{ "_id": "6a489a8de06c18f0a6542dbd", "Package": "popkin", "Title": "Estimate Kinship and FST under Arbitrary Population Structure", "Version": "1.3.25.9000", "Authors@R": "c(\nperson(given = \"Alejandro\",\nfamily = \"Ochoa\",\nrole = c(\"aut\", \"cre\"),\nemail = \"alejandro.ochoa@duke.edu\",\ncomment = c(ORCID = \"0000-0003-4928-3403\")),\nperson(given = \"John D.\",\nfamily = \"Storey\",\nrole = c(\"aut\"),\nemail = \"jstorey@princeton.edu\",\ncomment = c(ORCID = \"0000-0001-5992-402X\"))\n)", "Description": "Provides functions to estimate the kinship matrix of\nindividuals from a large set of biallelic SNPs, and extract\ninbreeding coefficients and the generalized FST (Wright's\nfixation index). Method described in Ochoa and Storey (2021)\n.", "LazyData": "true", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://github.com/StoreyLab/popkin/", "BugReports": "https://github.com/StoreyLab/popkin/issues", "Repository": "https://storeylab.r-universe.dev", "Date/Publication": "2026-01-27 19:05:12 UTC", "RemoteUrl": "https://github.com/storeylab/popkin", "RemoteRef": "HEAD", "RemoteSha": "a5d45b5f26f6c88e01099356572c72c18e07a922", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 05:17:35 UTC", "User": "root" }, "Author": "Alejandro Ochoa [aut, cre] (ORCID:\n),\nJohn D. Storey [aut] (ORCID: )", "Maintainer": "Alejandro Ochoa ", "_user": "storeylab", "_type": "src", "_file": "popkin_1.3.25.9000.tar.gz", "_fileid": "https://r2.ropensci.org/cd95df9d1d43a78bc17372aec7d51aef5da2d06f48b062b493f08b970d7295f9", "_filesize": 1552702, "_sha256": "cd95df9d1d43a78bc17372aec7d51aef5da2d06f48b062b493f08b970d7295f9", "_expires": "2026-10-12T05:30:51.000Z", "_created": "2026-07-04T05:17:35.000Z", "_published": "2026-07-04T05:30:53.150Z", "_jobs": [ { "job": 85105556897, "time": 128, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8078613758" }, { "job": 85105556875, "time": 122, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8078612763" }, { "job": 85105556858, "time": 80, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8078666637" }, { "job": 85105556864, "time": 85, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8078687175" }, { "job": 85105377536, "time": 163, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8078597625" }, { "job": 85105556855, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8078614393" }, { "job": 85105556861, "time": 65, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8078606008" }, { "job": 85105556887, "time": 76, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8078607183" }, { "job": 85105556860, "time": 70, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8078606514" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414", "_status": "success", "_upstream": "https://github.com/storeylab/popkin", "_commit": { "id": "a5d45b5f26f6c88e01099356572c72c18e07a922", "author": "Alejandro Ochoa Garcia ", "committer": "Alejandro Ochoa Garcia ", "message": "Function `plot_popkin` added options `xlab`, `xlab_adj`, `xlab_line`, and `xlab_side`\n", "time": 1769540712 }, "_maintainer": { "name": "Alejandro Ochoa", "email": "alejandro.ochoa@duke.edu", "login": "alexviiia", "orcid": "0000-0003-4928-3403", "description": "Statistical geneticist, computational biologist. Well-rounded nerd, also love languages and music.", "uuid": 12603341 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "BEDMatrix", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "bnpsd", "role": "Suggests" } ], "_owner": "storeylab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-01", "n": 1 }, { "week": "2026-05", "n": 1 } ], "_tags": [], "_stars": 21, "_contributors": [ { "user": "alexviiia", "count": 172, "uuid": 12603341 } ], "_userbio": { "uuid": 8007641, "type": "organization", "name": "Storey Lab", "followers": 21, "description": "Storey Lab at Princeton University" }, "_downloads": { "count": 381, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/popkin" }, "_mentions": 2, "_devurl": "https://github.com/storeylab/popkin", "_searchresults": 107, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/popkin.