{ "_id": "6a16992dacfb0bcc41d7d6a1", "Package": "whoa", "Type": "Package", "Title": "Evaluation of Genotyping Error in Genotype-by-Sequencing Data", "Version": "0.0.2", "Authors@R": "c(\nperson(given = c(\"Eric\", \"C.\"), family = \"Anderson\", email = \"eric.anderson@noaa.gov\", role = c(\"aut\", \"cre\"))\n)", "Maintainer": "Eric C. Anderson ", "Description": "This is a small, lightweight package that lets users\ninvestigate the distribution of genotypes in\ngenotype-by-sequencing (GBS) data where they expect (by and\nlarge) Hardy-Weinberg equilibrium, in order to assess rates of\ngenotyping errors and the dependence of those rates on read\ndepth. It implements a Markov chain Monte Carlo (MCMC) sampler\nusing 'Rcpp' to compute a Bayesian estimate of what we call the\nheterozygote miscall rate for restriction-associated digest\n(RAD) sequencing data and other types of reduced representation\nGBS data. It also provides functions to generate plots of\nexpected and observed genotype frequencies. Some background on\nthese topics can be found in a recent paper \"Recent advances in\nconservation and population genomics data analysis\" by\nHendricks et al. (2018) , and another\npaper describing the MCMC approach is in preparation with\nGordon Luikart and Thierry Gosselin.", "License": "CC0", "Encoding": "UTF-8", "LazyData": "TRUE", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://eriqande.r-universe.dev", "Date/Publication": "2021-08-09 22:55:58 UTC", "RemoteUrl": "https://github.com/eriqande/whoa", "RemoteRef": "HEAD", "RemoteSha": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-27 07:04:09 UTC", "User": "root" }, "Author": "Eric C. Anderson [aut, cre]", "MD5sum": "1e98031e14969c08ed30e12c0326b71e", "_user": "eriqande", "_type": "src", "_file": "whoa_0.0.2.tar.gz", "_fileid": "17d8ac1bf61952781adc8d77219699208be3f8d3cb159971a43dc68d9c16cb23", "_filesize": 631110, "_sha256": "17d8ac1bf61952781adc8d77219699208be3f8d3cb159971a43dc68d9c16cb23", "_created": "2026-05-27T07:04:09.000Z", "_published": "2026-05-27T07:11:41.088Z", "_distro": "noble", "_jobs": [ { "job": 78025070319, "time": 155, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7234022779" }, { "job": 78025070295, "time": 148, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7234021028" }, { "job": 78025070280, "time": 144, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7234019897" }, { "job": 78025070292, "time": 186, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7234031861" }, { "job": 78025070258, "time": 150, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7234014089" }, { "job": 78025070270, "time": 404, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7234081810" }, { "job": 78025070283, "time": 154, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7234017070" }, { "job": 78025070293, "time": 407, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7234083260" }, { "job": 78024571999, "time": 213, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7233978936" }, { "job": 78025070287, "time": 118, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7234012107" }, { "job": 78025070269, "time": 124, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7234013977" }, { "job": 78025070261, "time": 117, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7234011854" }, { "job": 78025070256, "time": 118, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7234012425" } ], "_buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/eriqande/whoa", "_commit": { "id": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "author": "Eric C. Anderson ", "committer": "Eric C. Anderson ", "message": "update cran comments\n", "time": 1628549758 }, "_maintainer": { "name": "Eric C. Anderson", "email": "eric.anderson@noaa.gov", "login": "eriqande", "description": "", "uuid": 2035238 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.16", "role": "Imports" }, { "package": "vcfR", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "eriqande", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 6, "_contributors": [ { "user": "eriqande", "count": 30, "uuid": 2035238 } ], "_userbio": { "uuid": 2035238, "type": "user", "name": "Eric C. Anderson" }, "_downloads": { "count": 747, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/whoa" }, "_mentions": 2, "_devurl": "https://github.com/eriqande/whoa", "_searchresults": 17, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/whoa.html", "manual.pdf" ], "_homeurl": "https://github.com/eriqande/whoa", "_realowner": "eriqande", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2019-08-02" }, { "version": "0.0.2", "date": "2021-08-11" } ], "_exports": [ "bin_depths", "exp_and_obs_geno_freqs", "geno_freq_boundaries", "geno_freq_calc_single", "geno_freqs_scatter", "infer_m", "make_it_012", "posteriors_plot", "prep_vcf_for_est_m_rd", "tidy_m_ests" ], "_datasets": [ { "name": "lobster_buz_2000", "title": "Restriction-associated digest (RAD) sequence data from 36 lobsters at 2000 single nucleotide polymorphisms (SNPs)", "object": "lobster_buz_2000", "class": [ "vcfR" ], "fields": [], "table": false, "tojson": false }, { "name": "lobster_buz_2000_as_012_matrix", "title": "An 012 matrix from (RAD) sequence data from 36 lobsters at 2000 single nucleotide polymorphisms (SNPs)", "object": "lobster_buz_2000_as_012_matrix", "class": [ "matrix", "array" ], "fields": {}, "rows": 2000, "table": true, "tojson": true } ], "_help": [ { "page": "exp_and_obs_geno_freqs", "title": "Computed