{ "_id": "6ad09d70576abc75bd5cda5f", "Package": "castgen", "Title": "Estimate Sample Size for Population Genomic Studies", "Version": "1.0.2", "Authors@R": "person(\"Alexander M.\", \"Sandercock\", , \"ams866@cornell.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"https://orcid.org/0000-0001-6897-1856\"))", "Description": "Estimate sample sizes needed to capture target levels of\ngenetic diversity from a population (multivariate allele\nfrequencies) for applications like germplasm conservation and\nbreeding efforts. Compares bootstrap samples to a full\npopulation using linear regression, employing the R-squared\nvalue to represent the proportion of diversity captured.\nIteratively increases sample size until a user-defined target\nR-squared is met. Offers a parallelized R implementation of a\npreviously developed 'python' method. All ploidy levels are\nsupported. For more details, see Sandercock et al. (2024)\n.", "License": "Apache License (>= 2)", "URL": "https://github.com/alex-sandercock/castgen", "BugReports": "https://github.com/alex-sandercock/castgen/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://alex-sandercock.r-universe.dev", "Date/Publication": "2025-04-02 20:01:46 UTC", "RemoteUrl": "https://github.com/alex-sandercock/castgen", "RemoteRef": "HEAD", "RemoteSha": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-15 09:16:11 UTC", "User": "root" }, "Author": "Alexander M. Sandercock [aut, cre] (ORCID:\n)", "Maintainer": "Alexander M. Sandercock ", "_user": "alex-sandercock", "_type": "src", "_file": "castgen_1.0.2.tar.gz", "_fileid": "https://r2.ropensci.org/1251be473d13a2a706cf558349366dfbbb13e8cc97d81b9f5732fd678629ecbd", "_filesize": 96908, "_sha256": "1251be473d13a2a706cf558349366dfbbb13e8cc97d81b9f5732fd678629ecbd", "_expires": "2027-01-23T09:31:26.000Z", "_created": "2026-10-15T09:16:11.000Z", "_published": "2026-10-15T09:31:27.943Z", "_buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116344510830, "time": 133, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11961625674" }, { "job": 116344510874, "time": 139, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11960373607" }, { "job": 116344510764, "time": 202, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11960484371" }, { "job": 116344510850, "time": 168, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11961568378" }, { "job": 116343287360, "time": 174, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11961121322" }, { "job": 116344510935, "time": 93, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11960692357" }, { "job": 116344510727, "time": 99, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11960652321" }, { "job": 116344510806, "time": 92, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11960802291" }, { "job": 116344510720, "time": 97, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11961027203" } ], "_upstream": "https://github.com/alex-sandercock/castgen", "_commit": { "id": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "author": "Alexander Sandercock <39815775+alex-sandercock@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #2 from alex-sandercock/development\n\nv1.0.2", "time": 1743624106 }, "_maintainer": { "name": "Alexander M. Sandercock", "email": "ams866@cornell.edu", "login": "amsande", "description": "", "uuid": 222830770, "orcid": "0000-0001-6897-1856" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "doParallel", "version": ">= 1.0.17", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.2", "role": "Imports" }, { "package": "foreach", "version": ">= 1.5.2", "role": "Imports" }, { "package": "parallel", "version": ">= 4.0.0", "role": "Imports" }, { "package": "Rdpack", "version": ">= 0.7", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "vcfR", "version": ">= 1.15.0", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "alex-sandercock", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "breeding", "conservation", "genomics" ], "_stars": 1, "_contributors": [ { "user": "alex-sandercock", "count": 25, "uuid": 39815775 } ], "_userbio": { "uuid": 39815775, "type": "user", "name": "Alexander Sandercock", "followers": 6, "description": "UF|IFAS Assistant Scientist and Genomics Coordinator @Breeding-Insight " }, "_downloads": { "count": 304, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/castgen" }, "_devurl": "https://github.com/alex-sandercock/castgen", "_searchresults": 3, "_rbuild": "4.6.1", "_assets": [ "extra/castgen.html", "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" ], "_homeurl": "https://github.com/alex-sandercock/castgen", "_realowner": "alex-sandercock", "_cranurl": true, "_releases": [ { "version": "1.0.2", "date": "2025-04-02" } ], "_exports": [ "capture_diversity.Gmat", "capture_diversity.VCF" ], "_help": [ { "page": "capture_diversity.Gmat", "title": "Estimate Minimum Number of Individuals to Sample to Capture Population Genomic Diversity (Genotype Matrix)", "topics": [ "capture_diversity.Gmat" ] }, { "page": "capture_diversity.VCF", "title": "Estimate Minimum Number of Individuals to Sample to Capture Population Genomic Diversity (VCF)", "topics": [ "capture_diversity.VCF" ] } ], "_readme": "https://github.com/alex-sandercock/castgen/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "cluster", "codetools", "digest", "doParallel", "dplyr", "foreach", "generics", "glue", "iterators", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memuse", "mgcv", "nlme", "permute", "pillar", "pinfsc50", "pkgconfig", "R6", "rbibutils", "Rcpp", "Rdpack", "rlang", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vcfR", "vctrs", "vegan", "viridisLite", "withr" ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "castgen", "_universes": [ "alex-sandercock", "amsande" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2", "date": "2026-10-15T09:18:04.000Z", "distro": "resolute", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/095eba35733fd7bcc87f9abdc3ec64b4d3b11b2a91270619f6c0599a99b6a3fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" }, { "r": "4.6.1", "os": "linux", "version": "1.0.2", "date": "2026-10-15T09:18:10.000Z", "distro": "resolute", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/61affb2ecfab343775cd72d881e9e9c6b38d2b350afab35ca8aca43a7b105d43", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2", "date": "2026-10-15T09:27:33.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/4257649fe43752428fb2d8da236338cd31e0a9bcd37c2a1f28cafb45c368cc8c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" }, { "r": "4.6.1", "os": "mac", "version": "1.0.2", "date": "2026-10-15T09:30:02.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/fa09e13b1a56abaa8ae0cfb7fc10f505a722cdd69799cc93f232679814a548e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2", "date": "2026-10-15T09:18:02.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/6fc4fdee4b5fe01ece248c260d4789ace5ec24ee421a272da4f60a37a4466f0e", "status": "success", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" }, { "r": "4.7.0", "os": "win", "version": "1.0.2", "date": "2026-10-15T09:17:27.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/e6e15383b3920e56e49038324847cab89ad473ab98bfe134a77efad1ff704fef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" }, { "r": "4.5.3", "os": "win", "version": "1.0.2", "date": "2026-10-15T09:17:21.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/aa8f1ca47c726bd6a0606bdaca1c77342b192369f8c9abb82ab45c56e15f4d83", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" }, { "r": "4.6.1", "os": "win", "version": "1.0.2", "date": "2026-10-15T09:17:22.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "https://r2.ropensci.org/55b0239297cde6b054e355b3b923c2fea54b1faaf3c63f06bddc6cf2c02a4c69", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/38711329602" } ] }