{ "_id": "6a1041e9acfb0bcc41c9d9ba", "Package": "MCMCtreeR", "Title": "Prepare MCMCtree Analyses and Plot Bayesian Divergence Time\nAnalyses Estimates on Trees", "Version": "1.1", "Author": "Mark Puttick [aut,cre], Pascal Title [ctb]", "Maintainer": "Mark Puttick ", "Description": "Provides functions to prepare time priors for 'MCMCtree'\nanalyses in the 'PAML' software from Yang\n(2007) and plot time-scaled\nphylogenies from any Bayesian divergence time analysis. Most\ntime-calibrated node prior distributions require user-specified\nparameters. The package provides functions to refine these\nparameters, so that the resulting prior distributions\naccurately reflect confidence in known, usually fossil, time\ninformation. These functions also enable users to visualise\ndistributions and write 'MCMCtree' ready input files.\nAdditionally, the package supplies flexible functions to\nvisualise age uncertainty on a plotted tree with using node\nbars, using branch widths proportional to the age uncertainty,\nor by plotting the full posterior distributions on nodes.\nTime-scaled phylogenetic plots can be visualised with absolute\nand geological timescales . All plotting functions are\napplicable with output from any Bayesian software, not just\n'MCMCtree'.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 07:34:27 UTC", "User": "root" }, "Repository": "https://markmark-zz.r-universe.dev", "Date/Publication": "2019-05-21 21:20:31 UTC", "RemoteUrl": "https://github.com/cran/MCMCtreeR", "RemoteRef": "HEAD", "RemoteSha": "2477103e8e9483eb9d4b50f0ff87801601abc1f1", "MD5sum": "b6be45cfb17be18b16dd3bac7bfc2b5a", "_user": "markmark-zz", "_type": "src", "_file": "MCMCtreeR_1.1.tar.gz", "_fileid": "7d3eabdbfa712ae331140a5b7b6c9f976297dbf30f4379ce26567180a67b031c", "_filesize": 3530709, "_sha256": "7d3eabdbfa712ae331140a5b7b6c9f976297dbf30f4379ce26567180a67b031c", "_created": "2026-05-11T07:34:27.000Z", "_published": "2026-05-22T11:45:45.514Z", "_distro": "noble", "_jobs": [ { "job": 77373008178, "time": 126, "config": 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"estimateGamma", "title": "Estimate Gamma Distribution for MCMCtree analysis", "topics": [ "estimateGamma" ] }, { "page": "estimateSkewNormal", "title": "Estimate Skew Normal for MCMCtree analysis", "topics": [ "estimateSkewNormal" ] }, { "page": "estimateSkewT", "title": "Estimate Skew-t Distribution for MCMCtree analysis", "topics": [ "estimateSkewT" ] }, { "page": "estimateUpper", "title": "Estimate Upper Age for MCMCtree analysis", "topics": [ "estimateUpper" ] }, { "page": "MCMC.tree.plot", "title": "Plot time-scaled phylogenies", "topics": [ "MCMC.tree.plot" ] }, { "page": "MCMCtree.output", "title": "MCMCtree.output", "topics": [ "MCMCtree.output" ] }, { "page": "MCMCtreePhy", "title": "MCMCtreePhy", "topics": [ "MCMCtreePhy" ] }, { "page": "nodeToPhy", "title": "Add Node Constraints to Tree in MCMCtree Format", "topics": [ "nodeToPhy" ] }, { "page": "plotMCMCtree", "title": "Plot distribution from MCMCtree node estimations", "topics": [ "plotMCMCtree" ] }, { "page": 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