markophylo: Markov Chain Models for Phylogenetic Trees
Version 1.0.4

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.

AuthorUtkarsh J. Dang and G. Brian Golding
Date of publication2015-12-31 08:29:14
MaintainerUtkarsh J. Dang <udang@mcmaster.ca>
LicenseGPL (>= 2)
Version1.0.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("markophylo")

Getting started

Package overview
Markov Chain Analysis on Phylogenetic Trees

Popular man pages

estimaterates: Estimate substitution rate matrix.
markophylo-package: Markov chain models for phylogenetic trees.
patterns: Unique phyletic patterns with counts.
plottree: Plot the tree used with different hypothesized branch...
print.markophylo: Print summary information for the model fit.
simdata1: Simulated data.
See all...

All man pages Function index File listing

Man pages

estimaterates: Estimate substitution rate matrix.
markophylo-package: Markov chain models for phylogenetic trees.
patterns: Unique phyletic patterns with counts.
plottree: Plot the tree used with different hypothesized branch...
print.markophylo: Print summary information for the model fit.
simdata1: Simulated data.

Functions

cat_loopC Source code
checkbglist Source code
colMeansC Source code
estimaterates Man page Source code
expm Source code
loopC Source code
markophylo Man page
markophylo-package Man page
part_loopC Source code
patterns Man page Source code
plottree Man page Source code
print.markophylo Man page Source code
simdata1 Man page
simdata2 Man page
simdata3 Man page
simdata4 Man page
simdata5 Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/estimaterates.R
inst/doc/estimaterates.html
inst/doc/estimaterates.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-main.R
src
src/Makevars
src/loopC-general4.cpp
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/simdata5.rda
data/simdata4.rda
data/simdata2.rda
data/simdata1.rda
data/simdata3.rda
R
R/custom-general14.R
R/RcppExports.R
vignettes
vignettes/estimaterates.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/plottree.Rd
man/estimaterates.Rd
man/print.markophylo.Rd
man/markophylo-package.Rd
man/simdata1.Rd
man/patterns.Rd
markophylo documentation built on May 19, 2017, 10:22 p.m.

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