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/storeylab/popkin", "_realowner": "storeylab", "_cranurl": true, "_releases": [ { "version": "1.0.4", "date": "2018-01-15" }, { "version": "1.0.5", "date": "2018-01-26" }, { "version": "1.1.2", "date": "2019-02-14" }, { "version": "1.2.2", "date": "2019-05-13" }, { "version": "1.3.0", "date": "2019-12-18" }, { "version": "1.3.7", "date": "2021-02-09" }, { "version": "1.3.8", "date": "2021-02-11" }, { "version": "1.3.13", "date": "2021-07-27" }, { "version": "1.3.17", "date": "2022-01-27" }, { "version": "1.3.23", "date": "2023-01-07" } ], "_exports": [ "admix_label_cols", "admix_order_cols", "avg_kinship_subpops", "fst", "inbr", "inbr_diag", "mean_kinship", "n_eff", "plot_admix", "plot_phylo", "plot_popkin", "popkin", "popkin_A", "popkin_A_min_subpops", "popkin_af", "pwfst", "rescale_popkin", "validate_kinship", "weights_subpops" ], "_datasets": [ { "name": "hgdp_subset", "title": "HGDP subset", "object": "hgdp_subset", "class": [ "matrix", "array" ], "fields": [ "EUROPE", "EUROPE", "EUROPE", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "AFRICA", "AFRICA", "AFRICA", "AFRICA", "AFRICA", "AFRICA", "EUROPE", "EUROPE", "EUROPE", "MIDDLE_EAST", "MIDDLE_EAST", "MIDDLE_EAST", "AFRICA", "AFRICA", "AFRICA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "AMERICA", "AMERICA", "AMERICA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "MIDDLE_EAST", "MIDDLE_EAST", "MIDDLE_EAST", "EUROPE", "EUROPE", "EUROPE", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EUROPE", "EUROPE", "EUROPE", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "AMERICA", "AMERICA", "AMERICA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "AFRICA", "AFRICA", "AFRICA", "AMERICA", "AMERICA", "AMERICA", "AFRICA", "AFRICA", "AFRICA", "OCEANIA", "OCEANIA", "OCEANIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "MIDDLE_EAST", "MIDDLE_EAST", "MIDDLE_EAST", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EUROPE", "EUROPE", "EUROPE", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "MIDDLE_EAST", "MIDDLE_EAST", "MIDDLE_EAST", "OCEANIA", "OCEANIA", "OCEANIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "AMERICA", "AMERICA", "AMERICA", "EUROPE", "EUROPE", "EUROPE", "AFRICA", "AFRICA", "AFRICA", "EUROPE", "EUROPE", "EUROPE", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "AMERICA", "AMERICA", "AMERICA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EUROPE", "EUROPE", "EUROPE", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "CENTRAL_SOUTH_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "EAST_ASIA", "AFRICA", "AFRICA", "AFRICA" ], "rows": 5000, "table": true, "tojson": true } ], "_help": [ { "page": "popkin-package", "title": "A package for estimating kinship and FST under arbitrary population structure", "topics": [ "popkin-package" ] }, { "page": "admix_label_cols", "title": "Label ancestries based on best match to individual labels", "topics": [ "admix_label_cols" ] }, { "page": "admix_order_cols", "title": "Reorder admixture matrix columns", "topics": [ "admix_order_cols" ] }, { "page": "avg_kinship_subpops", "title": "Calculate a kinship matrix between subpopulations by averaging individual data", "topics": [ "avg_kinship_subpops" ] }, { "page": "fst", "title": "Calculate FST from a population-level kinship matrix or vector of inbreeding coefficients", "topics": [ "fst" ] }, { "page": "hgdp_subset", "title": "HGDP subset", "topics": [ "hgdp_subset" ] }, { "page": "inbr", "title": "Extract inbreeding coefficients from a kinship matrix", "topics": [ "inbr" ] }, { "page": "inbr_diag", "title": "Replace kinship diagonal with inbreeding coefficients", "topics": [ "inbr_diag" ] }, { "page": "mean_kinship", "title": "Calculate the weighted mean kinship", "topics": [ "mean_kinship" ] }, { "page": "n_eff", "title": "Calculates the effective sample size of the data", "topics": [ "n_eff" ] }, { "page": "plot_admix", "title": "Make a structure/admixture plot", "topics": [ "plot_admix" ] }, { "page": "plot_phylo", "title": "Plot a 'phylo' tree object", "topics": [ "plot_phylo" ] }, { "page": "plot_popkin", "title": "Visualize one or more kinship matrices and other related objects", "topics": [ "plot_popkin" ] }, { "page": "popkin", "title": "Estimate kinship from a genotype matrix and subpopulation assignments", "topics": [ "popkin" ] }, { "page": "popkin_A", "title": "Compute popkin's 'A' and 'M' matrices from genotypes", "topics": [ "popkin_A" ] }, { "page": "popkin_A_min_subpops", "title": "Estimate the minimum expected value of a matrix 'A' using subpopulations", "topics": [ "popkin_A_min_subpops" ] }, { "page": "popkin_af", "title": "Estimate coancestry from an allele frequency matrix and subpopulation assignments", "topics": [ "popkin_af" ] }, { "page": "pwfst", "title": "Estimate the individual-level pairwise FST matrix", "topics": [ "pwfst" ] }, { "page": "rescale_popkin", "title": "Rescale kinship matrix to set a given kinship value to zero.", "topics": [ "rescale_popkin" ] }, { "page": "validate_kinship", "title": "Validate a kinship matrix", "topics": [ "validate_kinship" ] }, { "page": "weights_subpops", "title": "Get weights for individuals that balance subpopulations", "topics": [ "weights_subpops" ] } ], "_pkglogo": "https://github.com/storeylab/popkin/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/storeylab/popkin/raw/HEAD/README.md", "_rundeps": [ "ape", "digest", "lattice", "nlme", "RColorBrewer", "Rcpp" ], "_vignettes": [ { "source": "popkin.Rmd", "filename": "popkin.html", "title": "Estimate Kinship and FST under Arbitrary Population Structure with popkin", "author": "Alejandro Ochoa and John D. Storey", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Kinship and inbreeding coefficients", "The generalized $\\Fst$", "The individual-level pairwise $\\Fst$", "Sample usage", "Input genotype data", "Load and clean sample data", "Estimate and visualize kinship using genotypes and subpopulations", "Estimate $\\Fst$ and individual inbreeding from a kinship matrix", "Estimate individual-level pairwise $\\Fst$ matrix from a kinship matrix", "Rescale kinship matrix in a subset of the data", "Plot multiple kinship matrices together", "Plot kinship matrices with multiple levels of labels", "Coancestry estimation from allele frequencies", "Admixture plot example", "References" ], "created": "2017-05-05 21:33:53", "modified": "2023-01-06 23:35:36", "commits": 22 } ], "_score": 6.6526330680831105, "_indexed": true, "_nocasepkg": "popkin", "_universes": [ "storeylab", "alexviiia" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.25.9000", "date": "2026-07-04T05:19:43.000Z", "distro": "resolute", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/1ec4812820c1fd03865f217844ef7e0878e66694abad32fa92c1abe0bebfdea3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" }, { "r": "4.6.1", "os": "linux", "version": "1.3.25.9000", "date": "2026-07-04T05:19:38.000Z", "distro": "resolute", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/eebc81385d80fa02c27c16c78e4f25aedaf835084b8bfa318ef4256de43b359b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" }, { "r": "4.5.3", "os": "mac", "version": "1.3.25.9000", "date": "2026-07-04T05:27:15.000Z", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/d8c8a6e863cf5d548234551778241cb2704f200a8f9e9392294a5167dc1e2ba3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" }, { "r": "4.6.1", "os": "mac", "version": "1.3.25.9000", "date": "2026-07-04T05:30:21.000Z", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/7f175684c0c2a54fe0891b287a48a6595a8b9ebff2468f34b384cf3b9666922a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.25.9000", "date": "2026-07-04T05:20:05.000Z", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/39c77cd3913ddafcd35f80b85aedc4383ead058a016b4cbc0ccab4de7bad6c31", "status": "success", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" }, { "r": "4.7.0", "os": "win", "version": "1.3.25.9000", "date": "2026-07-04T05:18:37.000Z", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/db7aabff147b93442b45966b0270c41b402482032eadab26d90ac82736e39851", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" }, { "r": "4.5.3", "os": "win", "version": "1.3.25.9000", "date": "2026-07-04T05:18:45.000Z", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/5fb689d49e66599623c778cc7cbc52f4b5635a6a2c66b0467f3c24d29b93c3b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" }, { "r": "4.6.1", "os": "win", "version": "1.3.25.9000", "date": "2026-07-04T05:18:40.000Z", "commit": "a5d45b5f26f6c88e01099356572c72c18e07a922", "fileid": "https://r2.ropensci.org/5de6745b72f9d5a2f1a5c191fd39bf52a7c35f6a70be8f9bf793f66c7267ad1b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/storeylab/actions/runs/28695933414" } ] }