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  "Description": "Designed to ease the application and comparison of\nmultiple hypothesis testing procedures for FWER, gFWER, FDR and\nFDX. Methods are standardized and usable by the accompanying\n'mutossGUI'.",
  "License": "GPL",
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  "BugReports": "https://github.com/kornl/mutoss/issues/",
  "Repository": "https://kornl.r-universe.dev",
  "Date/Publication": "2025-12-26 10:03:33 UTC",
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  "Author": "MuToss Coding Team [aut] (Berlin 2010),\nGilles Blanchard [aut],\nThorsten Dickhaus [aut],\nNiklas Hack [aut],\nFrank Konietschke [aut],\nKornelius Rohmeyer [aut, cre],\nJonathan Rosenblatt [aut],\nMarsel Scheer [aut],\nWiebke Werft [aut]",
  "Maintainer": "Kornelius Rohmeyer <rohmeyer@small-projects.de>",
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    "author": "Kornelius Rohmeyer <rohmeyer@small-projects.de>",
    "committer": "Kornelius Rohmeyer <rohmeyer@small-projects.de>",
    "message": "Fixes for CRAN warnings 2025.\n",
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  "_devurl": "https://github.com/kornl/mutoss",
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  "_assets": [
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    "extra/mutoss.html",
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    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
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  "_homeurl": "https://github.com/kornl/mutoss",
  "_realowner": "kornl",
  "_cranurl": true,
  "_releases": [
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      "version": "0.1-1",
      "date": "2010-08-18"
    },
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  "_exports": [
    "ABH_pi0_est",
    "adaptiveBH",
    "adaptiveSTS",
    "adjPValuesPlot",
    "aorc",
    "augmentation",
    "BH",
    "BL",
    "BlaRoq",
    "bonferroni",
    "BR_pi0_est",
    "BY",
    "calculateBetaAdjustment",
    "compareMutoss",
    "fisher22_fast",
    "fisher22.marginal",
    "fisher22.model",
    "fisher23_fast",
    "fisher23.marginal",
    "fisher23.model",
    "ftest.marginal",
    "ftest.model",
    "gao",
    "gatherParameters",
    "gatherStatistics",
    "hochberg",
    "holm",
    "hommel",
    "indepBR",
    "jointCDF.orderedUnif",
    "linearStepUp",
    "mu.compare.adjusted",
    "mu.compare.critical",
    "mu.compare.summary",
    "multcomp.wrapper",
    "multiple.down",
    "multiple.down.adjust",
    "mutoss.apply",
    "mutoss.plotCI",
    "nparcomp",
    "nparcomp.wrapper",
    "onesamp.marginal",
    "onesamp.model",
    "oracleBH",
    "paired.marginal",
    "paired.model",
    "printRejected",
    "pval2locfdr",
    "pval2qval",
    "pValuesPlot",
    "Qvalue",
    "ranktruncated",
    "regwq",
    "requireLibrary",
    "rom",
    "SD",
    "sidak",
    "SidakSD",
    "simulation",
    "snk",
    "storey_pi0_est",
    "SU",
    "SUD",
    "TSBKY_pi0_est",
    "tukey.wrapper",
    "two.stage",
    "twosamp.marginal",
    "twosamp.model",
    "twostageBR"
  ],
  "_datasets": [
    {
      "name": "notterman",
      "title": "Notterman data set",
      "object": "notterman",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Tumor.27",
        "Tumor.29",
        "Tumor.34",
        "Tumor.28",
        "Tumor.35",
        "Tumor.8",
        "Tumor.3",
        "Tumor.9",
        "Tumor.4",
        "Tumor.32",
        "Tumor.39",
        "Tumor.10",
        "Tumor.33",
        "Tumor.5",
        "Tumor.11",
        "Tumor.6",
        "Tumor.12",
        "Tumor.40",
        "Normal.27",
        "Normal.29",
        "Normal.34",
        "Normal.28",
        "Normal.35",
        "Normal.8",
        "Normal.3",
        "Normal.9",
        "Normal.4",
        "Normal.32",
        "Normal.39",
        "Normal.10",
        "Normal.33",
        "Normal.5",
        "Normal.11",
        "Normal.6",
        "Normal.12",
        "Normal.40"
      ],
      "rows": 7457,
      "table": true,
      "tojson": true
    },
    {
      "name": "notterman.grpLabel",
      "title": "Notterman data set",
      "object": "notterman.grpLabel",
      "class": [
        "factor"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "T.Test.tumor.vs.normal",
      "title": "Notterman data set",
      "object": "T.Test.tumor.vs.normal",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ABH_pi0_est",
      "title": "Lowest Slope Line (LSL) method of Hochberg and Benjamini for estimating pi0",
      "topics": [
        "ABH_pi0_est"
      ]
    },
    {
      "page": "adaptiveBH",
      "title": "Benjamini-Hochberg (2000) adaptive linear step-up procedure",
