{ "_id": "6a173505acfb0bcc41d9491d", "Package": "qch", "Title": "Query Composite Hypotheses", "Version": "2.1.3", "Authors@R": "c(\nperson(\"Tristan\", \"Mary-Huard\", , \"tristan.mary-huard@agroparistech.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3839-9067\")),\nperson(\"Annaig\", \"De Walsche\", , \"annaig.de-walsche@inrae.fr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0603-1716\")),\nperson(\"Franck\", \"Gauthier\", , \"franck.gauthier@inrae.fr\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-0574-065X\"))\n)", "Author": "Tristan Mary-Huard [aut, cre] (ORCID:\n), Annaig De Walsche\n[aut] (ORCID: ), Franck\nGauthier [ctb] (ORCID: )", "Maintainer": "Tristan Mary-Huard ", "Description": "Provides functions for the joint analysis of Q sets of\np-values obtained for the same list of items. This joint\nanalysis is performed by querying a composite hypothesis, i.e.\nan arbitrary complex combination of simple hypotheses, as\ndescribed in Mary-Huard et al. (2021)\n and De Walsche et\nal.(2025) . In this approach, the\nQ-uplet of p-values associated with each item is distributed as\na multivariate mixture, where each of the 2^Q components\ncorresponds to a specific combination of simple hypotheses. The\ndependence between the p-value series is considered using a\nGaussian copula function. A p-value for the composite\nhypothesis test is derived from the posterior probabilities.", "License": "GPL-3", "biocViews": "", "Encoding": "UTF-8", "LazyData": "true", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-27 18:13:06 UTC", "User": "root" }, "RoxygenNote": "7.3.3", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-05-27 16:48:21 UTC", "RemoteUrl": "https://github.com/cran/qch", "RemoteRef": "HEAD", "RemoteSha": "a83f980907989f947612e01086f40bb220abc87d", "MD5sum": "cbe9f518875b4c433e4578107d73794f", "_user": "cran", "_type": "src", "_file": "qch_2.1.3.tar.gz", "_fileid": "c7bc475620072ad172ed2ece94819ae068bddc7e1763b627e3c036589797ccb9", "_filesize": 562904, "_sha256": "c7bc475620072ad172ed2ece94819ae068bddc7e1763b627e3c036589797ccb9", "_created": "2026-05-27T18:13:06.000Z", "_published": "2026-05-27T18:16:37.573Z", "_distro": "noble", "_jobs": [ { "job": 78143387440, "time": 144, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", 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"name": "Tristan Mary-Huard", "email": "tristan.mary-huard@agroparistech.fr", "login": "tmaryhuard", "description": "", "uuid": 71508740, "orcid": "0000-0002-3839-9067" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "copula", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "ks", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-27", "n": 1 }, { "week": "2026-08", "n": 1 }, { "week": "2026-22", "n": 1 } ], "_tags": [ { "name": "2.1.0", "date": "2025-07-04" }, { "name": "2.1.2", "date": "2026-02-16" }, { "name": "2.1.3", "date": "2026-05-27" } ], "_stars": 0, "_contributors": [ { "user": "tmaryhuard", "count": 5, "uuid": 71508740 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 228, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/qch" }, "_searchresults": 6, "_topics": [ "openblas", "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/qch.html", "manual.pdf" ], "_realowner": "tmaryhuard", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2021-05-07" }, { "version": "2.0.0", "date": "2024-03-29" }, { "version": "2.1.0", "date": "2025-07-04" }, { "version": "2.1.2", "date": "2026-02-16" }, { "version": "2.1.3", "date": "2026-05-27" } ], "_exports": [ "GetH1AtLeast", "GetH1Equal", "GetHconfig", "qch.fit", "qch.test" ], "_datasets": [ { "name": "PvalSets", "title": "Synthetic example to illustrate the main qch functions", "object": "PvalSets", "class": [ "data.frame" ], "fields": [ "Pval1", "Pval2", "Class" ], "rows": 10000, "table": true, "tojson": true }, { "name": "PvalSets_cor", "title": "Synthetic example to illustrate the main qch functions using Gaussian copula", "object": "PvalSets_cor", "class": [ "data.table", "data.frame" ], "fields": [ "Pval1", "Pval2", "Class" ], "rows": 