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]
First Published: 2015-07-07
Latest Update: 2023-08-19
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 01 May. 2025.
Previous versions and publish date:
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
04/0104/0204/0304/0404/0504/0604/0704/0804/0904/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/2004/2104/2204/2304/2404/2504/2604/2704/2804/2904/30Downloads for markophylo024681012141618TrendBars

Today's Hot Picks in Authors and Packages

dCUR  
Dimension Reduction with Dynamic CUR
Dynamic CUR (dCUR) boosts the CUR decomposition (Mahoney MW., Drineas P. (2009) ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
pander  
An R 'Pandoc' Writer
Contains some functions catching all messages, 'stdout' and other useful information while evaluati ...
Download / Learn more Package Citations See dependency  
geofabrik  
Downloading Open Street Map Data
Download OpenStreetMap data from geofabrik servers httpsdownload.geofabrik.de. This approach usesonl ...
Download / Learn more Package Citations See dependency  
dsm  
Density Surface Modelling of Distance Sampling Data
Density surface modelling of line transect data. A Generalized Additive Model-based approach is use ...
Download / Learn more Package Citations See dependency  
fbar  
An Extensible Approach to Flux Balance Analysis
A toolkit for Flux Balance Analysis and related metabolic modeling techniques. Functions are provid ...
Download / Learn more Package Citations See dependency  

24,142

R Packages

207,311

Dependencies

65,176

Author Associations

24,143

Publication Badges

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