{ "_id": "6adb26331206290b6ab7642f", "Package": "AdmixPoly", "Type": "Package", "Title": "Global and Local Admixture Inference in Polyploids", "Version": "1.0.1", "Authors@R": "c(\nperson(\"Simon\", \"Rio\", , \"simon.rio@cirad.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7014-8789\")),\nperson(\"Tristan\", \"Mary-Huard\", , \"tristan.mary-huard@agroparistech.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-3839-9067\")),\nperson(\"Franck\", \"Gauthier\", , \"franck.gauthier@inrae.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0574-065X\"))\n)", "Description": "Provides functions to perform global (genome-wide) and\nlocal admixture inference from bi- and multi-allelic marker\ndosages (discrete or continuous) in polyploid species.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "NeedsCompilation": "yes", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Language": "en-US", "SystemRequirements": "A system with a C++ compiler supporting OpenMP", "Config/testthat/edition": "3", "Packaged": { "Date": "2026-10-23 09:11:40 UTC", "User": "root" }, "Author": "Simon Rio [aut, cre] (ORCID:\n), Tristan Mary-Huard\n[aut] (ORCID: ), Franck\nGauthier [aut] (ORCID: )", "Maintainer": "Simon Rio ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-06-17 21:40:14 UTC", "RemoteUrl": "https://github.com/cran/AdmixPoly", "RemoteRef": "HEAD", "RemoteSha": "9f516f85921599adf9a16121252a8c8451f644ce", "_user": "cran", "_type": "src", "_file": "AdmixPoly_1.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/f6b23d2afdabff94490467c650a6932243aa5a96c82c0486cef0c031cdc13045", "_filesize": 419186, "_sha256": "f6b23d2afdabff94490467c650a6932243aa5a96c82c0486cef0c031cdc13045", "_expires": "2027-01-31T09:17:37.000Z", "_created": "2026-10-23T09:11:40.000Z", "_published": "2026-10-23T09:17:39.265Z", "_upstream": "https://github.com/cran/AdmixPoly", "_status": "success", "_maintainer": { "name": "Simon Rio", "email": "simon.rio@cirad.fr", "login": "simonrio", "description": "", "uuid": 74704960, "orcid": "0000-0001-7014-8789" }, "_jobs": [ { "job": 120336324701, "time": 138, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12491063421" }, { "job": 120336324859, "time": 237, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12490973717" }, { "job": 120336324932, "time": 141, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12490938602" }, { "job": 120336324839, "time": 183, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12491361650" }, { "job": 120334548368, "time": 261, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12491027897" }, { "job": 120336324729, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12491251867" }, { "job": 120336324805, "time": 275, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12491148715" }, { "job": 120336324912, "time": 219, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12491108315" }, { "job": 120336324853, "time": 264, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12491019060" }, { "job": 120336324772, "time": 195, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12491068426" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391", "_commit": { "id": "9f516f85921599adf9a16121252a8c8451f644ce", "author": "Simon Rio ", "committer": "cran-robot ", "message": "version 1.0.1\n", "time": 1781732414 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.1.0", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-24", "n": 1 }, { "week": "2026-25", "n": 1 } ], "_tags": [ { "name": "1.0.0", "date": "2026-06-08" }, { "name": "1.0.1", "date": "2026-06-17" } ], "_stars": 1, "_contributors": [ { "user": "simonrio", "count": 2, "uuid": 74704960 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 438, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/AdmixPoly" }, "_searchresults": 0, "_topics": [ "openblas", "cpp", "openmp" ], "_rbuild": "4.6.1", "_assets": [ "extra/AdmixPoly.