10000, "table": true, "tojson": true } ], "_help": [ { "page": "Copula.Hconfig_gaussian_density", "title": "Gaussian copula density for each H-configuration.", "topics": [ "Copula.Hconfig_gaussian_density" ] }, { "page": "EM_calibration_gaussian", "title": "EM calibration in the case of the Gaussian copula (unsigned)", "topics": [ "EM_calibration_gaussian" ] }, { "page": "EM_calibration_gaussian_memory", "title": "EM calibration in the case of the Gaussian copula (unsigned) with memory management", "topics": [ "EM_calibration_gaussian_memory" ] }, { "page": "EM_calibration_indep", "title": "EM calibration in the case of conditional independence", "topics": [ "EM_calibration_indep" ] }, { "page": "EM_calibration_indep_memory", "title": "EM calibration in the case of conditional independence with memory management (unsigned)", "topics": [ "EM_calibration_indep_memory" ] }, { "page": "f1_separation_signed", "title": "Signed case function: Separate f1 into f+ and f-", "topics": [ "f1_separation_signed" ] }, { "page": "FastKerFdr_signed", "title": "FastKerFdr signed", "topics": [ "FastKerFdr_signed" ] }, { "page": "FastKerFdr_unsigned", "title": "FastKerFdr unsigned", "topics": [ "FastKerFdr_unsigned" ] }, { "page": "fHconfig_sum_update_gaussian_copula_ptr_parallel", "title": "Computation of the sum sum_c(w_c*psi_c) using Gaussian copula parallelized version", "topics": [ "fHconfig_sum_update_gaussian_copula_ptr_parallel" ] }, { "page": "fHconfig_sum_update_ptr_parallel", "title": "Computation of the sum sum_c(w_c*psi_c) parallelized version", "topics": [ "fHconfig_sum_update_ptr_parallel" ] }, { "page": "gaussian_copula_density", "title": "Gaussian copula density", "topics": [ "gaussian_copula_density" ] }, { "page": "GetH1AtLeast", "title": "Specify the configurations corresponding to the composite H_1 test \"AtLeast\".", "topics": [ "GetH1AtLeast" ] }, { "page": "GetH1Equal", "title": "Specify the configurations corresponding to the composite H_1 test \"Equal\".", "topics": [ "GetH1Equal" ] }, { "page": "GetHconfig", "title": "Generate the H_0/H_1 configurations.", "topics": [ "GetHconfig" ] }, { "page": "last_incomplete_trapezoid_arma", "title": "This function is a re-implementation of the initial R loop computing last incomplete trapezoid. See R function integral.kde_adapted().", "topics": [ "last_incomplete_trapezoid_arma" ] }, { "page": "prior_update_arma_ptr_parallel", "title": "Update of the prior estimate in EM algo parallelized version", "topics": [ "prior_update_arma_ptr_parallel" ] }, { "page": "prior_update_gaussian_copula_ptr_parallel", "title": "Update of the prior estimate in EM algo using Gaussian copula, parallelized version", "topics": [ "prior_update_gaussian_copula_ptr_parallel" ] }, { "page": "PvalSets", "title": "Synthetic example to illustrate the main qch functions", "topics": [ "PvalSets" ] }, { "page": "PvalSets_cor", "title": "Synthetic example to illustrate the main qch functions using Gaussian copula", "topics": [ "PvalSets_cor" ] }, { "page": "qch.fit", "title": "Infer posterior probabilities of H_0/H_1 configurations.", "topics": [ "qch.fit" ] }, { "page": "qch.test", "title": "Perform composite hypothesis testing.", "topics": [ "qch.test" ] }, { "page": "R_MLE_update_gaussian_copula_ptr_parallel", "title": "Update the estimate of R correlation matrix of the gaussian copula, parallelized version", "topics": [ "R_MLE_update_gaussian_copula_ptr_parallel" ] }, { "page": "R.MLE", "title": "Gaussian copula correlation matrix Maximum Likelihood estimator.", "topics": [ "R.MLE" ] }, { "page": "R.MLE.check", "title": "Check the Gaussian copula correlation matrix Maximum Likelihood estimator", "topics": [ "R.MLE.check" ] }, { "page": "R.MLE.memory", "title": "Gaussian copula correlation matrix Maximum Likelihood estimator (memory handling)", "topics": [ "R.MLE.memory" ] }, { "page": "remove_decreasing_values_cpp", "title": "Same as function above but does not handle the index ordering of the vector q. 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