Other packages > Find by keyword >

MCMCtreeR  

Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees
View on CRAN: Click here


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]
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 18 Sep. 2026.
Previous versions and publish date:
0.1 (2019-03-24 09:46), 1.0 (2019-05-20 14:00), 1.1 (2019-05-22 00:20), (2026-07-09 08:09)
Other packages that cited MCMCtreeR R package
View MCMCtreeR citation profile
Other R packages that MCMCtreeR depends, imports, suggests or enhances
Complete documentation for MCMCtreeR
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

data360r  
Wrapper for 'TCdata360' and 'Govdata360' API
Makes it easy to engage with the Application Program Interface (API) of the 'TCdata360' and 'Govdat ...
Download / Learn more Package Citations See dependency  
downlit  
Syntax Highlighting and Automatic Linking
Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pk ...
Download / Learn more Package Citations See dependency  
eyelinker  
Import ASC Files from EyeLink Eye Trackers
Imports plain-text ASC data files from EyeLink eye trackers into (relatively) tidy data frames for ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
hmeasure  
The H-Measure and Other Scalar Classification Performance Metrics
Classification performance metrics that are derived from the ROC curve of a classifier. The package ...
Download / Learn more Package Citations See dependency  
injectoR  
R Dependency Injection
R dependency injection framework. Dependency injection allows a program design to follow the depend ...
Download / Learn more Package Citations See dependency  

28,565

R Packages

239,283

Dependencies

75,677

Author Associations

28,566

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA