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-4.7-arm64)Rphylopars_0.3.10.tar.gz(r-4.7-x86_64)Rphylopars_0.3.10.tar.gz(r-4.6-arm64)Rphylopars_0.3.10.tar.gz(r-4.6-x86_64)
Rphylopars_0.3.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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 from:83f849c8b4. Checks:6 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 197 | ||
| linux-devel-x86_64 | OK | 192 | ||
| source / vignettes | OK | 215 | ||
| linux-release-arm64 | OK | 193 | ||
| linux-release-x86_64 | OK | 193 | ||
| wasm-release | OK | 140 |
Exports:anc.reconanova.phylopars.lmfast.SSClogLik.phyloparslogLik.phylopars.lmphyloparsphylopars.lmprint.phyloparsprint.phylopars.lmprint.SSCsimtraitssummary.phyloparssummary.phylopars.lmwrite.phylopars
Dependencies:apebackportsbootbroomcliclusterGenerationcodacodetoolscolorspacecombinatcowplotcpp11DEoptimDerivdigestdoBydoParalleldplyrexpmfarverfastmatchforeachforecastfracdifffuturefuture.applygenericsggplot2globalsgluegtableigraphisobanditeratorslabelinglatticelifecyclelistenvlmtestmagrittrmapsMASSMatrixmicrobenchmarkmnormtmodelrnlmennetnumDerivoptimParallelparallellyphangornphylolmphytoolspillarpkgconfigpurrrquadprogR6RColorBrewerRcppRcppArmadillorlangS7scalesscatterplot3dstringistringrtibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo
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 |
