Analysis of Evolutionary Diversification
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Documentation for package ‘geiger’ version 2.0.11
Help Pages
A B C D E F G H I K L M N O P R S T U V W
| geiger-package | GEIGER |
-- A --
| aicm | Akaike's Information Criterion for MCMC samples (AICM) |
| aicw | determining Akaike weights |
| amphibia | example datasets |
| aov.phylo | phylogenetic ANOVA and MANOVA |
| area.between.curves | deprecated functions in GEIGER |
| argn | internal geiger functions |
| argn.bm | internal geiger functions |
| argn.default | internal geiger functions |
| argn.mkn | internal geiger functions |
| argn<- | internal geiger functions |
| argn<-.bm | internal geiger functions |
| as.phylo.hphylo | internal geiger functions |
| as.Qmatrix.gfit | Model fitting for discrete comparative data |
-- B --
| bd.km | estimate net diversification rate |
| bd.ms | estimate net diversification rate |
| BDsim | deprecated functions in GEIGER |
| bf | internal geiger functions |
| birthdeath.tree | deprecated functions in GEIGER |
| bm.lik | internal geiger functions |
-- C --
| calibrate.mecca | calibrating MECCA |
| calibrate.proposalwidth | deprecated functions in GEIGER |
| calibrate.rjmcmc | initialize proposal width |
| caniformia | example datasets |
| carnivores | example datasets |
| caudata | example datasets |
| chelonia | example datasets |
| cherries | internal geiger functions |
| coef.gfit | internal geiger functions |
| coef.gfits | internal geiger functions |
| compare.rates | deprecated functions in GEIGER |
| congruify.phylo | ultrametricization of trees from a supplied timetree |
| constrain | internal geiger functions |
| constrain.k | internal geiger functions |
| constrain.m | internal geiger functions |
| crown.limits | estimate net diversification rate |
| crown.p | estimate net diversification rate |
-- D --
| dcount | prior densities for truncated discrete random variable |
| deltaTree | deprecated functions in GEIGER |
| disp.calc | deprecated functions in GEIGER |
| disparity | disparity-through-time |
| dlunif | internal geiger functions |
| drop.extinct | prune specified taxa from a phylogenetic tree |
| drop.random | prune specified taxa from a phylogenetic tree |
| drop.tip | internal geiger functions |
| dtpois | internal geiger functions |
| dtt | disparity-through-time |
| dtt.full | deprecated functions in GEIGER |
-- E --
| edgelabels.auteur | internal geiger functions |
| edges.phylo | internal geiger functions |
| ess | internal geiger functions |
| ex.jumpsimulator | internal geiger functions |
| ex.ratesimulator | internal geiger functions |
| ex.traitgram | internal geiger functions |
| exemplar.phylo | internal geiger functions |
| exponentialchangeTree | deprecated functions in GEIGER |
-- F --
| fitContinuous | Model fitting for continuous comparative data |
| fitContinuousMCMC | Fit models of continuous trait evolution to comparative data using MCMC |
| fitDiscrete | Model fitting for discrete comparative data |
| fitDiversification | internal geiger functions |
| fitSplitModel | internal geiger functions |
-- G --
| gbcontain | NCBI taxonomy |
| gbresolve | NCBI taxonomy |
| gbresolve.default | internal geiger functions |
| gbresolve.phylo | NCBI taxonomy |
| gbtaxdump | internal geiger functions |
| geiger | GEIGER |
| gen | internal geiger functions |
| geospiza | example datasets |
| get.simulation.matrix | deprecated functions in GEIGER |
| getAncStates | deprecated functions in GEIGER |
| getBD | internal geiger functions |
| getDiversificationModel | internal geiger functions |
| getFullSplitModel | internal geiger functions |
| glomogram.phylo | Blending information from taxonomies and trees |
-- H --
| hash.node | internal geiger functions |
| hashes.phylo | internal geiger functions |
| hashes.rjmcmc | internal geiger functions |
| hdr | internal geiger functions |
| heights | internal geiger functions |
| heights.multiPhylo | internal geiger functions |
| heights.phylo | internal geiger functions |
| hme | internal geiger functions |
-- I --
| ic.sigma | deprecated functions in GEIGER |
| intercalate.samples | deprecated functions in GEIGER |
| is.constrained | internal geiger functions |
| is.extinct | prune specified taxa from a phylogenetic tree |
| is.phylo | internal geiger functions |
| is.root | internal geiger functions |
-- K --
| kappaTree | deprecated functions in GEIGER |
| kendallmoran.rate | internal geiger functions |
-- L --
| lambdaTree | deprecated functions in GEIGER |
