markophylo: Markov Chain Models for Phylogenetic Trees

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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.

Author
Utkarsh J. Dang and G. Brian Golding
Date of publication
2015-12-31 08:29:14
Maintainer
Utkarsh J. Dang <udang@mcmaster.ca>
License
GPL (>= 2)
Version
1.0.4

View on CRAN

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.

Files in this package

markophylo
markophylo/inst
markophylo/inst/CITATION
markophylo/inst/doc
markophylo/inst/doc/estimaterates.R
markophylo/inst/doc/estimaterates.html
markophylo/inst/doc/estimaterates.Rmd
markophylo/tests
markophylo/tests/testthat.R
markophylo/tests/testthat
markophylo/tests/testthat/test-main.R
markophylo/src
markophylo/src/Makevars
markophylo/src/loopC-general4.cpp
markophylo/src/Makevars.win
markophylo/src/RcppExports.cpp
markophylo/NAMESPACE
markophylo/NEWS
markophylo/data
markophylo/data/simdata5.rda
markophylo/data/simdata4.rda
markophylo/data/simdata2.rda
markophylo/data/simdata1.rda
markophylo/data/simdata3.rda
markophylo/R
markophylo/R/custom-general14.R
markophylo/R/RcppExports.R
markophylo/vignettes
markophylo/vignettes/estimaterates.Rmd
markophylo/MD5
markophylo/build
markophylo/build/vignette.rds
markophylo/DESCRIPTION
markophylo/man
markophylo/man/plottree.Rd
markophylo/man/estimaterates.Rd
markophylo/man/print.markophylo.Rd
markophylo/man/markophylo-package.Rd
markophylo/man/simdata1.Rd
markophylo/man/patterns.Rd