{ "_id": "6a19c7f3ad7a21ec8945fb4d", "Package": "admix", "Title": "Package Admix for Admixture (aka Contamination) Models", "Version": "2.6.1", "Authors@R": "c(\nperson(\"Xavier\", \"Milhaud\", , \"xavier.milhaud.research@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Pierre\", \"Vandekerkhove\", role = \"ctb\"),\nperson(\"Denys\", \"Pommeret\", role = \"ctb\"),\nperson(\"Yahia\", \"Salhi\", role = \"ctb\")\n)", "Description": "Implements techniques to estimate the unknown quantities\nrelated to two-component admixture models, where the two\ncomponents can belong to any distribution (note that in the\ncase of multinomial mixtures, the two components must belong to\nthe same family). Estimation methods depend on the assumptions\nmade on the unknown component density; see Bordes and\nVandekerkhove (2010) , Patra and\nSen (2016) , and Milhaud, Pommeret,\nSalhi, Vandekerkhove (2024) . In\npractice, one can estimate both the mixture weight and the\nunknown component density in a wide variety of frameworks. On\ntop of that, hypothesis tests can be performed in one and\ntwo-sample contexts to test the unknown component density (see\nMilhaud, Pommeret, Salhi and Vandekerkhove (2022)\n, and Milhaud, Pommeret, Salhi,\nVandekerkhove (2024) ). Finally,\nclustering of unknown mixture components is also feasible in a\nK-sample setting (see Milhaud, Pommeret, Salhi, Vandekerkhove\n(2024) ).", "License": "GPL (>= 3)", "URL": "https://github.com/XavierMilhaud/admix-Rpackage", "BugReports": "https://github.com/XavierMilhaud/admix-Rpackage/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "LazyData": "true", "RdMacros": "Rdpack", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make", "Repository": "https://xaviermilhaud.r-universe.dev", "Date/Publication": "2026-05-29 14:00:02 UTC", "RemoteUrl": "https://github.com/xaviermilhaud/admix-rpackage", "RemoteRef": "HEAD", "RemoteSha": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 17:01:23 UTC", "User": "root" }, "Author": "Xavier Milhaud [aut, cre],\nPierre Vandekerkhove [ctb],\nDenys Pommeret [ctb],\nYahia Salhi [ctb]", "Maintainer": "Xavier Milhaud ", "MD5sum": "581aecf03fd93bf40092c184776c5be9", "_user": "xaviermilhaud", "_type": "src", "_file": "admix_2.6.1.tar.gz", "_fileid": "130e3090a0cbf91e5d928d1612e8914fa159433e20dd7932edeb4a98114dd77f", "_filesize": 2537872, "_sha256": "130e3090a0cbf91e5d928d1612e8914fa159433e20dd7932edeb4a98114dd77f", "_created": "2026-05-29T17:01:23.000Z", "_published": "2026-05-29T17:08:03.927Z", "_distro": "noble", "_jobs": [ { "job": 78548381756, "time": 192, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7296467834" }, { "job": 78548381945, "time": 358, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7296522952" }, { "job": 78548381805, "time": 209, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7296472941" }, { "job": 78548381773, "time": 191, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7296467413" }, { "job": 78548381856, "time": 119, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7296444255" }, { "job": 78548381973, "time": 291, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7296500283" }, { "job": 78548381834, "time": 134, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7296449248" }, { "job": 78548381852, "time": 305, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7296504815" }, { "job": 78547717863, "time": 241, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7296404243" }, { "job": 78548381732, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7296447949" }, { "job": 78548381754, "time": 176, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7296462938" }, { "job": 78548381775, "time": 175, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7296462538" }, { "job": 78548381784, "time": 239, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7296482917" } ], "_buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/xaviermilhaud/admix-rpackage", "_commit": { "id": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "author": "XavierMilhaud ", "committer": "XavierMilhaud ", "message": "Improve param init for optimization in the BVdk estimation method\n", "time": 1780063202 }, "_maintainer": { "name": "Xavier Milhaud", "email": "xavier.milhaud.research@gmail.com", "login": "xaviermilhaud", "description": "I am a researcher in Applied Mathematics, Statistics and Probability", "uuid": 30351126 