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:Dwueng-Chwuan Jhwueng [aut, cre], Brian C. O'Meara [aut]

BMhyb_2.1.5.tar.gz
BMhyb_2.1.5.zip(r-4.7-any)BMhyb_2.1.5.zip(r-4.6-any)BMhyb_2.1.5.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
BMhyb/json (API)

# Install 'BMhyb' in R:

install.packages('BMhyb', repos = c('https://bomeara.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bomeara/bmhyb/issues

Datasets:

cichlid - Cichlid dataset
nicotiana - Nicotiana dataset

On CRAN:

2.84 score 137 scripts 15 downloads 10 exports 84 dependencies

Last updated from:22709ce279. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	224
source / vignettes	OK	179
linux-release	NOTE	184
macos-release	NOTE	182
macos-oldrel	NOTE	148
windows-devel	NOTE	200
windows-release	NOTE	263
windows-oldrel	NOTE	284
wasm-release	OK	149

Exports:AddHybridization BMhyb BMhybExhaustive ComputeLikelihood ComputeVCV ConvertEvonetToIgraphWithNodeNumbers CreateHybridlessEvonet MergeExhaustiveForPlotting SimulateNetwork SimulateTips

Dependencies:ape backports cachem checkmate class classInt cli clusterGeneration coda codetools colorspace combinat corpcor cowplot cpp11 data.table DBI DEoptim deSolve digest doParallel e1071 expm farver fastmap fastmatch foreach Formula formula.tools geiger generics ggplot2 glue gridExtra gtable igraph isoband iterators KernSmooth labeling lattice lhs lifecycle lubridate magrittr maps MASS Matrix memoise metR mnormt mvtnorm ncbit nlme numDeriv operator.tools optimParallel phangorn phytools pkgconfig plyr proxy purrr quadprog R6 RColorBrewer Rcpp rlang s2 S7 scales scatterplot3d sf stringi stringr subplex timechange TreeSim units vctrs viridis viridisLite withr wk

Citation

Development and contributors

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