bomeara. See also theR-universe documentation.Package: BMhyb 2.1.5
Dwueng-Chwuan Jhwueng
BMhyb: Comparative Methods for Phylogenetic Networks
Analyze the phenotypic evolution of species of hybrid origin on a phylogenetic network. This can detect a burst of variation at the formation of a hybrid as well as an increase or decrease in trait value at a hybridization event. Parameters are estimated by maximum likelihood, and model averaging can be done automatically. Users need to enter a comparative data set and a phylogenetic network.
Authors:
BMhyb_2.1.5.tar.gz
BMhyb_2.1.5.zip(r-4.5)BMhyb_2.1.5.zip(r-4.4)BMhyb_2.1.5.zip(r-4.3)
BMhyb_2.1.5.tgz(r-4.4-any)BMhyb_2.1.5.tgz(r-4.3-any)
BMhyb_2.1.5.tar.gz(r-4.5-noble)BMhyb_2.1.5.tar.gz(r-4.4-noble)
BMhyb_2.1.5.tgz(r-4.4-emscripten)BMhyb_2.1.5.tgz(r-4.3-emscripten)
BMhyb.pdf |BMhyb.html✨
BMhyb/json (API)
NEWS
| # Install 'BMhyb' in R: |
| install.packages('BMhyb', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bomeara/bmhyb/issues
Last updated 3 years agofrom:22709ce279. Checks:OK: 1 NOTE: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 16 2024 |
| R-4.5-win | NOTE | Dec 16 2024 |
| R-4.5-linux | NOTE | Dec 16 2024 |
| R-4.4-win | NOTE | Dec 16 2024 |
| R-4.4-mac | NOTE | Dec 16 2024 |
| R-4.3-win | NOTE | Dec 16 2024 |
| R-4.3-mac | NOTE | Dec 16 2024 |
Exports:AddHybridizationBMhybBMhybExhaustiveComputeLikelihoodComputeVCVConvertEvonetToIgraphWithNodeNumbersCreateHybridlessEvonetMergeExhaustiveForPlottingSimulateNetworkSimulateTips
Dependencies:apebackportscachemcheckmateclassclassIntcliclusterGenerationcodacodetoolscolorspacecombinatcorpcorcowplotcpp11data.tableDBIDEoptimdeSolvedigestdoParallele1071expmfansifarverfastmapforeachFormulaformula.toolsgeigergenericsggplot2gluegridExtragtableigraphisobanditeratorsKernSmoothlabelinglatticelhslifecyclelubridatemagrittrmapsMASSMatrixmemoisemetRmgcvmnormtmunsellmvtnormncbitnlmenumDerivoperator.toolsoptimParallelphangornphytoolspillarpkgconfigplyrproxypurrrquadprogR6RColorBrewerRcppRcppArmadillorlangs2scalesscatterplot3dsfstringistringrsubplextibbletimechangeTreeSimunitsutf8vctrsviridisviridisLitewithrwk
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add hybrid events to a phy.graph | AddHybridization |
| Optimize model | BMhyb |
| Exhaustively evaluate models | BMhybExhaustive |
| Cichlid dataset | cichlid |
| Compute the likelihood for a set of parameters | ComputeLikelihood |
| Compute the variance-covariance matrix | ComputeVCV |
| Convert an evonet object into igraph | ConvertEvonetToIgraphWithNodeNumbers |
| Convert phylo object to evonet | CreateHybridlessEvonet |
| Get convex hull at a given threshold | GetConvexHull |
| Function to merge adaptive sampling sims for plotting | MergeExhaustiveForPlotting |
| Nicotiana dataset | nicotiana |
| Plot BMhybExhaustive result | plot.BMhybExhaustiveResult |
| Plot BMhyb result | plot.BMhybResult |
| Print BMhybExhaustive result | print.BMhybExhaustiveResult |
| Print BMhyb result | print.BMhybResult |
| Simulate a phylogenetic network | SimulateNetwork |
| Simulate trait data | SimulateTips |
| Summarize BMhybExhaustive result | summary.BMhybExhaustiveResult |
| Summarize BMhyb result | summary.BMhybResult |