| likfx.bm | internal geiger functions |
| linearchangeTree | deprecated functions in GEIGER |
| Linnaean | internal geiger functions |
| load | internal geiger functions |
| load.rjmcmc | posterior samples from single or multiple MCMC runs |
| logLik.gfit | internal geiger functions |
| logLik.gfits | internal geiger functions |
| lookup.phylo | Blending information from taxonomies and trees |
-- M --
| make.bm.relaxed | internal geiger functions |
| make.gbm | tailor reversible-jump Markov chain Monte Carlo sampling |
| mecca | running a MECCA analysis |
| medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC |
| mkn.lik | internal geiger functions |
-- N --
| name.check | Compares taxa in data and tree |
| nh.test | using the Freckleton and Harvey node-height test |
| node.leaves | deprecated functions in GEIGER |
| node.sons | deprecated functions in GEIGER |
| nodelabel.phylo | Blending information from taxonomies and trees |
-- O --
| ouTree | deprecated functions in GEIGER |
-- P --
| PATHd8.phylo | internal geiger functions |
| phy.anova | deprecated functions in GEIGER |
| phy.manova | deprecated functions in GEIGER |
| phylo.clades | Blending information from taxonomies and trees |
| phylo.lookup | Blending information from taxonomies and trees |
| plot.auteurMCMC | internal geiger functions |
| plot.auteurMCMCMC | internal geiger functions |
| plot.medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC |
| plot.rjmcmc | internal geiger functions |
| plot.rjmcmc.list | internal geiger functions |
| plotDiversificationSurface | internal geiger functions |
| pool.rjmcmcsamples | deprecated functions in GEIGER |
| pp.mcmc | using posterior predictive MCMC for modeling quantitative trait evolution |
| primates | example datasets |
| print.auteurRAW | internal geiger functions |
| print.bayesfactor | internal geiger functions |
| print.bm | internal geiger functions |
| print.constraint.m | internal geiger functions |
| print.glnL | internal geiger functions |
| print.gprior | internal geiger functions |
| print.mcmc.list | internal geiger functions |
| print.medusa | MEDUSA: modeling evolutionary diversification using stepwise AIC |
| print.mkn | internal geiger functions |
| print.rbm | internal geiger functions |
| print.rjmcmc | internal geiger functions |
| print.rjmcmcmc | internal geiger functions |
| print.taxdump | internal geiger functions |
| print.transformer | internal geiger functions |
| prune.extinct.taxa | deprecated functions in GEIGER |
| prune.random.taxa | deprecated functions in GEIGER |
-- R --
| r8s.phylo | call r8s from geiger |
| rate.estimate | deprecated functions in GEIGER |
| ratematrix | evolutionary VCV matrix |
| rc | relative cladogenesis test |
| rescale.phylo | Rescale object of class '"phylo"' |
| rescaleTree | deprecated functions in GEIGER |
| resplitEdgeMatrixGeiger | internal geiger functions |
| rjmcmc.bm | Bayesian sampling of shifts in trait evolution: relaxed Brownian motion |
| root.phylo | internal geiger functions |
| runMedusa | deprecated functions in GEIGER |
-- S --
| sem | internal geiger functions |
| shifts.plot | deprecated functions in GEIGER |
| sim.bd | birth-death population simulator |
| sim.bdtree | birth-death tree simulator |
| sim.char | simulate character evolution |
| sim.mecca | internal geiger functions |
| span.phylo | internal geiger functions |
| speciationalTree | deprecated functions in GEIGER |
| splitEdgeMatrixGeiger | internal geiger functions |
| startingpt.mecca | starting values for MECCA |
| stem.limits | estimate net diversification rate |
| stem.p | estimate net diversification rate |
| subset.phylo | blending information from taxonomies and trees |
-- T --
| tip.disparity | deprecated functions in GEIGER |
| tips | descendents of a given node in a phylogenetic tree |
| to.auteur | conversion of MCMC samples between auteur and coda |
| to.coda | conversion of MCMC samples between auteur and coda |
| tracer | deprecated functions in GEIGER |
| transform.phylo | deprecated functions in GEIGER |
| treedata | compare taxa in data and tree |
| tworateTree | deprecated functions in GEIGER |
-- U --
| ultrametricize.phylo | internal geiger functions |
| unique.phylo | internal geiger functions |
| uniqueMultiPhylo | internal geiger functions |
-- V --
| vmat | deprecated functions in GEIGER |
-- W --
| whales | example datasets |
| white.mkn | internal geiger functions |
| write.pathd8 | internal geiger functions |
| write.r8s | internal geiger functions |
| write.treePL | internal geiger functions |