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  "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<https://orcid.org/0000-0002-3839-9067>), Annaig De Walsche\n[aut] (ORCID: <https://orcid.org/0000-0003-0603-1716>), Franck\nGauthier [ctb] (ORCID: <https://orcid.org/0000-0003-0574-065X>)",
  "Maintainer": "Tristan Mary-Huard <tristan.mary-huard@agroparistech.fr>",
  "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<doi:10.1093/bioinformatics/btab592> and De Walsche et\nal.(2025) <doi: 10.1093/nargab/lqaf118>. 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",
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  "Repository": "https://tmaryhuard.r-universe.dev",
  "Date/Publication": "2026-05-27 16:48:21 UTC",
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  "_topics": [
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    "cpp",
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  "_assets": [
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    "extra/citation.json",
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    "qch.test"
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      "name": "PvalSets",
      "title": "Synthetic example to illustrate the main qch functions",
      "object": "PvalSets",
      "class": [
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      ],
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        "Pval2",
        "Class"
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      "name": "PvalSets_cor",
      "title": "Synthetic example to illustrate the main qch functions using Gaussian copula",
      "object": "PvalSets_cor",
      "class": [
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        "data.frame"
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    {
      "page": "Copula.Hconfig_gaussian_density",
      "title": "Gaussian copula density for each H-configuration.",
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        "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"
      ]
    },
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      "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"
      ]
    },
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      "page": "R.MLE.check",
      "title": "Check the Gaussian copula correlation matrix Maximum Likelihood estimator",
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      ]
    },
    {
      "page": "R.MLE.memory",
      "title": "Gaussian copula correlation matrix Maximum Likelihood estimator (memory handling)",
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