Package: Rphylopars 0.3.10
Eric W. Goolsby
Rphylopars: Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data (Goolsby et al. 2017). Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
Authors:
Rphylopars_0.3.10.tar.gz
Rphylopars_0.3.10.tar.gz(r-4.5-noble)Rphylopars_0.3.10.tar.gz(r-4.4-noble)
Rphylopars_0.3.10.tgz(r-4.4-emscripten)Rphylopars_0.3.10.tgz(r-4.3-emscripten)
Rphylopars.pdf |Rphylopars.html✨
Rphylopars/json (API)
| # Install 'Rphylopars' in R: |
| install.packages('Rphylopars', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ericgoolsby/rphylopars/issues
Last updated 9 months agofrom:83f849c8b4. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 15 2024 |
| R-4.5-linux-x86_64 | OK | Oct 15 2024 |
Exports:anc.reconanova.phylopars.lmfast.SSClogLik.phyloparslogLik.phylopars.lmphyloparsphylopars.lmprint.phyloparsprint.phylopars.lmprint.SSCsimtraitssummary.phyloparssummary.phylopars.lmwrite.phylopars
Dependencies:apebackportsbootbroomcliclusterGenerationcodacodetoolscolorspacecombinatcowplotcpp11DEoptimDerivdigestdoBydoParalleldplyrexpmfansifarverfastmatchforeachfuturefuture.applygenericsggplot2globalsgluegtableigraphisobanditeratorslabelinglatticelifecyclelistenvmagrittrmapsMASSMatrixmgcvmicrobenchmarkmnormtmodelrmunsellnlmenumDerivoptimParallelparallellyphangornphylolmphytoolspillarpkgconfigpurrrquadprogR6RColorBrewerRcppRcppArmadillorlangscalesscatterplot3dstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Phylogenetic Comparative Tools for Missing Data and Within-Species Variation | Rphylopars-package |
| Ultra-fast maximum likelihood ancestral state reconstruction | anc.recon |
| Phylopars regression ANOVA | anova.phylopars.lm |
| Fast Phylogenetic Signal Using Sum of Squared Changes (SSC) | fast.SSC |
| Extract Log_likelihood | logLik.phylopars |
| Extract Log_likelihood | logLik.phylopars.lm |
| Estimation of phylogenetic and phenotypic covariance parameters | phylopars |
| Rphylopars regression | phylopars.lm |
| Print phylopars | print.phylopars |
| Print phylopars.lm | print.phylopars.lm |
| Print SSC | print.SSC |
| Simulate traits for phylopars estimation | simtraits |
| Phylopars summary | summary.phylopars |
| phylopars.lm summary | summary.phylopars.lm |
| Write data and tree files for Python phylopars compatability. | write.phylopars |