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "base", "role": "Imports" }, { "package": "cubature", "role": "Imports" }, { "package": "fdrtool", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "Iso", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "orthopolynom", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "Rdpack", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "doParallel", "role": "Suggests" }, { "package": "doRNG", "role": "Suggests" }, { "package": "evd", "role": "Suggests" }, { "package": "flexsurv", "role": "Suggests" }, { "package": "foreach", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "lattice", "role": "Suggests" }, { "package": "logitnorm", "role": "Suggests" }, { "package": "plyr", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rmutil", "role": "Suggests" }, { "package": "mockery", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "xaviermilhaud", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 3 }, { "week": "2025-27", "n": 4 }, { "week": "2025-32", "n": 4 }, { "week": "2025-35", "n": 1 }, { "week": "2025-36", "n": 5 }, { "week": "2025-39", "n": 2 }, { "week": "2025-40", "n": 4 }, { "week": "2025-42", "n": 1 }, { "week": "2026-02", "n": 1 }, { "week": "2026-19", "n": 1 }, { "week": "2026-20", "n": 4 }, { "week": "2026-21", "n": 2 }, { "week": "2026-22", "n": 1 } ], "_tags": [], "_stars": 3, "_contributors": [ { "user": "xaviermilhaud", "count": 165, "uuid": 30351126 } ], "_userbio": { "uuid": 30351126, "type": "user", "name": "XavierMilhaud", "description": "I am a researcher in Applied Mathematics, Statistics and Probability" }, "_downloads": { "count": 672, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/admix" }, "_mentions": 2, "_devurl": "https://github.com/xaviermilhaud/admix-rpackage", "_searchresults": 22, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/admix.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/xaviermilhaud/admix-rpackage", "_realowner": "xaviermilhaud", "_cranurl": true, "_releases": [ { "version": "0.3.2", "date": "2021-06-14" }, { "version": "0.4.0", "date": "2022-03-24" }, { "version": "2.1-0", "date": "2023-03-23" }, { "version": "2.1-1", "date": "2023-07-06" }, { "version": "2.1-2", "date": "2023-07-13" }, { "version": "2.1-3", "date": "2024-04-25" }, { "version": "2.3.1", "date": "2024-10-24" }, { "version": "2.3.2", "date": "2024-11-05" }, { "version": "2.3.3", "date": "2024-11-08" }, { "version": "2.3.4", "date": "2025-03-07" }, { "version": "2.4", "date": "2025-05-27" }, { "version": "2.4.2", "date": "2025-07-05" }, { "version": "2.4.3", "date": "2025-08-21" }, { "version": "2.5.1", "date": "2025-09-05" }, { "version": "2.5.2", "date": "2026-01-08" } ], "_exports": [ "admix_cluster", "admix_estim", "admix_model", "admix_test", "decontaminated_cdf", "decontaminated_density", "detect_support_type", "distribution_type", "get_cluster_members", "get_cluster_sizes", "get_discrepancy_matrix", "get_discrepancy_rank", "get_distribution_parameters", "get_known_component", "get_mixing_weights", "get_mixture_data", "get_statistic_components", "get_tabulated_dist", "is_equal_knownComp", "reject_nullHyp", "twoComp_mixt", "validate_distribution", "which_rank" ], "_datasets": [ { "name": "allGalaxies", "title": "Measurements of heliocentric velocities", "object": "allGalaxies", "class": [ "data.frame" ], "fields": [ "Target", "HV", "Name" ], "rows": 8862, "table": true, "tojson": true }, { "name": "milkyWay", "title": "Dataset of heliocentric velocity for the Milky Way", "object": "milkyWay", "class": [ "data.frame" ], "fields": [ "V1" ], "rows": 170601, "table": true, "tojson": true }, { "name": "mortality_sample", "title": "Dataset of deaths statistics in 11 european countries", "object": "mortality_sample", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "stmf_small", "title": "Dataset of Short-term Mortality Fluctuations (STMF) from HMD", "object": "stmf_small", "class": [ "data.frame" ], "fields": [ "CountryCode", "Year", "Week", "Sex", "D0_14", "D15_64", "D65_74", "D75_84", "D85p", "DTotal", "R0_14", "R15_64", "R65_74", "R75_84", "R85p", "RTotal", "Split", "SplitSex", "Forecast" ], "rows": 15252, "table": true, "tojson": true } ], "_help": [ { "page": "admix_cluster", "title": "Cluster K populations following admixture models", "topics": [ "admix_cluster" ] }, { "page": "admix_estim", "title": "Estimate the unknown weight in an admixture model", "topics": [ "admix_estim" ] }, { "page": "admix_model", "title": "Define the distribution/parameter(s) of the known component", "topics": [ "admix_model" ] }, { "page": "admix_test", "title": "Hypothesis test for the unknown component(s) in admixture model(s)", "topics": [ "admix_test" ] }, { "page": "allGalaxies", "title": "Measurements of heliocentric velocities", "topics": [ "allGalaxies" ] }, { "page": "decontaminated_density", "title": "Probability density function of the unknown component", "topics": [ "decontaminated_density" ] }, { "page": "detect_support_type", "title": "Detect the type of support of some