API for uyedaj/bayou
Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
| Global functions | |
|---|---|
| .D.from.theta | Source code |
| .OU.asr | Source code |
| .OU.lik | Source code |
| .addColorBar | Source code |
| .addshift2map | Source code |
| .adjustTheta | Source code |
| .allnodes.W | Source code |
| .ancestorBranches | Source code |
| .auteur.W | Source code |
| .branchRegime | Source code |
| .buildControl | Source code |
| .colorRamp | Source code |
| .computelnr | Source code |
| .discard.burnin | Source code |
| .fchain.local | Source code |
| .getSimDists | Source code |
| .getTipMap | Source code |
| .imputePredBM | Source code |
| .jointHalflifeVyProposal | Source code |
| .lastpar | Source code |
| .make.monitorFn | Source code |
| .multiplierProposal | Source code |
| .optima.ages | Source code |
| .ou.next | Source code |
| .ouMatrix | Source code |
| .parmap.W | Source code |
| .pars2map | Source code |
| .posterior.Q | Source code |
| .prepare.ou.univariate | Source code |
| .proposalFn | Source code |
| .pruningwise.branching.times | Source code |
| .pruningwise.distFromRoot | Source code |
| .pull.rsample | Source code |
| .sim.OU | Source code |
| .simOU.onmap | Source code |
| .simmap.W | Source code |
| .slide | Source code |
| .slide2 | Source code |
| .slidespace | Source code |
| .slidingWindowProposal | Source code |
| .splitmerge | Source code |
| .splitmergeGreen | Source code |
| .splitmergePrior | Source code |
| .splitmergePriorMultiplier | Source code |
| .splitmergePriorSlidingWindow | Source code |
| .splitmergebd | Source code |
| .store.bayou | Source code |
| .store.bayou2 | Source code |
| .tipregime | Source code |
| .toSimmap | Source code |
| .tune.D | Source code |
| .updateControl | Source code |
| .vcv.asrOU | Source code |
| .vectorMultiplier | Source code |
| .vectorSlidingWindow | Source code |
| .vectorSlidingWindowSplit | Source code |
| C_threepoint | Source code |
| C_transf_branch_lengths | Source code |
| C_weightmatrix | Source code |
| Lposterior | Man page Source code |
| OU.lik | Man page Source code |
| OU.repar | Man page Source code |
| OUphenogram | Man page Source code |
| OUwie2bayou | Man page Source code |
| QG.alpha | Man page Source code |
| QG.sig2 | Man page Source code |
| bayou | Man page |
| bayou-deprecated | Man page |
| bayou-package | Man page |
| bayou.checkModel | Man page Source code |
| bayou.lik | Man page Source code |
| bayou.makeMCMC | Man page Source code |
| bayou.mcmc | Man page Source code |
| bayou2OUwie | Man page Source code |
| cdpois | Man page Source code |
| combine.chains | Man page Source code |
| dataSim | Man page Source code |
| dhalfcauchy | Man page Source code |
| dloc | Man page Source code |
| dsb | Man page Source code |
| gelman.R | Man page Source code |
| getPreValues | Source code |
| identifyBranches | Man page Source code |
| load.bayou | Man page Source code |
| make.powerposteriorFn | Man page Source code |
| make.prior | Man page Source code |
| make.refFn | Man page Source code |
| makeBayouModel | Man page Source code |
| makeTransparent | Man page Source code |
| model.OU | Man page |
| parmap.W | Man page Source code |
| pars2simmap | Man page Source code |
| phalfcauchy | Man page Source code |
| phenogram.density | Man page Source code |
| plot.bayouMCMC | Man page Source code |
| plot.ssMCMC | Man page Source code |
| plotBayoupars | Man page Source code |
| plotBranchHeatMap | Man page Source code |
| plotOUtreesim | Man page Source code |
| plotRegimes | Man page Source code |
| plotShiftSummaries | Man page Source code |
| plotSimmap.mcmc | Man page Source code |
| powerPosteriorFn | Source code |
| print.bayouFit | Man page Source code |
| print.bayouMCMC | Man page Source code |
| print.priorFn | Man page Source code |
| print.refFn | Man page Source code |
| print.ssMCMC | Man page Source code |
| priorSim | Man page Source code |
| pull.pars | Man page Source code |
| qhalfcauchy | Man page Source code |
| rdpois | Man page Source code |
| regime.plot | Man page Source code |
| rhalfcauchy | Man page Source code |
| rloc | Man page Source code |
| rsb | Man page Source code |
| set.burnin | Man page Source code |
| set.runpars | Source code |
| shiftSummaries | Man page Source code |
| simmap.W | Man page Source code |
| summary.bayouMCMC | Man page Source code |
