{ "_id": "6a2c82d43efcd9bda42debd1", "Package": "evobiR", "Type": "Package", "Title": "Evolutionary Biology in R", "Version": "2.2", "Date": "2025-02-20", "Author": "Michelle M. Jonika, Maximos Chin, Nathan Anderson, Richard H.\nAdams, Jeffery P. Demuth, and Heath Blackmon", "Maintainer": "Heath Blackmon ", "URL": "https://github.com/coleoguy/evobir", "BugReports": "https://github.com/coleoguy/evobir/issues", "Description": "Comparative analysis of continuous traits influencing\ndiscrete states, and utility tools to facilitate comparative\nanalyses. Implementations of ABBA/BABA type statistics to test\nfor introgression in genomic data.", "License": "GPL (>=2)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "libglpk-dev make libxml2-dev zlib1g-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2026-04-30 14:17:42 UTC", "RemoteUrl": "https://github.com/coleoguy/evobir", "RemoteRef": "HEAD", "RemoteSha": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-12 22:02:29 UTC", "User": "root" }, "MD5sum": "5ada75a7c8eed2dd132deee1ac375c34", "_user": "phylotastic", "_type": "src", "_file": "evobiR_2.2.tar.gz", "_fileid": "667a3ef7922dd32a10b04f97ef73855f48bcadd7f5e9d4cbd48d55a7c1ab0929", "_filesize": 1190493, "_sha256": "667a3ef7922dd32a10b04f97ef73855f48bcadd7f5e9d4cbd48d55a7c1ab0929", "_created": "2026-06-12T22:02:29.000Z", "_published": "2026-06-12T22:06:12.804Z", "_distro": "noble", "_jobs": [ { "job": 81129826725, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7603596208" }, { "job": 81129826589, "time": 172, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7603594292" }, { "job": 81129826655, "time": 135, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7603583162" }, { "job": 81129826591, "time": 99, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7603572759" }, { "job": 81129278177, "time": 224, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7603543040" }, { "job": 81129826584, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7603581743" }, { "job": 81129826622, "time": 133, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7603582496" }, { "job": 81129826594, "time": 127, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7603580697" }, { "job": 81129826617, "time": 139, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7603584528" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/coleoguy/evobir", "_commit": { "id": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "author": "Heath Blackmon ", "committer": "Heath Blackmon ", "message": "Add LICENSE file (GPL-2)\n\nDESCRIPTION already declares GPL (>= 2). Adding the canonical license\ntext so GitHub displays the license badge correctly and the repo can\nbe unambiguously redistributed.\n\nCo-Authored-By: Claude Opus 4.7 (1M context) \n", "time": 1777558662 }, "_maintainer": { "name": "Heath Blackmon", "email": "coleoguy@gmail.com", "login": "coleoguy", "orcid": "0000-0002-5433-4036", "description": "Evolutionary Biologist studying sex chromosomes, genomics, and trait evolution.", "uuid": 4976546 }, "_registered": true, "_dependencies": [ { "package": "seqinr", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "castor", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "expm", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "coleoguy", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-40", "n": 1 }, { "week": "2026-08", "n": 2 }, { "week": "2026-09", "n": 4 }, { "week": "2026-12", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [ { "name": "v3", "date": "2026-03-20" } ], "_topics": [ "comparative-methods", "evolutionary-biology", "phylogenetics" ], "_stars": 21, "_contributors": [ { "user": "coleoguy", "count": 198, "uuid": 4976546 }, { "user": "michellejonika", "count": 5, "uuid": 44213878 }, { "user": "seanchien4", "count": 5, "uuid": 115194066 }, { "user": "maxchin0701", "count": 5, "uuid": 80797134 }, { "user": "nw-anderson", "count": 2, "uuid": 50749568 }, { "user": "thejoyofcode", "count": 1, "uuid": 10440239 }, { "user": "chromartie", "count": 1, "uuid": 13067802 }, { "user": "mcconnellmmeghann-mugo", "count": 1, "uuid": 234062684 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 43, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/evobiR" }, "_mentions": 3, "_devurl": "https://github.com/coleoguy/evobir", "_searchresults": 140, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/evobiR.