bomeara. To fix this you can add URL: https://phylotastic.r-universe.dev/BMhyb to the package DESCRIPTION file. 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-4.7)BMhyb_2.1.5.zip(r-4.6)BMhyb_2.1.5.zip(r-4.5)
BMhyb_2.1.5.tgz(r-4.6-any)BMhyb_2.1.5.tgz(r-4.5-any)
BMhyb_2.1.5.tar.gz(r-4.7-any)BMhyb_2.1.5.tar.gz(r-4.6-any)
BMhyb_2.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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 from:22709ce279. Checks:7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 274 | ||
| source / vignettes | OK | 185 | ||
| linux-release-x86_64 | NOTE | 330 | ||
| macos-release-arm64 | NOTE | 208 | ||
| macos-oldrel-arm64 | NOTE | 188 | ||
| windows-devel | NOTE | 273 | ||
| windows-release | NOTE | 259 | ||
| windows-oldrel | NOTE | 269 | ||
| wasm-release | OK | 148 |
Exports:AddHybridizationBMhybBMhybExhaustiveComputeLikelihoodComputeVCVConvertEvonetToIgraphWithNodeNumbersCreateHybridlessEvonetMergeExhaustiveForPlottingSimulateNetworkSimulateTips
Dependencies:apebackportscachemcheckmateclassclassIntcliclusterGenerationcodacodetoolscolorspacecombinatcorpcorcowplotcpp11data.tableDBIDEoptimdeSolvedigestdoParallele1071expmfarverfastmapforeachFormulaformula.toolsfuturefuture.applygeigergenericsggplot2globalsgluegridExtragtableigraphisobanditeratorsKernSmoothlabelinglatticelhslifecyclelistenvlubridatemagrittrmapsMASSMatrixmemoisemetRmnormtmvtnormncbitnlmenumDerivoperator.toolsoptimParallelosqpparallellyphangornphytoolspkgconfigplyrprogressrproxypurrrR6RColorBrewerRcppRcppArmadillorlangs2S7scalesscatterplot3dsfstringistringrsubplextimechangeTreeSimunitsvctrsviridisviridisLitewithrwk
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 |