API for mwpennell/geiger-v2
Analysis of Evolutionary Diversification
| Global functions | |
|---|---|
| .CI | Source code |
| .Qmatrix.from.gfit | Source code |
| .acegram | Source code |
| .adjustjump | Source code |
| .adjustrate | Source code |
| .adjustshift | Source code |
| .adjustvalue | Source code |
| .ard.matrix | Source code |
| .area.between.curves | Source code |
| .assess.lnR | Source code |
| .assigndescendants | Source code |
| .basename.noext | Source code |
| .bf.interpreter | Source code |
| .bm.lik.fn.reml | Source code |
| .bm.lik.fn.vcv | Source code |
| .bm.phylo | Source code |
| .bm.rate.mle | Source code |
| .bm.smartstart | Source code |
| .bnd.hessian | Source code |
| .branching.depth | Source code |
| .branching.heights | Source code |
| .build_calibrations | Source code |
| .build_classification | Source code |
| .cache.descendants | Source code |
| .cache.y.nodes | Source code |
| .check.Qmatrix | Source code |
| .check.control.mkn | Source code |
| .check.control.ode | Source code |
| .check.gbm | Source code |
| .check.info.ode | Source code |
| .check.integer | Source code |
| .check.lim | Source code |
| .check.loaded.symbol | Source code |
| .check.parallel | Source code |
| .check.pars.nonnegative | Source code |
| .check.prior | Source code |
| .check.root | Source code |
| .check.scalar | Source code |
| .check.states | Source code |
| .check.states.quasse | Source code |
| .check.stoppingcrit | Source code |
| .check.tree | Source code |
| .cleanup.rjmcmc | Source code |
| .compile_taxonomy | Source code |
| .constrain | Source code |
| .constrain.k | Source code |
| .constrain.m | Source code |
| .constrain.parse | Source code |
| .cont.foo | Source code |
| .default.argn.bm | Source code |
| .default.argn.mk2 | Source code |
| .default.argn.mkn | Source code |
| .defunctify | Source code |
| .delta.cache | Source code |
| .delta.phylo | Source code |
| .deprecate | Source code |
| .depth.phylo | Source code |
| .detachDiversitree | Source code |
| .disparity | Source code |
| .dlnratio | Source code |
| .drop.tip | Source code |
| .dt.tips.ordered | Source code |
| .dtt | Source code |
| .dtt.polygon | Source code |
| .dunifn | Source code |
| .eb.cache | Source code |
| .eb.phylo | Source code |
| .edger | Source code |
| .er.matrix | Source code |
| .error.rjmcmc | Source code |
| .ests.parlog.rjmcmc | Source code |
| .exemplar.default | Source code |
| .fetch_gbhierarchy.above | Source code |
| .fill.taxonomy | Source code |
| .fix.rjmcmc.matrix | Source code |
| .fix.root.bm | Source code |
| .format.levels.print | Source code |
| .gb_anc_worker | Source code |
| .gb_des_worker | Source code |
| .gbm.prior.lik | Source code |
| .geigerwarn | Source code |
| .get.ancestor.of.node | Source code |
| .get.ancestors.of.node | Source code |
| .get.children | Source code |
| .get.desc.of.node | Source code |
| .get.descendants.of.node | Source code |
| .get.ordering | Source code |
| .get.simulation.matrix | Source code |
| .hash.tip | Source code |
| .ic.sigma | Source code |
| .initial.tip.bm.pruning | Source code |
| .intercalate.rjmcmc | Source code |
| .is.wholenumber | Source code |
| .jumps.edgewise | Source code |
| .jumps.plot | Source code |
| .kappa.cache | Source code |
| .kappa.phylo | Source code |
| .kendallmoran.rate | Source code |
| .lambda.cache | Source code |
| .lambda.phylo | Source code |
| .link.root | Source code |
| .lnpriorhastings_ratio.merge | Source code |
| .lnpriorhastings_ratio.split | Source code |
| .load.rjmcmc | Source code |
| .lrate.phylo | Source code |
| .make.bm.relaxed.pic | Source code |
| .make.bm.relaxed.vcv | Source code |
| .make.cache | Source code |
| .make.cache.bm | Source code |
| .make.cache.mkn | Source code |
| .make.info.bm | Source code |
| .make.info.mkn | Source code |
| .make.modelmatrix | Source code |
| .make.ode.deSolve | Source code |
| .make.pars.mkn | Source code |
| .make.pij.mkn | Source code |
| .matrix.to.list | Source code |
| .md5 | Source code |
| .meristic.matrix | Source code |
| .mrca | Source code |
| .namespace | Source code |
| .nodefind.phylo | Source code |
| .nrate.phylo | Source code |
