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:Mark Puttick [aut,cre], Pascal Title [ctb]

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-4.5-any)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'))
Datasets:
  • MCMCtree.output - MCMCtree.output
  • apeData - ApeData Ape phylogeny in ape format, monophyletic clades, and maximum and minimum ages

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.31 score 34 scripts 199 downloads 3 mentions 13 exports 15 dependencies

Last updated 6 years agofrom:2477103e8e. Checks:3 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 22 2025
R-4.5-winNOTEMar 22 2025
R-4.5-macNOTEMar 22 2025
R-4.5-linuxNOTEMar 22 2025
R-4.4-winNOTEMar 22 2025
R-4.4-macNOTEMar 22 2025
R-4.4-linuxNOTEMar 22 2025
R-4.3-winOKMar 22 2025
R-4.3-macOKMar 22 2025

Exports:estimateBoundestimateCauchyestimateFixedestimateGammaestimateSkewNormalestimateSkewTestimateUpperMCMC.tree.plotMCMCtreePhyplotMCMCtreepriorPosteriorreadMCMCtreetipDes

Dependencies:apecodadigestlatticeMASSMatrixMatrixModelsmnormtnlmenumDerivquantregRcppsnSparseMsurvival

MCMCtreeR

Rendered fromMCMCtree.Rmdusingknitr::rmarkdownon Mar 22 2025.

Last update: 2019-05-20
Started: 2019-05-20

MCMCtreeR: plotting time trees

Rendered fromMCMCtree_plot.Rmdusingknitr::rmarkdownon Mar 22 2025.

Last update: 2019-05-20
Started: 2019-05-20