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MCMCtreeR
View on CRAN: Click
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Download and install MCMCtreeR package within the R console
Install from CRAN:
install.packages("MCMCtreeR")
Install from Github:
library("remotes")
install_github("cran/MCMCtreeR")
Install by package version:
library("remotes")
install_version("MCMCtreeR", "1.1")
Attach the package and use:
library("MCMCtreeR")
Maintained by
Mark Puttick
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-03-24
Latest Update: 2019-05-21
Description:
Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007) 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'.
How to cite:
Mark Puttick (2019). MCMCtreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees. R package version 1.1, https://cran.r-project.org/web/packages/MCMCtreeR. Accessed 22 Dec. 2024.
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Other R packages that MCMCtreeR depends,
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Complete documentation for MCMCtreeR
Functions, R codes and Examples using
the MCMCtreeR R package
Some associated functions: MCMC.tree.plot . MCMCtree.output . MCMCtreePhy . apeData . estimateBound . estimateCauchy . estimateFixed . estimateGamma . estimateSkewNormal . estimateSkewT . estimateUpper . nodeToPhy . plotMCMCtree . priorPosterior . readMCMCtree . tipDes .
Some associated R codes: MCMC.tree.plot.R . MCMCPhyOneNode.R . MCMCtree.output.R . MCMCtreePhy.R . apeData.R . cauchyMCMCtree.R . estimateBound.R . estimateCauchy.R . estimateFixed.R . estimateGamma.R . estimateSkewNormal.R . estimateSkewT.R . estimateUpper.R . nodeTimes.R . nodeToPhy.R . plotMCMCtree.R . priorPosterior.R . read.in.mrbayes.R . read.in.revbayes.R . readMCMCtree.R . time.colour.R . tipDes.R . uniformMCMCtree.R . Full MCMCtreeR package functions and examples
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