonia geospiza primates whales
deprecated functions in GEIGERarea.between.curves BDsim birthdeath.tree calibrate.proposalwidth compare.rates deltaTree disp.calc dtt.full exponentialchangeTree geiger-defunct get.simulation.matrix getAncStates ic.sigma intercalate.samples kappaTree lambdaTree linearchangeTree node.leaves node.sons ouTree phy.anova phy.manova pool.rjmcmcsamples prune.extinct.taxa prune.random.taxa rate.estimate rescaleTree runMedusa shifts.plot speciationalTree tip.disparity tracer transform.phylo tworateTree vmat
internal geiger functionsex.jumpsimulator ex.ratesimulator ex.traitgram
posterior samples from single or multiple MCMC runsload.rjmcmc
tailor reversible-jump Markov chain Monte Carlo samplingmake.gbm
running a MECCA analysismecca
MEDUSA: modeling evolutionary diversification using stepwise AICmedusa print.medusa
Compares taxa in data and treename.check
using the Freckleton and Harvey node-height testnh.test
Blending information from taxonomies and treesglomogram.phylo lookup.phylo nodelabel.phylo phylo.clades phylo.lookup
MEDUSA: modeling evolutionary diversification using stepwise AICplot.medusa
using posterior predictive MCMC for modeling quantitative trait evolutionpp.mcmc
call r8s from geigerr8s.phylo
evolutionary VCV matrixratematrix
relative cladogenesis testrc
Rescale object of class '"phylo"'rescale.phylo
Bayesian sampling of shifts in trait evolution: relaxed Brownian motionrjmcmc.bm
birth-death population simulatorsim.bd
birth-death tree simulatorsim.bdtree
simulate character evolutionsim.char
starting values for MECCAstartingpt.mecca
blending information from taxonomies and treessubset.phylo
descendents of a given node in a phylogenetic treetips
conversion of MCMC samples between auteur and codato.auteur to.coda
compare taxa in data and treetreedata