      "topics": [
        "adaptiveBH"
      ]
    },
    {
      "page": "adaptiveSTS",
      "title": "Storey-Taylor-Siegmund (2004) adaptive step-up procedure",
      "topics": [
        "adaptiveSTS"
      ]
    },
    {
      "page": "adjPValuesPlot",
      "title": "A function plotting adjusted p-values...",
      "topics": [
        "adjPValuesPlot"
      ]
    },
    {
      "page": "aorc",
      "title": "Step-up-down test based on the asymptotically optimal rejection curve.",
      "topics": [
        "aorc"
      ]
    },
    {
      "page": "augmentation",
      "title": "Wrapper function to the augmentation methods of the multtest package.",
      "topics": [
        "augmentation"
      ]
    },
    {
      "page": "BH",
      "title": "Benjamini-Hochberg (1995) linear step-up procedure",
      "topics": [
        "BH"
      ]
    },
    {
      "page": "BL",
      "title": "Benjamini-Liu (1999) step-down procedure",
      "topics": [
        "BL"
      ]
    },
    {
      "page": "BlaRoq",
      "title": "Blanchard-Roquain (2008) step-up Procedure for arbitrary dependent p-Values...",
      "topics": [
        "BlaRoq"
      ]
    },
    {
      "page": "bonferroni",
      "title": "Bonferroni correction...",
      "topics": [
        "bonferroni"
      ]
    },
    {
      "page": "BR_pi0_est",
      "title": "Estimate of pi0 using the one-step Blanchard-Roquain procedure",
      "topics": [
        "BR_pi0_est"
      ]
    },
    {
      "page": "BY",
      "title": "Benjamini-Yekutieli (2001) step-up procedure",
      "topics": [
        "BY"
      ]
    },
    {
      "page": "calculateBetaAdjustment",
      "title": "Calculating the beta adjustment factor for the asymptotically optimal rejection curve.",
      "topics": [
        "calculateBetaAdjustment"
      ]
    },
    {
      "page": "compareMutoss",
      "title": "Functions for comparing outputs of different procedures.",
      "topics": [
        "compareMutoss",
        "mu.compare.adjusted",
        "mu.compare.critical",
        "mu.compare.summary"
      ]
    },
    {
      "page": "ErrorControl",
      "title": "Class ErrorControl",
      "topics": [
        "ErrorControl-class"
      ]
    },
    {
      "page": "fisher22_fast",
      "title": "Fisher (2x2) table association analysis for calculating one (marginal) p-value...",
      "topics": [
        "fisher22_fast"
      ]
    },
    {
      "page": "fisher22.marginal",
      "title": "Fisher (2x2) table association analysis for calculating all marginal p-values...",
      "topics": [
        "fisher22.marginal"
      ]
    },
    {
      "page": "fisher23_fast",
      "title": "Fisher-type (2x3) table association analysis for calculating one (marginal) p-value...",
      "topics": [
        "fisher23_fast"
      ]
    },
    {
      "page": "fisher23.marginal",
      "title": "Fisher-type (2x3) table association analysis for calculating all marginal p-values...",
      "topics": [
        "fisher23.marginal"
      ]
    },
    {
      "page": "ftest.marginal",
      "title": "Marginal F test",
      "topics": [
        "ftest.marginal"
      ]
    },
    {
      "page": "gao",
      "title": "Xin Gao's non-parametric multiple test procedure is applied to Data.",
      "topics": [
        "gao",
        "gao.wrapper"
      ]
    },
    {
      "page": "gatherParameters",
      "title": "Extracts the parameters from the simulation()-Object",
      "topics": [
        "gatherParameters"
      ]
    },
    {
      "page": "gatherStatistics",
      "title": "Gathering statistics from simulation()-Object",
      "topics": [
        "gatherStatistics"
      ]
    },
    {
      "page": "hochberg",
      "title": "Hochberg (1988) step-up procedure",
      "topics": [
        "hochberg"
      ]
    },
    {
      "page": "holm",
      "title": "Holm's (1979) step-down-procedure",
      "topics": [
        "holm"
      ]
    },
    {
      "page": "hommel",
      "title": "Hommel's (1988) step-up-procedure",
      "topics": [
        "hommel"
      ]
    },
    {
      "page": "indepBR",
      "title": "Blanchard-Roquain (2009) 1-stage adaptive step-up",
      "topics": [
        "indepBR"
      ]
    },
    {
      "page": "jointCDF.orderedUnif",
      "title": "Joint cumulative distribution function of order statistics of n iid. U(0,1)-distributed random variables",
      "topics": [
        "jointCDF.orderedUnif"
      ]
    },
    {
      "page": "linearStepUp",
      "title": "Linear Step Up Service Function...",
      "topics": [
        "linearStepUp"
      ]
    },
    {
      "page": "mu.test.class",
      "title": "Test for compatible classes for comparison...",
      "topics": [
