{ "_id": "6a169ce4acfb0bcc41d7ead5", "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": "2026-05-27 07:15:08 UTC", "User": "root" }, "Author": "Alexander M. Sandercock [aut, cre] (ORCID:\n)", "Maintainer": "Alexander M. Sandercock ", "MD5sum": "782a8829929fb36715cc578e5e51d36c", "_user": "alex-sandercock", "_type": "src", "_file": "castgen_1.0.2.tar.gz", "_fileid": "b29a845cccee88bd6f936d201eb312fc952174a153b165ef2d40501fceff44b1", "_filesize": 95692, "_sha256": "b29a845cccee88bd6f936d201eb312fc952174a153b165ef2d40501fceff44b1", "_created": "2026-05-27T07:15:08.000Z", "_published": "2026-05-27T07:27:32.378Z", "_distro": "noble", "_jobs": [ { "job": 78026549291, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7234209442" }, { "job": 78026549255, "time": 149, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7234204157" }, { "job": 78026549292, "time": 192, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7234364671" }, { "job": 78026549312, "time": 235, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7234325555" }, { "job": 78025891797, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7234158490" }, { "job": 78026549343, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7234189078" }, { "job": 78026549289, "time": 123, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7234196301" }, { "job": 78026549437, "time": 95, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7234187129" }, { "job": 78026549360, "time": 107, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7234191583" } ], "_buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615", "_status": "success", "_host": "GitHub-Actions", "_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" }, "_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", "description": "Genomics Coordinator @Breeding-Insight " }, "_downloads": { "count": 164, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/castgen" }, "_devurl": "https://github.com/alex-sandercock/castgen", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/castgen.html", "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", "manual.pdf" ], "_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": "2026-05-27T07:17:34.000Z", "distro": "noble", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "a374adc50a464f0efb60335fc036a901f2d99a326c96fadc9fe919633e3a485a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" }, { "r": "4.6.0", "os": "linux", "version": "1.0.2", "date": "2026-05-27T07:17:17.000Z", "distro": "noble", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "e6ad35b5ae4b3fcec4bc23cac63446579096fc8cfcb561efc44fa34c17e61851", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2", "date": "2026-05-27T07:26:16.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "ea06084c5c815d02b5defcbe6e5fdfc5c66f512e194a732de5b64a8758dd5c80", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" }, { "r": "4.6.0", "os": "mac", "version": "1.0.2", "date": "2026-05-27T07:23:47.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "020e67ccc89e35a7933a17d6e2f127e5e39590f0ed46483ff52a93c62a26fbc9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2", "date": "2026-05-27T07:17:07.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "2083e741fa899d3882d6255d36498a8acb84c7fc91349715ec5784170ee150a8", "status": "success", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" }, { "r": "4.7.0", "os": "win", "version": "1.0.2", "date": "2026-05-27T07:16:50.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "a52b1bc99044ed18b6111da71ace9224feff216adc206db3c6b29ffbb69e2cd6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" }, { "r": "4.5.3", "os": "win", "version": "1.0.2", "date": "2026-05-27T07:16:19.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "83d8201be6f8e6ded03528fce312e18dd667d0ad13267271d559c555500525da", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" }, { "r": "4.6.0", "os": "win", "version": "1.0.2", "date": "2026-05-27T07:16:32.000Z", "commit": "2a218145cea3ebebad9d8a54fdcbb688bf883e46", "fileid": "44c7267d0490a352d68073e215ee90fd5ffb6ec7d42cc624e3d6136b231c7845", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alex-sandercock/actions/runs/26496488615" } ] }