Package: geiger 2.0.11
Luke Harmon
geiger: Analysis of Evolutionary Diversification
Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Authors:
geiger_2.0.11.tar.gz
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geiger.pdf |geiger.html✨
geiger/json (API)
| # Install 'geiger' in R: |
| install.packages('geiger', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mwpennell/geiger-v2/issues
- amphibia - Example datasets
- caniformia - Example datasets
- carnivores - Example datasets
- caudata - Example datasets
- chelonia - Example datasets
- geospiza - Example datasets
- primates - Example datasets
- whales - Example datasets
Last updated 2 years agofrom:a6b589fc07. Checks:OK: 4 NOTE: 5. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 05 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 05 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 05 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 05 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 05 2024 |
| R-4.3-win-x86_64 | OK | Nov 05 2024 |
| R-4.3-mac-x86_64 | OK | Nov 05 2024 |
| R-4.3-mac-aarch64 | OK | Nov 05 2024 |
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:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcppRcppArmadillorlangscatterplot3dsubplexvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GEIGER | geiger-package geiger |
| Akaike's Information Criterion for MCMC samples (AICM) | aicm |
| determining Akaike weights | aicw |
| phylogenetic ANOVA and MANOVA | aov.phylo |
| estimate net diversification rate | bd.km bd.ms crown.limits crown.p stem.limits stem.p |
| calibrating MECCA | calibrate.mecca |
| initialize proposal width | calibrate.rjmcmc |
| ultrametricization of trees from a supplied timetree | congruify.phylo |
| prior densities for truncated discrete random variable | dcount |
| prune specified taxa from a phylogenetic tree | drop.extinct drop.random is.extinct |
| disparity-through-time | disparity dtt |
| Model fitting for continuous comparative data | fitContinuous |
| Fit models of continuous trait evolution to comparative data using MCMC | fitContinuousMCMC |
| Model fitting for discrete comparative data | as.Qmatrix.gfit fitDiscrete |
| NCBI taxonomy | gbcontain gbresolve gbresolve.phylo |
| example datasets | amphibia caniformia carnivores caudata chelonia geospiza primates whales |
| deprecated functions in GEIGER | area.between.curves BDsim birthdeath.tree calibrate.proposalwidth compare.rates deltaTree disp.calc dtt.full exponentialchangeTree 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 functions | ex.jumpsimulator ex.ratesimulator ex.traitgram |
| internal geiger functions | argn argn.bm argn.default argn.mkn argn<- argn<-.bm as.phylo.hphylo bf bm.lik cherries coef.gfit coef.gfits constrain constrain.k constrain.m dlunif drop.tip dtpois edgelabels.auteur edges.phylo ess exemplar.phylo fitDiversification fitSplitModel gbresolve.default gbtaxdump gen getBD getDiversificationModel getFullSplitModel hash.node hashes.phylo hashes.rjmcmc hdr heights heights.multiPhylo heights.phylo hme is.constrained is.phylo is.root kendallmoran.rate likfx.bm Linnaean load logLik.gfit logLik.gfits make.bm.relaxed mkn.lik PATHd8.phylo plot.auteurMCMC plot.auteurMCMCMC plot.rjmcmc plot.rjmcmc.list plotDiversificationSurface print.auteurRAW print.bayesfactor print.bm print.constraint.m print.glnL print.gprior print.mcmc.list print.mkn print.rbm print.rjmcmc print.rjmcmcmc print.taxdump print.transformer resplitEdgeMatrixGeiger root.phylo sem sim.mecca span.phylo splitEdgeMatrixGeiger ultrametricize.phylo unique.phylo uniqueMultiPhylo white.mkn write.pathd8 write.r8s write.treePL |
| posterior samples from single or multiple MCMC runs | load.rjmcmc |
| tailor reversible-jump Markov chain Monte Carlo sampling | make.gbm |
| running a MECCA analysis | mecca |
| MEDUSA: modeling evolutionary diversification using stepwise AIC | medusa print.medusa |
| Compares taxa in data and tree | name.check |
| using the Freckleton and Harvey node-height test | nh.test |
| Blending information from taxonomies and trees | glomogram.phylo lookup.phylo nodelabel.phylo phylo.clades phylo.lookup |
| MEDUSA: modeling evolutionary diversification using stepwise AIC | plot.medusa |
| using posterior predictive MCMC for modeling quantitative trait evolution | pp.mcmc |
| call r8s from geiger | r8s.phylo |
| evolutionary VCV matrix | ratematrix |
| relative cladogenesis test | rc |
| Rescale object of class '"phylo"' | rescale.phylo |
| Bayesian sampling of shifts in trait evolution: relaxed Brownian motion | rjmcmc.bm |
| birth-death population simulator | sim.bd |
| birth-death tree simulator | sim.bdtree |
| simulate character evolution | sim.char |
| starting values for MECCA | startingpt.mecca |
| blending information from taxonomies and trees | subset.phylo |
| descendents of a given node in a phylogenetic tree | tips |
| conversion of MCMC samples between auteur and coda | to.auteur to.coda |
| compare taxa in data and tree | treedata |
