Other packages > Find by keyword >

markophylo  

Markov Chain Models for Phylogenetic Trees
View on CRAN: Click here


Download and install markophylo package within the R console
Install from CRAN:
install.packages("markophylo")

Install from Github:
library("remotes")
install_github("cran/markophylo")

Install by package version:
library("remotes")
install_version("markophylo", "1.0.9")



Attach the package and use:
library("markophylo")
Maintained by
Utkarsh J. Dang
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-07-07
Latest Update: 2023-09-19
Description:
Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc. See Dang and Golding (2016) for more details.
How to cite:
Utkarsh J. Dang (2015). markophylo: Markov Chain Models for Phylogenetic Trees. R package version 1.0.9, https://cran.r-project.org/web/packages/markophylo. Accessed 07 Aug. 2026.
Previous versions and publish date:
(2026-07-09 06:28), 1.0.1 (2015-07-07 18:11), 1.0.2 (2015-08-31 23:34), 1.0.3 (2015-11-06 01:09), 1.0.4 (2015-12-31 08:29), 1.0.6 (2018-01-30 18:14), 1.0.7 (2019-03-22 16:00), 1.0.8 (2020-07-05 19:40)
Other packages that cited markophylo R package
View markophylo citation profile
Other R packages that markophylo depends, imports, suggests or enhances
Complete documentation for markophylo
Functions, R codes and Examples using the markophylo R package
Some associated functions: estimaterates . estimaterates_f . markophylo-package . patterns . plottree . print.markophylo . simdata1 . 
Some associated R codes: RcppExports.R . custom-general14.R . estimatesrates_f.R .  Full markophylo package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

modelwordcloud  
Model Word Clouds
Makes a word cloud of text, sized by the frequency of the word, and colored either by user-specified ...
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  
BayesESS  
Determining Effective Sample Size
Determines effective sample size of a parametric prior distribution in Bayesian models. For a web-b ...
Download / Learn more Package Citations See dependency  
bbricks  
Bayesian Methods and Graphical Model Structures for Statistical Modeling
A set of frequently used Bayesian parametric and nonparametric model structures, as well as a set of ...
Download / Learn more Package Citations See dependency  
enrichwith  
Methods to Enrich R Objects with Extra Components
Provides the "enrich" method to enrich list-like R objects with new, relevant components. The curren ...
Download / Learn more Package Citations See dependency  

28,083

R Packages

239,283

Dependencies

74,457

Author Associations

28,084

Publication Badges

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