Package: markophylo 1.0.9
Utkarsh J. Dang
markophylo: Markov Chain Models for Phylogenetic Trees
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) <doi:10.1093/bioinformatics/btv541> for more details.
Authors:
markophylo_1.0.9.tar.gz
markophylo_1.0.9.tar.gz(r-4.5-noble)markophylo_1.0.9.tar.gz(r-4.4-noble)
markophylo_1.0.9.tgz(r-4.4-emscripten)markophylo_1.0.9.tgz(r-4.3-emscripten)
markophylo.pdf |markophylo.html✨
markophylo/json (API)
NEWS
| # Install 'markophylo' in R: |
| install.packages('markophylo', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:82c21cfa0c. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-linux-x86_64 | OK | Sep 13 2024 |
Exports:estimateratesestimaterates_fpatternsplottreeprint.markophylo
Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmfastmatchforeachgeigergenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcppRcppArmadillorlangscatterplot3dsubplexvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Markov chain models for phylogenetic trees. | markophylo-package markophylo |
| Estimate substitution rate matrix. | estimaterates |
| Estimate substitution rate matrix. | estimaterates_f |
| Unique phyletic patterns with counts. | patterns |
| Plot the tree used with different hypothesized branch groupings (or clades) following unique rates coloured differently. | plottree |
| Print summary information for the model fit. | print.markophylo |
| Simulated data. | simdata1 simdata2 simdata3 simdata4 simdata5 |