Package: MCMCtreeR 1.1
MCMCtreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees
Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot time-scaled phylogenies from any Bayesian divergence time analysis. Most time-calibrated node prior distributions require user-specified parameters. The package provides functions to refine these parameters, so that the resulting prior distributions accurately reflect confidence in known, usually fossil, time information. These functions also enable users to visualise distributions and write 'MCMCtree' ready input files. Additionally, the package supplies flexible functions to visualise age uncertainty on a plotted tree with using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. Time-scaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.
Authors:
MCMCtreeR_1.1.tar.gz
MCMCtreeR_1.1.zip(r-4.5)MCMCtreeR_1.1.zip(r-4.4)MCMCtreeR_1.1.zip(r-4.3)
MCMCtreeR_1.1.tgz(r-4.4-any)MCMCtreeR_1.1.tgz(r-4.3-any)
MCMCtreeR_1.1.tar.gz(r-4.5-noble)MCMCtreeR_1.1.tar.gz(r-4.4-noble)
MCMCtreeR_1.1.tgz(r-4.4-emscripten)MCMCtreeR_1.1.tgz(r-4.3-emscripten)
MCMCtreeR.pdf |MCMCtreeR.html✨
MCMCtreeR/json (API)
| # Install 'MCMCtreeR' in R: |
| install.packages('MCMCtreeR', repos = c('https://markmark-zz.r-universe.dev', 'https://cloud.r-project.org')) |
- MCMCtree.output - MCMCtree.output
- apeData - ApeData Ape phylogeny in ape format, monophyletic clades, and maximum and minimum ages
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:2477103e8e. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 21 2024 |
| R-4.5-win | NOTE | Aug 21 2024 |
| R-4.5-linux | NOTE | Aug 21 2024 |
| R-4.4-win | NOTE | Aug 21 2024 |
| R-4.4-mac | NOTE | Aug 21 2024 |
| R-4.3-win | OK | Aug 21 2024 |
| R-4.3-mac | OK | Aug 21 2024 |
Exports:estimateBoundestimateCauchyestimateFixedestimateGammaestimateSkewNormalestimateSkewTestimateUpperMCMC.tree.plotMCMCtreePhyplotMCMCtreepriorPosteriorreadMCMCtreetipDes
Dependencies:apecodadigestlatticeMASSMatrixMatrixModelsmnormtnlmenumDerivquantregRcppsnSparseMsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ApeData Ape phylogeny in ape format, monophyletic clades, and maximum and minimum ages | apeData |
| Estimate a Uniform Distribution for MCMCtree | estimateBound |
| Estimate Cauchy Distribution for MCMCtree | estimateCauchy |
| Fixed Age for MCMCtree analysis input | estimateFixed |
| Estimate Gamma Distribution for MCMCtree analysis | estimateGamma |
| Estimate Skew Normal for MCMCtree analysis | estimateSkewNormal |
| Estimate Skew-t Distribution for MCMCtree analysis | estimateSkewT |
| Estimate Upper Age for MCMCtree analysis | estimateUpper |
| Plot time-scaled phylogenies | MCMC.tree.plot |
| MCMCtree.output | MCMCtree.output |
| MCMCtreePhy | MCMCtreePhy |
| Add Node Constraints to Tree in MCMCtree Format | nodeToPhy |
| Plot distribution from MCMCtree node estimations | plotMCMCtree |
| priorPosterior | priorPosterior |
| Read MCMCtree output tree into R | readMCMCtree |
| Find Descendent Tips From A Common Ancestor | tipDes |