expected and observed genotype frequencies from a `vcfR' object", "topics": [ "exp_and_obs_geno_freqs" ] }, { "page": "geno_freqs_scatter", "title": "return a `ggplot2' plot object of observed and expected genotype freqs", "topics": [ "geno_freqs_scatter" ] }, { "page": "infer_m", "title": "get posterior estimates for m from different read depth categories", "topics": [ "infer_m" ] }, { "page": "lobster_buz_2000", "title": "Restriction-associated digest (RAD) sequence data from 36 lobsters at 2000 single nucleotide polymorphisms (SNPs)", "topics": [ "lobster_buz_2000" ] }, { "page": "lobster_buz_2000_as_012_matrix", "title": "An 012 matrix from (RAD) sequence data from 36 lobsters at 2000 single nucleotide polymorphisms (SNPs)", "topics": [ "lobster_buz_2000_as_012_matrix" ] }, { "page": "make_it_012", "title": "just a quick function for making an 012 matrix from a character matrix", "topics": [ "make_it_012" ] }, { "page": "posteriors_plot", "title": "return a `ggplot2' plot object of the posterior esimates for heterozyote miscall rates", "topics": [ "posteriors_plot" ] }, { "page": "whoa", "title": "whoa: Evaluation of genotyping error in genotype by sequencing data", "topics": [ "whoa" ] } ], "_readme": "https://github.com/eriqande/whoa/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "cluster", "cpp11", "digest", "dplyr", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memuse", "mgcv", "nlme", "permute", "pillar", "pinfsc50", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vcfR", "vctrs", "vegan", "viridis", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "whoa_tutorial.Rmd", "filename": "whoa_tutorial.html", "title": "whoa Tutorial", "author": "Eric C. Anderson", "engine": "knitr::rmarkdown", "headings": [ "A quick run", "Packages", "Lobster data", "Make a quick genotype frequency scatter plot", "Now infer an overall heterozygote miscall rate.", "Now infer a miscall rate for read depth bins" ], "created": "2018-09-05 18:46:40", "modified": "2019-08-01 19:19:24", "commits": 4 } ], "_score": 5.008600171761918, "_indexed": true, "_nocasepkg": "whoa", "_universes": [ "eriqande" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.2", "date": "2026-05-27T07:06:36.000Z", "distro": "noble", "arch": "aarch64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "72df869fd7654fa9162b078bcc37eb880a56c88511f3653a88878f0c229fbeb4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.7.0", "os": "linux", "version": "0.0.2", "date": "2026-05-27T07:06:29.000Z", "distro": "noble", "arch": "x86_64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "d5c32668d0baec3b1db47b18d09e36dd36bcce8e39cb5c28ffc229d7bebd6024", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.6.0", "os": "linux", "version": "0.0.2", "date": "2026-05-27T07:06:31.000Z", "distro": "noble", "arch": "aarch64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "0d61cc39dcc8e7edfebf0dfcc797dd1c4f2192bd8d8104765e1f369b5108cb91", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.6.0", "os": "linux", "version": "0.0.2", "date": "2026-05-27T07:07:07.000Z", "distro": "noble", "arch": "x86_64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "52291ded5eb46a51d23513cb5a63c037db548752858a755849794d6b4e3a3fcb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.5.3", "os": "mac", "version": "0.0.2", "date": "2026-05-27T07:06:18.000Z", "arch": "aarch64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "06709ffb08024f7f335a667a394e870bd974172ed873e7e796d1693b8837940f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.5.3", "os": "mac", "version": "0.0.2", "date": "2026-05-27T07:09:27.000Z", "arch": "x86_64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "f1936744cc4506cc97412f56d89536d145045fb31fec81c772ec9e16a52edc47", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.6.0", "os": "mac", "version": "0.0.2", "date": "2026-05-27T07:06:22.000Z", "arch": "aarch64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "a8bdd60787a47cf67722b636284f2117f3c43da910407d444cc382cd414330f6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.6.0", "os": "mac", "version": "0.0.2", "date": "2026-05-27T07:08:58.000Z", "arch": "x86_64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "29f89338dc26ee888e3711fb260fdc4a8bbd0b26ddda9c6a82e0cd5bf11d023a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.2", "date": "2026-05-27T07:06:24.000Z", "arch": "emscripten", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "2bf24ea35b963f0c6b3e2b53a6770bd25f4da2c96792532bc045e2eca6bd5ec1", "status": "success", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.7.0", "os": "win", "version": "0.0.2", "date": "2026-05-27T07:05:41.000Z", "arch": "x86_64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "b99d55832ca33735d2e26b8a04f810ab4c4911c3f6163f3ba923a0236d3bd69b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.5.3", "os": "win", "version": "0.0.2", "date": "2026-05-27T07:05:35.000Z", "arch": "x86_64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "9fa5ad233c7243b13bfbc4a116792f0ddb657b0a8eb6248e260bf9d0d7e76ca5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" }, { "r": "4.6.0", "os": "win", "version": "0.0.2", "date": "2026-05-27T07:05:33.000Z", "arch": "x86_64", "commit": "831f589d21e7ed2ad34ae46eff635dbab95c4271", "fileid": "d0b67bda95115691741577a6e59a93b2d2df5016c3127f2bb24da20ff87be5b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eriqande/actions/runs/26496079103" } ] }