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| add.transparency | internal auteur functions |
| adjustjump | internal auteur functions |
| adjustrate | internal auteur functions |
| adjustshift | internal auteur functions |
| adjustvalue | internal auteur functions |
| assess.lnR | internal auteur functions |
| assigndescendants | internal auteur functions |
| auteur | main: Bayesian Inference of Trait Evolutionary Process |
| bm.lik.fn | internal auteur functions |
| bm.phenogram | trait evolution along phylogenies |
| bm.reml.fn | internal auteur functions |
| branchcol.plot | internal auteur functions |
| calibrate.proposalwidth | initialize proposal width |
| checkrates | internal auteur functions |
| chelonia | example datasets for auteur |
| choose.one | internal auteur functions |
| cleanup.files | internal auteur functions |
| collect.nodes | internal auteur functions |
| compare.rates | statistical comparison of posterior rate estimates |
| determine.accepted.proposal | internal auteur functions |
| edgelabels.rj | internal auteur functions |
| find.relatives | internal auteur functions |
| fit.continuous | internal auteur functions |
| fit.hansen | internal auteur functions |
| generate.error.message | internal auteur functions |
| generate.log | internal auteur functions |
| generate.starting.point | internal auteur functions |
| get.ancestor.of.node | internal auteur functions |
| get.ancestors | internal auteur functions |
| get.ancestors.of.node | internal auteur functions |
| get.desc.of.node | internal auteur functions |
| get.descendants.of.node | internal auteur functions |
| get.epochs | internal auteur functions |
| get.times | internal auteur functions |
| hdr | internal auteur functions |
| infer.y | internal auteur functions |
| intercalate.samples | pool data |
| is.root | internal auteur functions |
| jumps.edgewise | internal auteur functions |
| levy.phenogram | trait evolution along phylogenies |
| levyevolver | internal auteur functions |
| lnprior.exp | internal auteur functions |
| nearest.pair | internal auteur functions |
| ou.lik.fn | internal auteur functions |
| oumat | internal auteur functions |
| ouweights | internal auteur functions |
| parlogger | internal auteur functions |
| pathlengths | internal auteur functions |
| phenogram | trait evolution along phylogenies |
| pic_variance | internal auteur functions |
| pool.rjmcmcsamples | combining posterior samples from Bayesian analysis |
| prepare.data.bm | internal auteur functions |
| primates | example datasets for auteur |
| priorratio.exp | internal auteur functions |
| proposal.multiplier | internal auteur functions |
| proposal.slidingwindow | internal auteur functions |
| prunelastsplit | internal auteur functions |
| ptpois | internal auteur functions |
| randomization.test | statistical comparison of sets of values by randomization |
| rjmcmc | main: Bayesian Inference of Trait Evolutionary Process |
| rjmcmc.bm | Bayesian sampling of shifts in trait-evolutionary rates: Brownian motion |
| rtpois | internal auteur functions |
| shifts.plot | plotting of Bayesian posterior samples |
| splitormerge | internal auteur functions |
| splitrate | internal auteur functions |
| splitvalue | internal auteur functions |
| summarize.run | internal auteur functions |
| table.print | internal auteur functions |
| trace.plot | plotting of Bayesian posterior samples |
| tracer | plotting of Bayesian posterior samples |
| tree.slide | internal auteur functions |
| tune.rate | internal auteur functions |
| tune.value | internal auteur functions |
| ultrametricize | internal auteur functions |
| unexcludeddescendants | internal auteur functions |
| updateJvcv | internal auteur functions |
| updateLvcv | internal auteur functions |
| updatetree | internal auteur functions |
| updatevcv | internal auteur functions |
| urodela | example datasets for auteur |
| vmat | computation of phylogenetic variance-covariance matrix |
| withinrange | internal auteur functions |