Package: evobiR 2.2

evobiR: Evolutionary Biology in R

Comparative analysis of continuous traits influencing discrete states, and utility tools to facilitate comparative analyses. Implementations of ABBA/BABA type statistics to test for introgression in genomic data.

Authors:Michelle M. Jonika, Maximos Chin, Nathan Anderson, Richard H. Adams, Jeffery P. Demuth, and Heath Blackmon

evobiR_2.2.tar.gz
evobiR_2.2.zip(r-4.6)evobiR_2.2.zip(r-4.5)
evobiR_2.2.tgz(r-4.6-any)evobiR_2.2.tgz(r-4.5-any)
evobiR_2.2.tar.gz(r-4.6-any)evobiR_2.2.tar.gz(r-4.5-any)
evobiR_2.2.tgz(r-4.5-emscripten)
evobiR.pdf |evobiR.html✨
evobiR/json (API)

# Install 'evobiR' in R:

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

Bug tracker:https://github.com/coleoguy/evobir/issues

Datasets:

hym.tree - Hymenoptera phylogenetic tree
mite.trait - Phenotype data for mites
trees - 10 phylogenetic trees for mites

On CRAN:

8.02 score 20 stars 125 scripts 280 downloads 3 mentions 18 exports 59 dependencies

Last updated from:2d0653466c. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	171
source / vignettes	OK	216
linux-release-x86_64	OK	200
macos-devel-arm64	OK	185
macos-release-arm64	OK	149
windows-devel	OK	121
windows-release	OK	232
windows-oldrel	OK	149
wasm-release	OK	122

Exports:AncCond AncCondFast CalcD CalcPopD countTrees fix.simmap FuzzyMatch getNe GetTipRates make.simmap2 pSAF ReOrderAlignment ResSel SampleTrees scaleTreeRates SlidingWindow SuperMatrix WinCalcD

Dependencies:ade4 ape castor cli clusterGeneration coda codetools combinat cpp11 DEoptim digest doParallel expm farver fastmatch foreach generics ggplot2 glue gridExtra gtable igraph isoband iterators jsonlite labeling lattice lifecycle magrittr maps MASS Matrix mnormt naturalsort nlme numDeriv optimParallel phangorn phytools pixmap pkgconfig quadprog R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang RSpectra S7 scales scatterplot3d segmented seqinr sp vctrs viridis viridisLite withr

Evolutionary biology in R (evobiR) tutorial

Michelle Jonika, Jeffery Demuth, Richard H. Adams, and Heath Blackmon

Rendered fromevolutionary.biology.in.R.Rmdusingknitr::rmarkdownon Mar 20 2026.

Last update: 2026-03-20
Started: 2015-10-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
evobiR: Evolutionary Biology in R	evobiR-package evobiR
Simulated SNP alignment data	1.fasta 3.fasta
Ancestral Condition Analysis	AncCond
Ancestral Condition Test (Parametric Bootstrap)	AncCondFast
Patterson's D-Statistic (ABBA-BABA Test)	CalcD
Population-Level Patterson's D-Statistic	CalcPopD
Count Tree Topologies in a Collection	countTrees
Fix Failed Branches in Stochastic Mapping	fix.simmap
Fuzzy Name Matching Between Tree and Data	FuzzyMatch
Effective Population Size from Census Numbers	getNe
Calculate Evolutionary Rates at Tree Tips	GetTipRates
Gnatocerus cornutus measurements	horn.beetle.csv
Hymenoptera phylogenetic tree	hym.tree
Enhanced Stochastic Character Mapping	make.simmap2
Phenotype data for mites	mite.trait
Plot a Rate-Scaled Phylogeny	plot.phyloscaled
Probability of Sex-Autosome Fusion	pSAF
Reorder Sequences in a FASTA Alignment	ReOrderAlignment
Residual Selection for Artificial Breeding Experiments	ResSel
Sample Trees from Bayesian MCMC Output	SampleTrees
Analyze Rate Heterogeneity in Discrete Character Evolution	scaleTreeRates
Sliding Window Analysis	SlidingWindow
Build a Supermatrix from Multiple Sequence Alignments	SuperMatrix
10 phylogenetic trees for mites	trees trees.mite
100 simulated phylogenetic trees	trees.nex
Windowed Patterson's D-Statistic	WinCalcD