random variables", "topics": [ "detect_support_type" ] }, { "page": "distribution_type", "title": "Determine the type of distribution under consideration", "topics": [ "distribution_type" ] }, { "page": "get_cluster_members", "title": "Extractor for members of clusters", "topics": [ "get_cluster_members" ] }, { "page": "get_cluster_sizes", "title": "Extractor for cluster sizes", "topics": [ "get_cluster_sizes" ] }, { "page": "get_discrepancy_matrix", "title": "Extractor for discrepancies b/w unknown components", "topics": [ "get_discrepancy_matrix" ] }, { "page": "get_discrepancy_rank", "title": "Extractor for pairwise discrepancy rankings", "topics": [ "get_discrepancy_rank" ] }, { "page": "get_distribution_parameters", "title": "Check the validity of the specified distributions", "topics": [ "get_distribution_parameters" ] }, { "page": "get_known_component", "title": "Extractor for known component(s) in admixture model(s)", "topics": [ "get_known_component" ] }, { "page": "get_mixing_weights", "title": "Extractor for estimated mixing weights", "topics": [ "get_mixing_weights" ] }, { "page": "get_mixture_data", "title": "Extractor for simulated data from two-component mixture", "topics": [ "get_mixture_data" ] }, { "page": "get_statistic_components", "title": "Extractor for components involved in test statistic", "topics": [ "get_statistic_components" ] }, { "page": "get_tabulated_dist", "title": "Extractor for tabulated distribution in the k-sample test", "topics": [ "get_tabulated_dist" ] }, { "page": "is_equal_knownComp", "title": "Equality of known components in two admixture models", "topics": [ "is_equal_knownComp" ] }, { "page": "milkyWay", "title": "Dataset of heliocentric velocity for the Milky Way", "topics": [ "milkyWay" ] }, { "page": "mortality_sample", "title": "Dataset of deaths statistics in 11 european countries", "topics": [ "mortality_sample" ] }, { "page": "plot.admix_model", "title": "Plot method for objects of class 'admix_model'", "topics": [ "plot.admix_model" ] }, { "page": "plot.decontaminated_density", "title": "Plot method for object of class 'decontaminated_density'", "topics": [ "plot.decontaminated_density" ] }, { "page": "plot.twoComp_mixt", "title": "Plot the empirical mixture pdf", "topics": [ "plot.twoComp_mixt" ] }, { "page": "print.admix_cluster", "title": "Print method for object of class 'admix_cluster'", "topics": [ "print.admix_cluster" ] }, { "page": "print.admix_estim", "title": "Print method for object of class 'admix_estim'", "topics": [ "print.admix_estim" ] }, { "page": "print.admix_model", "title": "Print method for objects of class 'admix_model'", "topics": [ "print.admix_model" ] }, { "page": "print.decontaminated_density", "title": "Print method for object of class 'decontaminated_density'", "topics": [ "print.decontaminated_density" ] }, { "page": "print.twoComp_mixt", "title": "Print method for objects 'twoComp_mixt'", "topics": [ "print.twoComp_mixt" ] }, { "page": "reject_nullHyp", "title": "Extractor for the test decision", "topics": [ "reject_nullHyp" ] }, { "page": "stmf_small", "title": "Dataset of Short-term Mortality Fluctuations (STMF) from HMD", "topics": [ "stmf_small" ] }, { "page": "summary.admix_cluster", "title": "Summary method for object of class 'admix_cluster'", "topics": [ "summary.admix_cluster" ] }, { "page": "summary.admix_estim", "title": "Summary method for object of class 'admix_estim'", "topics": [ "summary.admix_estim" ] }, { "page": "summary.admix_model", "title": "Summary method for objects of class 'admix_model'", "topics": [ "summary.admix_model" ] }, { "page": "summary.decontaminated_density", "title": "Summary method for object of class 'decontaminated_density'", "topics": [ "summary.decontaminated_density" ] }, { "page": "summary.twoComp_mixt", "title": "Summary method for objects 'twoComp_mixt'", "topics": [ "summary.twoComp_mixt" ] }, { "page": "twoComp_mixt", "title": "Simulation of a two-component mixture model", "topics": [ "twoComp_mixt" ] }, { "page": "validate_distribution", "title": "Check the validity of the specified distribution and parameter(s)", "topics": [ "validate_distribution" ] }, { "page": "which_rank", "title": "Extractor for the selected rank in the test statistic", "topics": [ "which_rank" ] } ], "_readme": "https://github.com/xaviermilhaud/admix-rpackage/raw/HEAD/README.md", "_rundeps": [ "cubature", "fdrtool", "Iso", "MASS", "orthopolynom", "polynom", "pracma", "rbibutils", "Rcpp", "Rdpack" ], "_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": "admixture-clustering.Rmd", "filename": "admixture-clustering.html", "title": "Clustering of unknown subpopulations in admixture models", "author": "Xavier