| .null.cache | Source code |
| .null.phylo | Source code |
| .oldestyle.gfit.continuous | Source code |
| .oldestyle.gfit.discrete | Source code |
| .ou.cache | Source code |
| .ou.phylo | Source code |
| .ou.smartstart | Source code |
| .ou.vcv | Source code |
| .parlog.rjmcmc | Source code |
| .paths.cache | Source code |
| .paths.phylo | Source code |
| .pic_variance.phylo | Source code |
| .polytomy.phylo | Source code |
| .pp.getproposal | Source code |
| .prep.glomogram | Source code |
| .prepare.bm.univariate | Source code |
| .prepare.gbm.univariate | Source code |
| .print.table | Source code |
| .proc.lnR | Source code |
| .process.jumps | Source code |
| .process.shifts | Source code |
| .proposal.multiplier | Source code |
| .proposal.slidingwindow | Source code |
| .rate.estimate | Source code |
| .rcount | Source code |
| .rcp | Source code |
| .read.ests.rjmcmc | Source code |
| .reml.lk | Source code |
| .repars | Source code |
| .replace.tip.with.subtree | Source code |
| .reshape.constraint.m | Source code |
| .resolve.executable | Source code |
| .rjmcmc.bm.multi | Source code |
| .root.bm.direct | Source code |
| .root.p.calc | Source code |
| .rootfunc.mkn | Source code |
| .samples.plot | Source code |
| .scale.brlen | Source code |
| .scale.edge.tree | Source code |
| .set.seed.clock | Source code |
| .shifts.plot | Source code |
| .slot.attribute | Source code |
| .splitormerge | Source code |
| .standardize.prior | Source code |
| .startingpt.bm | Source code |
| .subset.auteurRAW | Source code |
| .sym.matrix | Source code |
| .toC.int | Source code |
| .traceplot | Source code |
| .treeslide | Source code |
| .trend.cache | Source code |
| .trend.phylo | Source code |
| .tune.SE | Source code |
| .tune.rate | Source code |
| .tune.value | Source code |
| .unique.phylo | Source code |
| .uniquify_hashes | Source code |
| .white.cache | Source code |
| .white.phylo | Source code |
| BDsim | Man page Source code |
| Linnaean | Man page |
| PATHd8.phylo | Man page Source code |
| `argn<-` | Source code |
| aicm | Man page |
| aicw | Man page |
| amphibia | Man page |
| aov.phylo | Man page Source code |
| area.between.curves | Man page |
| argn | Man page Source code |
| argn.bm | Man page Source code |
| argn.default | Man page Source code |
| argn.mkn | Man page Source code |
| argn<- | Man page |
| argn<-.bm | Man page |
| as.Qmatrix.gfit | Man page Source code |
| as.phylo.hphylo | Man page Source code |
| bd.km | Man page Source code |
| bd.ms | Man page Source code |
| bf | Man page Source code |
| birthdeath.tree | Man page Source code |
| bm.lik | Man page Source code |
| calibrate.mecca | Man page |
| calibrate.proposalwidth | Man page |
| calibrate.rjmcmc | Man page Source code |
| caniformia | Man page |
| carnivores | Man page |
| caudata | Man page |
| chelonia | Man page |
| cherries | Man page Source code |
| coef.gfit | Man page Source code |
| coef.gfits | Man page Source code |
| compare.rates | Man page |
| congruify.phylo | Man page Source code |
| constrain | Man page |
| constrain.k | Man page |
| constrain.m | Man page |
| crown.limits | Man page Source code |
| crown.p | Man page Source code |
| dcount | Man page Source code |
| deltaTree | Man page Source code |
| disp.calc | Man page |
| disparity | Man page Source code |
| dlunif | Man page Source code |
| drop.extinct | Man page |
| drop.random | Man page |
| drop.tip | Man page |
| dtpois | Man page Source code |
| dtt | Man page Source code |
| dtt.full | Man page |
| edgelabels.auteur | Man page |
| edges.phylo | Man page Source code |
| ess | Man page Source code |
| ex.jumpsimulator | Man page Source code |
| ex.ratesimulator | Man page Source code |
| ex.traitgram | Man page Source code |
| exemplar.phylo | Man page Source code |
| exponentialchangeTree | Man page Source code |
| fitContinuous | Man page Source code |
| fitContinuousMCMC | Man page Source code |
| fitDiscrete | Man page Source code |
| fitDiversification | Man page |
| fitSplitModel | Man page |
| gbcontain | Man page Source code |
| gbresolve | Man page Source code |
| gbresolve.default | Man page Source code |
