Prepare MCMCtree Analyses and Plot Bayesian Divergence Time
Analyses Estimates on Trees
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Documentation for package ‘MCMCtreeR’ version 1.1
Help Pages
| apeData | ApeData Ape phylogeny in ape format, monophyletic clades, and maximum and minimum ages |
| estimateBound | Estimate a Uniform Distribution for MCMCtree |
| estimateCauchy | Estimate Cauchy Distribution for MCMCtree |
| estimateFixed | Fixed Age for MCMCtree analysis input |
| estimateGamma | Estimate Gamma Distribution for MCMCtree analysis |
| estimateSkewNormal | Estimate Skew Normal for MCMCtree analysis |
| estimateSkewT | Estimate Skew-t Distribution for MCMCtree analysis |
| estimateUpper | Estimate Upper Age for MCMCtree analysis |
| MCMC.tree.plot | Plot time-scaled phylogenies |
| MCMCtree.output | MCMCtree.output |
| MCMCtreePhy | MCMCtreePhy |
| nodeToPhy | Add Node Constraints to Tree in MCMCtree Format |
| plotMCMCtree | Plot distribution from MCMCtree node estimations |
| priorPosterior | priorPosterior |
| readMCMCtree | Read MCMCtree output tree into R |
| tipDes | Find Descendent Tips From A Common Ancestor |