Milhaud", "engine": "knitr::rmarkdown", "headings": [ "Algorithm", "Applications", "On $\\mathbb{R}^+$" ], "created": "2021-05-28 19:36:50", "modified": "2025-08-06 07:22:57", "commits": 13 }, { "source": "admixture-weight-estimation.Rmd", "filename": "admixture-weight-estimation.html", "title": "Estimation of unknown elements in admixture models", "author": "Xavier Milhaud", "engine": "knitr::rmarkdown", "headings": [ "Estimation of the unknown component weight in an admixture model", "The one-sample case", "Case of symmetric unknown density", "Other cases", "The two-sample case", "Under the null hypothesis $H_0: F_1 = F_2$", "Under the alternative hypothesis $H_1: F_1 \\neq F_2$", "Estimation of the unknown cumulative distribution function", "References" ], "created": "2021-05-28 19:36:50", "modified": "2026-05-08 13:49:11", "commits": 13 }, { "source": "test-hypothesis.Rmd", "filename": "test-hypothesis.html", "title": "Hypothesis test in admixture models", "author": "Xavier Milhaud", "engine": "knitr::rmarkdown", "headings": [ "The one-sample case only available to symmetric unknown density", "The two-sample case", "Case of symmetric unknown densities", "Case of fully unknown densities", "The K-sample case", "References" ], "created": "2021-05-28 19:36:50", "modified": "2025-08-06 07:22:57", "commits": 17 } ], "_score": 6.410608542568368, "_indexed": true, "_nocasepkg": "admix", "_universes": [ "xaviermilhaud" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.6.1", "date": "2026-05-29T17:04:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "5741a659b8aa955261c8e06be1b83d95c82a7a4bbcd8f3e891d525d0fd65c097", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.7.0", "os": "linux", "version": "2.6.1", "date": "2026-05-29T17:06:47.000Z", "distro": "noble", "arch": "x86_64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "34011df25a8210ed4c857d2f2d1e987dc82aaaa1e6207715d97ccc95537f9a74", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.6.0", "os": "linux", "version": "2.6.1", "date": "2026-05-29T17:04:25.000Z", "distro": "noble", "arch": "aarch64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "0923f82705d75deb14eb0804a5f6ea1e8cdaf8c44c334d7f0dcff9188e6d0e7c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.6.0", "os": "linux", "version": "2.6.1", "date": "2026-05-29T17:04:01.000Z", "distro": "noble", "arch": "x86_64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "c6d5e2b7869f87e299c8d05aa88a35ea2e72eef0eedb0b240db38e8b69de8586", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.5.3", "os": "mac", "version": "2.6.1", "date": "2026-05-29T17:03:03.000Z", "arch": "aarch64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "4e43e2571b6d0310cf19d991857fa806bb51968b82e85e410d5d3b09a9fb71d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.5.3", "os": "mac", "version": "2.6.1", "date": "2026-05-29T17:04:56.000Z", "arch": "x86_64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "ba616eda24d2218e65c0e32513b6209a197d74c34bed559ac65bd9bcac664457", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.6.0", "os": "mac", "version": "2.6.1", "date": "2026-05-29T17:03:13.000Z", "arch": "aarch64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "2624d2f457efa34bcd2aa5d4f274c13604ec67f187b2b3259295cd89e57f20c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.6.0", "os": "mac", "version": "2.6.1", "date": "2026-05-29T17:05:06.000Z", "arch": "x86_64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "e6c32e5ea4e79c4ca55a9b3ec41cf0f075c2e068f02826138259c9804804e991", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.6.0", "os": "wasm", "version": "2.6.1", "date": "2026-05-29T17:03:52.000Z", "arch": "emscripten", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "8de59dfda02b60c694792bab3678cb579599b35a2fc51068483f7b7fa851ba01", "status": "success", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.7.0", "os": "win", "version": "2.6.1", "date": "2026-05-29T17:03:01.000Z", "arch": "x86_64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "e24143cd65e1c31345a82e0be18e43b36a44932053f9cc303df8ffa5073045f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.5.3", "os": "win", "version": "2.6.1", "date": "2026-05-29T17:02:56.000Z", "arch": "x86_64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "473507a8695384ab477d3a8c4d725d96d9d4cec6a44d41dd93fb7cfd4ec69bad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" }, { "r": "4.6.0", "os": "win", "version": "2.6.1", "date": "2026-05-29T17:03:38.000Z", "arch": "x86_64", "commit": "1c2249ed6b46ca0d5546a0fb965c05f3106bd04d", "fileid": "75325ded2ae8fb7604a0c069559dbc7f225d9bb29cd4c30446ccd7b35c0e0823", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xaviermilhaud/actions/runs/26650612482" } ] }