| gbresolve.phylo | Man page Source code |
| gbtaxdump | Man page |
| geiger | Man page |
| geiger-package | Man page |
| gen | Man page |
| geospiza | Man page |
| get.simulation.matrix | Man page |
| getAncStates | Man page Source code |
| getBD | Man page |
| getDiversificationModel | Man page |
| getFullSplitModel | Man page |
| getMDIp | Source code |
| glomogram.phylo | Man page Source code |
| hash.node | Man page Source code |
| hashes.phylo | Man page Source code |
| hashes.rjmcmc | Man page Source code |
| hdr | Man page |
| heights | Man page Source code |
| heights.multiPhylo | Man page Source code |
| heights.phylo | Man page Source code |
| hme | Man page Source code |
| ic.sigma | Man page Source code |
| intercalate.samples | Man page |
| is.constrained | Man page Source code |
| is.extinct | Man page |
| is.phylo | Man page Source code |
| is.root | Man page |
| kappaTree | Man page Source code |
| kendallmoran.rate | Man page |
| lambdaTree | Man page Source code |
| likfx.bm | Man page |
| linearchangeTree | Man page Source code |
| load | Man page |
| load.rjmcmc | Man page Source code |
| logLik.gfit | Man page Source code |
| logLik.gfits | Man page Source code |
| lookup.phylo | Man page Source code |
| make.bm.relaxed | Man page Source code |
| make.gbm | Man page Source code |
| mecca | Man page |
| medusa | Man page |
| mkn.lik | Man page Source code |
| name.check | Man page Source code Source code |
| nh.test | Man page Source code |
| node.leaves | Man page Source code |
| node.sons | Man page |
| nodelabel.phylo | Man page Source code |
| ouTree | Man page Source code |
| phy.anova | Man page |
| phy.manova | Man page |
| phylo.clades | Man page Source code |
| phylo.lookup | Man page Source code |
| plot.auteurMCMC | Man page Source code |
| plot.auteurMCMCMC | Man page Source code |
| plot.medusa | Man page |
| plot.rjmcmc | Man page |
| plot.rjmcmc.list | Man page |
| plotDiversificationSurface | Man page |
| pool.rjmcmcsamples | Man page |
| pp.mcmc | Man page Source code |
| primates | Man page |
| print.auteurRAW | Man page Source code |
| print.bayesfactor | Man page Source code |
| print.bm | Man page |
| print.constraint.m | Man page Source code |
| print.gfit | Source code |
| print.gfits | Source code |
| print.glnL | Man page Source code |
| print.gprior | Man page Source code |
| print.mcmc.list | Man page Source code |
| print.medusa | Man page |
| print.mkn | Man page |
| print.name.check | Source code |
| print.rbm | Man page |
| print.rjmcmc | Man page |
| print.rjmcmcmc | Man page |
| print.taxdump | Man page |
| print.transformer | Man page |
| prune.extinct.taxa | Man page Source code |
| prune.random.taxa | Man page Source code |
| r8s.phylo | Man page Source code |
| rate.estimate | Man page Source code |
| ratematrix | Man page Source code |
| rc | Man page Source code |
| rescale.phylo | Man page Source code |
| rescaleTree | Man page Source code |
| resplitEdgeMatrixGeiger | Man page |
| rjmcmc.bm | Man page |
| root.phylo | Man page |
| runMedusa | Man page Source code |
| sem | Man page Source code |
| shifts.plot | Man page |
| sim.bd | Man page |
| sim.bdtree | Man page |
| sim.char | Man page Source code |
| sim.mecca | Man page |
| span.phylo | Man page Source code |
| speciationalTree | Man page Source code |
| splitEdgeMatrixGeiger | Man page |
| startingpt.mecca | Man page |
| stem.limits | Man page Source code |
| stem.p | Man page Source code |
| subset.phylo | Man page Source code |
| summary.name.check | Source code |
| tip.disparity | Man page Source code |
| tips | Man page Source code |
| to.auteur | Man page Source code |
| to.coda | Man page Source code |
| tracer | Man page |
| transform.phylo | Man page |
| treePL.phylo | Source code |
| treedata | Man page Source code |
| tworateTree | Man page Source code |
| ultrametricize.phylo | Man page |
| unique.phylo | Man page Source code |
| uniqueMultiPhylo | Man page Source code |
| vmat | Man page |
| whales | Man page |
| white.mkn | Man page Source code |
| write.pathd8 | Man page Source code |
| write.r8s | Man page Source code |
| write.treePL | Man page Source code |