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2013-10-21" }, { "version": "1.1", "date": "2015-09-06" } ], "_exports": [ "AncCond", "AncCondFast", "CalcD", "CalcPopD", "countTrees", "fix.simmap", "FuzzyMatch", "getNe", "GetTipRates", "make.simmap2", "pSAF", "ReOrderAlignment", "ResSel", "SampleTrees", "scaleTreeRates", "SlidingWindow", "SuperMatrix", "WinCalcD" ], "_datasets": [ { "name": "hym.tree", "title": "Hymenoptera phylogenetic tree", "object": "hym.tree", "file": "hym.tree.rda", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "mite.trait", "title": "Phenotype data for mites", "object": "mite.trait", "file": "mite.trait.RData", "class": [ "data.frame" ], "fields": [ "X", "Fem2N", "ploidy" ], "rows": 109, "table": true, "tojson": true }, { "name": "trees", "title": "10 phylogenetic trees for mites", "object": "trees.mite", "file": "trees.mite.rda", "class": [ "multiPhylo" ], "fields": [], "table": true, "tojson": false } ], "_help": [ { "page": "evobiR-package", "title": "evobiR: Evolutionary Biology in R", "topics": [ "evobiR-package", "evobiR" ] }, { "page": "1.fasta", "title": "Simulated SNP alignment data", "topics": [ "1.fasta", "3.fasta" ] }, { "page": "AncCond", "title": "Ancestral Condition Analysis", "topics": [ "AncCond" ] }, { "page": "AncCondFast", "title": "Ancestral Condition Test (Parametric Bootstrap)", "topics": [ "AncCondFast" ] }, { "page": "CalcD", "title": "Patterson's D-Statistic (ABBA-BABA Test)", "topics": [ "CalcD" ] }, { "page": "CalcPopD", "title": "Population-Level Patterson's D-Statistic", "topics": [ "CalcPopD" ] }, { "page": "countTrees", "title": "Count Tree Topologies in a Collection", "topics": [ "countTrees" ] }, { "page": "fix.simmap", "title": "Fix Failed Branches in Stochastic Mapping", "topics": [ "fix.simmap" ] }, { "page": "FuzzyMatch", "title": "Fuzzy Name Matching Between Tree and Data", "topics": [ "FuzzyMatch" ] }, { "page": "getNe", "title": "Effective Population Size from Census Numbers", "topics": [ "getNe" ] }, { "page": "GetTipRates", "title": "Calculate Evolutionary Rates at Tree Tips", "topics": [ "GetTipRates" ] }, { "page": "horn.beetle", "title": "Gnatocerus cornutus measurements", "topics": [ "horn.beetle.csv" ] }, { "page": "hym.tree", "title": "Hymenoptera phylogenetic tree", "topics": [ "hym.tree" ] }, { "page": "make.simmap2", "title": "Enhanced Stochastic Character Mapping", "topics": [ "make.simmap2" ] }, { "page": "mite.trait", "title": "Phenotype data for mites", "topics": [ "mite.trait" ] }, { "page": "plot.phyloscaled", "title": "Plot a Rate-Scaled Phylogeny", "topics": [ "plot.phyloscaled" ] }, { "page": "pSAF", "title": "Probability of Sex-Autosome Fusion", "topics": [ "pSAF" ] }, { "page": "ReOrderAlignment", "title": "Reorder Sequences in a FASTA Alignment", "topics": [ "ReOrderAlignment" ] }, { "page": "ResSel", "title": "Residual Selection for Artificial Breeding Experiments", "topics": [ "ResSel" ] }, { "page": "SampleTrees", "title": "Sample Trees from Bayesian MCMC Output", "topics": [ "SampleTrees" ] }, { "page": "scaleTreeRates", "title": "Analyze Rate Heterogeneity in Discrete Character Evolution", "topics": [ "scaleTreeRates" ] }, { "page": "SlidingWindow", "title": "Sliding Window Analysis", "topics": [ "SlidingWindow" ] }, { "page": "SuperMatrix", "title": "Build a Supermatrix from Multiple Sequence Alignments", "topics": [ "SuperMatrix" ] }, { "page": "trees.mite", "title": "10 phylogenetic trees for mites", "topics": [ "trees", "trees.mite" ] }, { "page": "trees.nex", "title": "100 