        "mu.test.class"
      ]
    },
    {
      "page": "mu.test.name",
      "title": "Tests if all hypotheses have the same names.",
      "topics": [
        "mu.test.name"
      ]
    },
    {
      "page": "mu.test.rates",
      "title": "Tests that different procedures used the same error rates.",
      "topics": [
        "mu.test.rates"
      ]
    },
    {
      "page": "mu.test.same.data",
      "title": "Tests if the same pvalues were used by different procedures.",
      "topics": [
        "mu.test.same.data"
      ]
    },
    {
      "page": "mu.test.type",
      "title": "Tests that different procedures use the same error types.",
      "topics": [
        "mu.test.type"
      ]
    },
    {
      "page": "multcomp.wrapper",
      "title": "Simultaneous confidence intervals for arbitrary parametric contrasts in unbalanced one-way layouts.",
      "topics": [
        "multcomp.wrapper"
      ]
    },
    {
      "page": "multiple.down",
      "title": "Benjamini-Krieger-Yekutieli (2006) Multi-Stage Step-Down",
      "topics": [
        "multiple.down"
      ]
    },
    {
      "page": "multiple.down.adjust",
      "title": "A service function used by multiple...",
      "topics": [
        "multiple.down.adjust"
      ]
    },
    {
      "page": "Mutoss",
      "title": "Class Mutoss",
      "topics": [
        "Mutoss-class"
      ]
    },
    {
      "page": "mutoss.apply",
      "title": "Applies a function to a Mutoss object.",
      "topics": [
        "mutoss.apply"
      ]
    },
    {
      "page": "mutoss.models",
      "title": "Mutoss Models",
      "topics": [
        "fisher22.model",
        "fisher23.model",
        "ftest.model",
        "onesamp.model",
        "paired.model",
        "twosamp.model"
      ]
    },
    {
      "page": "mutoss.plotCI",
      "title": "mutoss.plotCI",
      "topics": [
        "mutoss.plotCI"
      ]
    },
    {
      "page": "MutossMethod",
      "title": "Class MutossMethod",
      "topics": [
        "MutossMethod",
        "MutossMethod-class"
      ]
    },
    {
      "page": "notterman",
      "title": "Notterman data set",
      "topics": [
        "notterman",
        "notterman.grpLabel",
        "T.Test.tumor.vs.normal"
      ]
    },
    {
      "page": "nparcomp",
      "title": "Simultaneous confidence intervals for relative contrast effects...",
      "topics": [
        "nparcomp"
      ]
    },
    {
      "page": "nparcomp.wrapper",
      "title": "Simultaneous confidence intervals for relative contrast effects...",
      "topics": [
        "nparcomp.wrapper"
      ]
    },
    {
      "page": "onesamp.marginal",
      "title": "Marginal one sample test",
      "topics": [
        "onesamp.marginal"
      ]
    },
    {
      "page": "oracleBH",
      "title": "Bejamini-Hochberg (2000) oracle linear step-up Procedure...",
      "topics": [
        "oracleBH"
      ]
    },
    {
      "page": "paired.marginal",
      "title": "Marginal paired two sample test",
      "topics": [
        "paired.marginal"
      ]
    },
    {
      "page": "printRejected",
      "title": "Internal MuTossProjekt-Function",
      "topics": [
        "printRejected"
      ]
    },
    {
      "page": "pval2locfdr",
      "title": "Strimmer et al.'s fdrtool-based local fdr",
      "topics": [
        "pval2locfdr"
      ]
    },
    {
      "page": "pval2qval",
      "title": "Strimmer et al.'s fdrtool-based q-values",
      "topics": [
        "pval2qval"
      ]
    },
    {
      "page": "pValuesPlot",
      "title": "A function plotting p-values...",
      "topics": [
        "pValuesPlot"
      ]
    },
    {
      "page": "Qvalue",
      "title": "Storey's (2001) q-value Procedure...",
      "topics": [
        "Qvalue"
      ]
    },
    {
      "page": "ranktruncated",
      "title": "Rank truncated p-Value procedure...",
      "topics": [
        "ranktruncated"
      ]
    },
    {
      "page": "regwq",
      "title": "REGWQ - Ryan / Einot and Gabriel / Welsch test procedure...",
      "topics": [
        "regwq"
      ]
    },
    {
      "page": "reject",
      "title": "reject",
      "topics": [
        "reject"
      ]
    },
    {
      "page": "requireLibrary",
      "title": "Tries to load a package.",
      "topics": [
        "requireLibrary"
      ]
    },
    {
      "page": "rom",
      "title": "Rom's (1990) step-up-procedure.",
      "topics": [
        "rom"
      ]
    },
    {
      "page": "SD",
      "title": "A general step-down procedure.",
      "topics": [
        "SD"
      ]
    },
    {
      "page": "sidak",
      "title": "Sidak correction",
      "topics": [
        "sidak"
      ]
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