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_realowner": "simonrio", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2026-06-08" }, { "version": "1.0.1", "date": "2026-06-17" } ], "_exports": [ "AdmixGlobal", "AdmixLocal", "GlobalPlot", "LocalPlot", "ReadHPA", "ReadVCF", "SimulatePop" ], "_help": [ { "page": "AdmixPoly-package", "title": "AdmixPoly: Global and Local Admixture Inference in Polyploids", "topics": [ "AdmixPoly-package", "AdmixPoly" ] }, { "page": "AdmixGlobal", "title": "Expectation-Maximization algorithm for global (genome-wide) admixture inference", "topics": [ "AdmixGlobal" ] }, { "page": "AdmixLocal", "title": "Forward-Backward algorithm for local admixture inference", "topics": [ "AdmixLocal" ] }, { "page": "ComputeLogLik", "title": "Calculate the log-likelihood", "topics": [ "ComputeLogLik" ] }, { "page": "GlobalPlot", "title": "Plot global admixture proportions", "topics": [ "GlobalPlot" ] }, { "page": "LocalPlot", "title": "Plot local ancestry dosages", "topics": [ "LocalPlot" ] }, { "page": "ReadHPA", "title": "Read Haplotype Presence-Absence (HPA) file", "topics": [ "ReadHPA" ] }, { "page": "ReadVCF", "title": "Read VCF file", "topics": [ "ReadVCF" ] }, { "page": "SimulatePop", "title": "Simulate an admixed polyploid population characterized for multi-allelic markers", "topics": [ "SimulatePop" ] }, { "page": "UpdateParam", "title": "Update Prop and Freq parameters for EM step", "topics": [ "UpdateParam" ] } ], "_readme": "https://github.com/cran/AdmixPoly/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "data.table", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "AdmixPoly-vignette.Rmd", "filename": "AdmixPoly-vignette.html", "title": "AdmixPoly-vignette", "author": "Simon Rio", "engine": "knitr::rmarkdown", "headings": [ "Simulate admixed population", "Unsupervised global admixture inference", "Semi-supervised global admixture inference", "Local admixture inference", "Import genotyping data" ], "created": "2026-06-08 19:30:20", "modified": "2026-06-08 19:30:20", "commits": 1 } ], "_score": 3, "_indexed": false, "_nocasepkg": "admixpoly", "_universes": [ "cran" ], "_indexurl": "https://simonrio.r-universe.dev/AdmixPoly", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-10-23T09:13:58.000Z", "distro": "resolute", "arch": "aarch64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/a8f08f8f5cfe4d9163edc3e2814550b473cf8e41e6466c31c238f0111835b6ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-10-23T09:15:18.000Z", "distro": "resolute", "arch": "x86_64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/37700de66430d43fa6073361103472a4d5bc6d9075293ecd4f1e829c0f3d4ee8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.6.1", "os": "linux", "version": "1.0.1", "date": "2026-10-23T09:14:01.000Z", "distro": "resolute", "arch": "aarch64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/02393b338250dabff66963d8a48c9b9c0af72c53846cbe963bb6e99db638a093", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.6.1", "os": "linux", "version": "1.0.1", "date": "2026-10-23T09:14:34.000Z", "distro": "resolute", "arch": "x86_64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/f0bc3878bea6091b544788c06047803f0588d425787357ea475699075e8e3d3a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-10-23T09:14:21.000Z", "arch": "emscripten", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/cb1173ca24594470b5ff0d6792a932b8af38dc5f9e1c43dedf33d804c15fdcf6", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-10-23T09:15:39.000Z", "arch": "aarch64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/2bab1bd21c04c5fa90619709138509d597feb0d599a9f31ae1ea5472dcea92b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-10-23T09:13:37.000Z", "arch": "x86_64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/6ff25276cb34f5b01bfbead78cd1a392bdfe3953cd0ed7efbccc5a711bee5c13", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.6.1", "os": "win", "version": "1.0.1", "date": "2026-10-23T09:15:32.000Z", "arch": "aarch64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/33b23e4c55fdfccf2f908eb89c50953048393b85b6841f08a1603d1a8dbad400", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" }, { "r": "4.6.1", "os": "win", "version": "1.0.1", "date": "2026-10-23T09:13:45.000Z", "arch": "x86_64", "commit": "9f516f85921599adf9a16121252a8c8451f644ce", "fileid": "https://r2.ropensci.org/0dc4bae9382ea0d0b7d648f82cd872e20d7e053a20ce29408316e382ddad146b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39929626391" } ] }