simulated phylogenetic trees", "topics": [ "trees.nex" ] }, { "page": "WinCalcD", "title": "Windowed Patterson's D-Statistic", "topics": [ "WinCalcD" ] } ], "_readme": "https://github.com/coleoguy/evobir/raw/HEAD/README.md", "_rundeps": [ "ade4", "ape", "backports", "castor", "checkmate", "cli", "clusterGeneration", "coda", "codetools", "combinat", "cpp11", "DEoptim", "digest", "doParallel", "expm", "farver", "foreach", "future", "future.apply", "generics", "ggplot2", "globals", "glue", "gridExtra", "gtable", "igraph", "isoband", "iterators", "jsonlite", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "maps", "MASS", "Matrix", "mnormt", "naturalsort", "nlme", "numDeriv", "optimParallel", "osqp", "parallelly", "phangorn", "phytools", "pixmap", "pkgconfig", "progressr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "rlang", "RSpectra", "S7", "scales", "scatterplot3d", "segmented", "seqinr", "sp", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "evolutionary.biology.in.R.Rmd", "filename": "evolutionary.biology.in.R.html", "title": "Evolutionary biology in R (evobiR) tutorial", "author": "Michelle Jonika, Jeffery Demuth, Richard H. Adams, and Heath Blackmon", "engine": "knitr::rmarkdown", "headings": [ "Installing", "Comparative Methods", "AncCond", "AncCondFast", "GetTipRates", "FuzzyMatch", "SampleTrees", "countTrees", "SuperMatrix", "Phylogenetic Rate Analysis", "scaleTreeRates & plot.phyloscaled", "make.simmap2 & fix.simmap", "Population Genetics", "CalcD & WinCalcD", "getNe", "pSAF", "Utility/Misc. Functions", "ReOrderAlignment", "Sliding window", "ResSel" ], "created": "2015-10-19 01:18:39", "modified": "2026-03-20 18:27:36", "commits": 33 } ], "_score": 7.188506633818115, "_indexed": false, "_nocasepkg": "evobir", "_universes": [ "phylotastic" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.2", "date": "2026-06-12T22:04:59.000Z", "distro": "noble", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "d1057ebe983563a78dfa25447ab5914e4aecd2ebeab628dbae0a0b6f5565c627", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" }, { "r": "4.6.0", "os": "linux", "version": "2.2", "date": "2026-06-12T22:04:52.000Z", "distro": "noble", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "4a34fbf62dad4980fed8d3e08a56eae958361b08783bcbc961af17e03eb6317f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" }, { "r": "4.5.3", "os": "mac", "version": "2.2", "date": "2026-06-12T22:04:25.000Z", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "9c9b79a74362cc19971ab62aea0e9903171deb8c90bd33bdfaf821d60da2b34d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" }, { "r": "4.6.0", "os": "mac", "version": "2.2", "date": "2026-06-12T22:04:00.000Z", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "7361eeaaae11a2747e5339e4396564d921d22a5efcbe4d7f09428ec8597ab217", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" }, { "r": "4.6.0", "os": "wasm", "version": "2.2", "date": "2026-06-12T22:05:01.000Z", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "a6b8d882bcb0ba9e8bc28ce56338606f025e6ca5ce18fb42c17cf57bdfb4a937", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" }, { "r": "4.7.0", "os": "win", "version": "2.2", "date": "2026-06-12T22:03:55.000Z", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "9cb103c0f8f0b822aad70add02241dd914f4244b309b352e4ddd4ff94581552e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" }, { "r": "4.5.3", "os": "win", "version": "2.2", "date": "2026-06-12T22:03:58.000Z", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "db1a82727e0f3eb2ec9b13688be72644878c70536ebc703e837aa28aac3e8114", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" }, { "r": "4.6.0", "os": "win", "version": "2.2", "date": "2026-06-12T22:04:08.000Z", "commit": "a6fea9862f710556c3bf4be2ef5d1a83c747cd8d", "fileid": "c69aafcae5bdaaa09766cab5f842fba70c7ef4f1a9b1155c3bc13eea07335524", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27445433921" } ] }