Package: rphylo 0.1.1
Vivian G. Li
rphylo: Phylogenetic Analysis with Dependent Discrete Models
Implementation of dependent discrete models (with reversible jump MCMC) derived from 'BayesTraits' V5.0.3 <https://github.com/AndrewPMeade/BayesTraits-Release/tree/Release>. Original software copyright Andrew Meade and contributors, distributed under GPL-3. Modifications for this package by Vivian G. Li <[email protected]>. The following articles should be referenced when using this package: Pagel, M., A. Meade and D. Barker (2004) "Bayesian estimation of ancestral character states on phylogenies" <doi:10.1080/10635150490522232>; Pagel, M. (1994) "Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters" <doi:10.1098/rspb.1994.0006>; Pagel, M. and A. Meade (2006) "Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo" <doi:10.1086/503444>.
Authors:
rphylo_0.1.1.tar.gz
rphylo_0.1.1.tar.gz(r-4.7-any)rphylo_0.1.1.tar.gz(r-4.6-any)
rphylo_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rphylo/json (API)
| # Install 'rphylo' in R: |
| install.packages('rphylo', 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 from:4fe9a951b6. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 154 | ||
| source / vignettes | OK | 162 | ||
| linux-release-x86_64 | OK | 142 | ||
| wasm-release | OK | 347 |
Exports:get_emp_freqrun_dep_modelscale_trees
Dependencies:apeclicpp11digestexpmfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmephangornpkgconfigquadprogRcpprlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Derive empirical frequencies of states | get_emp_freq |
| Print method for dep_model objects | print.dep_model |
| Run a dependent discrete-character model | run_dep_model |
| Scale branch lengths of phylogenetic trees | scale_trees |
| Example trait dataset | tdata |
| Example trait dataset (60 taxa) | tdata2 |
| Example phylogenetic tree | ttree |
| Example phylogenetic trees (500 trees) | ttree2 |
