Package: aphylo 0.3-4
aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees
Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Authors:
aphylo_0.3-4.tar.gz
aphylo_0.3-4.zip(r-4.5)aphylo_0.3-4.zip(r-4.4)aphylo_0.3-4.zip(r-4.3)
aphylo_0.3-4.tgz(r-4.4-x86_64)aphylo_0.3-4.tgz(r-4.4-arm64)aphylo_0.3-4.tgz(r-4.3-x86_64)aphylo_0.3-4.tgz(r-4.3-arm64)
aphylo_0.3-4.tar.gz(r-4.5-noble)aphylo_0.3-4.tar.gz(r-4.4-noble)
aphylo_0.3-4.tgz(r-4.4-emscripten)aphylo_0.3-4.tgz(r-4.3-emscripten)
aphylo.pdf |aphylo.html✨
aphylo/json (API)
NEWS
# Install 'aphylo' in R: |
install.packages('aphylo', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/uscbiostats/aphylo/issues
- fakeexperiment - Fake Experimental Data
- faketree - Fake Phylogenetic Tree
annotationsinferencephylogeneticsrcpparmadillo
Last updated 11 months agofrom:d11fc14f81. Checks:OK: 4 NOTE: 5. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 06 2024 |
R-4.5-win-x86_64 | NOTE | Sep 06 2024 |
R-4.5-linux-x86_64 | NOTE | Sep 06 2024 |
R-4.4-win-x86_64 | NOTE | Sep 06 2024 |
R-4.4-mac-x86_64 | NOTE | Sep 06 2024 |
R-4.4-mac-aarch64 | NOTE | Sep 06 2024 |
R-4.3-win-x86_64 | OK | Sep 06 2024 |
R-4.3-mac-x86_64 | OK | Sep 06 2024 |
R-4.3-mac-aarch64 | OK | Sep 06 2024 |
Exports:accuracy_sifteraphylo_cvAPHYLO_DEFAULT_MCMC_CONTROLaphylo_formulaaphylo_from_data_frameaphylo_mcmcaphylo_mleAPHYLO_PARAM_DEFAULTaucbalance_annbpriordist2rootget_postorderimputate_duplicationslist_offspringlist_parentsLogLikemislabelNannNannotatednew_aphylonew_aphylo_prunerNtreesplot_logLikplot_multivariatepredict_brute_forcepredict_pre_orderprediction_scoreraphylordrop_annotationsread_nhxread_pantherread_pliread.pantherrmultiAphylosim_fun_on_treesim_treestatesupriorwrite_pli
Dependencies:apeclicodadigestfmcmclatticeMASSMatrixnlmeRcpprlangxml2