{ "_id": "6ab0ec443d719c1f84084a42", "Package": "rhierbaps", "Type": "Package", "Title": "Clustering Genetic Sequence Data Using the HierBAPS Algorithm", "Version": "1.1.3", "Authors@R": "person(\"Gerry\", \"Tonkin-Hill\", email = \"g.tonkinhill@gmail.com\", role = c(\"cre\", \"aut\"))", "Description": "Implements the hierarchical Bayesian analysis of\npopulations structure (hierBAPS) algorithm of Cheng et al.\n(2013) for clustering DNA sequences\nfrom multiple sequence alignments in FASTA format. The\nimplementation includes improved defaults and plotting\ncapabilities and unlike the original 'MATLAB' version removes\nsingleton SNPs by default.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.0", "VignetteBuilder": "knitr", "URL": "https://github.com/gtonkinhill/rhierbaps", "BugReports": "https://github.com/gtonkinhill/rhierbaps/issues", "Repository": "https://gtonkinhill.r-universe.dev", "Date/Publication": "2026-02-23 05:32:54 UTC", "RemoteUrl": "https://github.com/gtonkinhill/rhierbaps", "RemoteRef": "HEAD", "RemoteSha": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-21 08:31:35 UTC", "User": "root" }, "Author": "Gerry Tonkin-Hill [cre, aut]", "Maintainer": "Gerry Tonkin-Hill ", "_user": "gtonkinhill", "_type": "src", "_file": "rhierbaps_1.1.3.tar.gz", "_fileid": "https://r2.ropensci.org/29d7a3f84f2bcb95a59052f936e463dc0c896e0cc90a22acc917eb6a29aa4c5e", "_filesize": 1457318, "_sha256": "29d7a3f84f2bcb95a59052f936e463dc0c896e0cc90a22acc917eb6a29aa4c5e", "_expires": "2026-12-30T08:35:14.000Z", "_created": "2026-09-21T08:31:35.000Z", "_published": "2026-09-21T08:35:16.080Z", "_jobs": [ { "job": 106265310385, "time": 158, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10628379514" }, { "job": 106265310452, "time": 160, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10628114960" }, { "job": 106265310490, "time": 176, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10629276492" }, { "job": 106265310481, "time": 165, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10629236517" }, { "job": 106263921102, "time": 302, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10628881104" }, { "job": 106265310337, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10629590117" }, { "job": 106265310538, "time": 89, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10628673842" }, { "job": 106265310383, "time": 76, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10629785178" }, { "job": 106265310430, "time": 118, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10628124638" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760", "_status": "success", "_upstream": "https://github.com/gtonkinhill/rhierbaps", "_commit": { "id": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "author": "Gerry Tonkin-Hill ", "committer": "GitHub ", "message": "Refactor R-CMD-check workflow for efficiency", "time": 1771824774 }, "_maintainer": { "name": "Gerry Tonkin-Hill", "email": "g.tonkinhill@gmail.com", "login": "gtonkinhill", "description": "Research group leader at Peter Mac & Doherty Institute\n| previously at UiO, Sanger & Cambridge\n| microbial genomics, statistics, machine learning", "uuid": 10625107 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "ape", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "ggtree", "role": "Suggests" }, { "package": "phytools", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "formatR", "role": "Suggests" } ], "_owner": "gtonkinhill", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-09", "n": 4 } ], "_tags": [], "_topics": [ "population-genetics", "population-genomics", "population-structure" ], "_stars": 36, "_contributors": [ { "user": "gtonkinhill", "count": 47, "uuid": 10625107 } ], "_userbio": { "uuid": 10625107, "type": "user", "name": "Gerry Tonkin-Hill", "followers": 178, "description": "Research group leader at Peter Mac & Doherty Institute\r\n| previously at UiO, Sanger & Cambridge\r\n| microbial genomics, statistics, machine learning" }, "_downloads": { "count": 357, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rhierbaps" }, "_mentions": 1, "_devurl": "https://github.com/gtonkinhill/rhierbaps", "_searchresults": 43, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/rhierbaps.html", "LICENSE" ], "_homeurl": "https://github.com/gtonkinhill/rhierbaps", "_realowner": "gtonkinhill", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2018-07-20" }, { "version": "1.1.0", "date": "2018-10-10" }, { "version": "1.1.2", "date": "2019-05-10" }, { "version": "1.1.3", "date": "2019-12-11" }, { "version": "1.1.4", "date": "2022-11-18" } ], "_exports": [ "hierBAPS", "load_fasta", "plot_sub_cluster", "save_lml_logs" ], "_help": [ { "page": "calc_change_in_ml", "title": "calc_change_in_ml", "topics": [ "calc_change_in_ml" ] }, { "page": "calc_log_ml", "title": "calc_log_ml", "topics": [ "calc_log_ml" ] }, { "page": "hierBAPS", "title": "hierBAPS", "topics": [ "hierBAPS" ] }, { "page": "join_units_2", "title": "join_units_2", "topics": [ "join_units_2" ] }, { "page": "load_fasta", "title": "load_fasta", "topics": [ "load_fasta" ] }, { "page": "model_search_parallel", "title": "model_search_parallel", "topics": [ "model_search_parallel" ] }, { "page": "move_units_1", "title": "move_units_1", "topics": [ "move_units_1" ] }, { "page": "plot_sub_cluster", "title": "plot_sub_cluster", "topics": [ "plot_sub_cluster" ] }, { "page": "preproc_alignment", "title": "preproc_alignment", "topics": [ "preproc_alignment" ] }, { "page": "reallocate_units_4", "title": "reallocate_units_4", "topics": [ "reallocate_units_4" ] }, { "page": "save_lml_logs", "title": "save_lml_logs", "topics": [ "save_lml_logs" ] }, { "page": "split_clusters_3", "title": "split_clusters_3", "topics": [ "split_clusters_3" ] } ], "_readme": "https://github.com/gtonkinhill/rhierbaps/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "cpp11", "digest", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "matrixStats", "nlme", "patchwork", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "introduction.Rmd", "filename": "introduction.html", "title": "Introduction to rhierbaps", "author": "Gerry Tonkin-Hill", "engine": "knitr::rmarkdown", "headings": [ "Libraries", "Loading data", "Running hierBAPS", "Plotting results", "Caculating assignment probabilities", "Saving results", "Citing rhierbaps", "References", "Session Information" ], "created": "2017-11-24 15:03:35", "modified": "2019-05-09 21:00:36", "commits": 14 } ], "_score": 5.888740960682893, "_indexed": true, "_nocasepkg": "rhierbaps", "_universes": [ "gtonkinhill" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.3", "date": "2026-09-21T08:34:04.000Z", "distro": "resolute", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/0f7070973589d699bbbcb15a63c5ed86e2f51c7084a4e44dd73eef5d257df0d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" }, { "r": "4.6.1", "os": "linux", "version": "1.1.3", "date": "2026-09-21T08:34:13.000Z", "distro": "resolute", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/cffe52a18093521fcb1fa4bd9986dfb2632e8fb003eeacc32866b50e01bfe5a9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" }, { "r": "4.5.3", "os": "mac", "version": "1.1.3", "date": "2026-09-21T08:34:02.000Z", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/79b1ad64778da52703462e59d33e0cec89db2d33dd97965586253b417d769762", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" }, { "r": "4.6.1", "os": "mac", "version": "1.1.3", "date": "2026-09-21T08:33:41.000Z", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/fc7f97a73b722a0c01d9536f055c8eb12d27d94a02563a0e670b4ee4283818b9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.3", "date": "2026-09-21T08:34:02.000Z", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/d6a692fe59482a69c7df3653e7b596ac447e0692f14b508ddad189a829701d2e", "status": "success", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" }, { "r": "4.7.0", "os": "win", "version": "1.1.3", "date": "2026-09-21T08:32:49.000Z", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/a054365444b35f0dba9794d0ed155cd4f45fee43e00ef021fcb7f36a54fc843e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" }, { "r": "4.5.3", "os": "win", "version": "1.1.3", "date": "2026-09-21T08:32:45.000Z", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/75b9771a67b31f48a29a6bc2ce508a10ecf4689f0554e8a949d7200d525aa5c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" }, { "r": "4.6.1", "os": "win", "version": "1.1.3", "date": "2026-09-21T08:33:26.000Z", "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544", "fileid": "https://r2.ropensci.org/508cd22d8f0a5ff83c8c87c70c5566cce75e914c87b5907b9b5bef8a0e7be0fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/35577912760" } ] }