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 21 Nov. 2024.
Previous versions and publish date:
0.1 (2019-03-24 09:46), 1.0 (2019-05-20 14:00)
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
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

SCBiclust  
Identifies Mean, Variance, and Hierarchically Clustered Biclusters
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency  
RcppHNSW  
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R int ...
Download / Learn more Package Citations See dependency  
crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency  
pkgdepends  
Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain ...
Download / Learn more Package Citations See dependency  
kgschart  
KGS Rank Graph Parser
Restore underlining numeric data from rating history graph of KGS (an online platform of the game o ...
Download / Learn more Package Citations See dependency  
deductive  
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from vali ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

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