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  "Package": "paweh",
  "Title": "Power and Sample Size Analysis for Genetic Studies with\nHeterogeneity and Misclassification",
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  "Description": "Provides prospective power and minimum sample size\nnecessary (MSSN) calculations for genetic and genomic\nassociation study design. Supported designs include\ncase-control studies, transmission disequilibrium tests with\naffected-child trios, and single- and multivariate\nquantitative-trait studies. The package emphasizes selected\ndepartures from idealized assumptions, including locus\nheterogeneity and supported forms of genotype and phenotype\nmisclassification. These factors can materially affect power\nand sample-size requirements but can be difficult to\nincorporate analytically. Published statistical-genetics\nmethods are implemented in a reproducible, primarily parameter-\nand model-based framework with static visualizations and an\noptional Shiny dashboard for interactive exploration. The\nsoftware supports prospective study planning; it does not\nperform downstream association testing.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://github.com/akilanthony/paweh,\nhttps://akilanthony.github.io/paweh/",
  "BugReports": "https://github.com/akilanthony/paweh/issues",
  "biocViews": "ExperimentalDesign, Genetics, GenomeWideAssociation,\nShinyApps",
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  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-09-17 13:18:55 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/paweh",
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  "Packaged": {
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    "User": "root"
  },
  "Author": "Akil Anthony [aut, cre] (ORCID:\n<https://orcid.org/0009-0008-8813-8560>),\nDerek Gordon [aut]",
  "Maintainer": "Akil Anthony <akilanthony19@gmail.com>",
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  "_created": "2026-10-17T10:43:49.000Z",
  "_published": "2026-10-17T10:49:59.589Z",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/39025771132",
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    "author": "Akil Anthony <akilanthony19@gmail.com>",
    "committer": "Akil Anthony <akilanthony19@gmail.com>",
    "message": "Fix cross-platform TDT-NGS numeric tests\n",
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    "cc_chisq_mssn_genotype_misclassification_2p",
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    "ngs_genotype_error_matrix",
    "paweh_app",
    "plot_cc_mssn",
    "plot_cc_power",
    "plot_ngs_mssn",
    "plot_ngs_power",
    "plot_qtl_anova_mssn",
    "plot_qtl_anova_power",
    "plot_qtl_genotype_distribution",
    "plot_qtl_threshold_chisq_mssn",
    "plot_qtl_threshold_chisq_power",
    "plot_tdt_mssn",
    "plot_tdt_mssn_locus_heterogeneity",
    "plot_tdt_mssn_phenotype_misclassification",
    "plot_tdt_power",
    "plot_tdt_power_locus_heterogeneity",
    "plot_tdt_power_phenotype_misclassification",
    "plot_tdt_surface3d",
    "qtl_anova_mssn",
    "qtl_anova_power",
    "qtl_falconer_parameters",
    "qtl_falconer_threshold_parameters",
    "qtl_multivariate_mssn_full",
    "qtl_multivariate_power_full",
    "qtl_threshold_chisq_mssn",
    "qtl_threshold_chisq_power",
    "tdt_expected_nontransmission_probability",
    "tdt_expected_transmission_counts",
    "tdt_expected_transmission_probability",
    "tdt_mssn",
    "tdt_mssn_from_model",
    "tdt_mssn_phenotype_misclassification_from_ncp",
    "tdt_ngs_mssn",
    "tdt_ngs_power",
    "tdt_power",
    "tdt_power_from_expected_counts",
    "tdt_power_from_model"
  ],
  "_help": [
    {
      "page": "case_control_genotype_misclassification",
      "title": "Specialized Case-Control Genotype Misclassification Functions",
      "topics": [
        "case_control_genotype_misclassification",
        "cc_chisq_mssn_genotype_misclassification_1p",
        "cc_chisq_mssn_genotype_misclassification_2p",
        "cc_chisq_mssn_genotype_misclassification_3p",
        "cc_chisq_mssn_genotype_misclassification_differential_3p",
        "cc_chisq_power_genotype_misclassification_1p",
        "cc_chisq_power_genotype_misclassification_2p",
        "cc_chisq_power_genotype_misclassification_3p",
        "cc_chisq_power_genotype_misclassification_differential_3p"
      ]
    },
    {
      "page": "case_control_locus_heterogeneity",
      "title": "Specialized Case-Control Locus-Heterogeneity Functions",
      "topics": [
        "case_control_locus_heterogeneity",
        "cc_chisq_mssn_locus_heterogeneity",
        "cc_chisq_power_locus_heterogeneity",
        "cc_trend_mssn_locus_heterogeneity",
        "cc_trend_power_locus_heterogeneity"
      ]
    },
    {
      "page": "case_control_phenotype_misclassification",
      "title": "Specialized Case-Control Phenotype Misclassification Functions",
      "topics": [
        "case_control_phenotype_misclassification",
        "cc_chisq_mssn_phenotype_misclassification",
        "cc_chisq_power_phenotype_misclassification"
      ]
    },
    {
      "page": "cc_mssn",
      "title": "Case-Control Minimum Sample Size for Conditional Genotype Frequencies",
      "topics": [
        "cc_mssn"
      ]
    },
    {
      "page": "cc_ngs_mssn",
      "title": "Analytic MSSN for a Case-Control Sequencing Study",
      "topics": [
        "cc_ngs_mssn"
      ]
    },
    {
      "page": "cc_ngs_power",
      "title": "Analytic Power for a Case-Control Sequencing Study",
      "topics": [
        "cc_ngs_power"
      ]
    },
    {
      "page": "cc_power",
      "title": "Case-Control Power for Conditional Genotype Frequencies",
      "topics": [
        "cc_power"
      ]
    },
    {
      "page": "lrtae_mssn",
      "title": "Minimum Total Sample Size for an LRTae Design",
      "topics": [
        "lrtae_mssn"
      ]
    },
    {
      "page": "lrtae_ncp",
      "title": "Noncentrality Parameter for Prospective LRTae Designs",
      "topics": [
        "lrtae_ncp"
      ]
    },
    {
      "page": "lrtae_power",
      "title": "Prospective Power for an LRTae Design",
      "topics": [
        "lrtae_power"
      ]
    },
    {
      "page": "ngs_genotype_error_matrix",
      "title": "Sequencing-Derived Genotype Error Matrix",
      "topics": [
        "ngs_genotype_error_matrix"
      ]
    },
    {
      "page": "paweh_app",
      "title": "Construct the paweh Shiny Dashboard",
      "topics": [
        "paweh_app"
      ]
    },
    {
      "page": "plot_cc_mssn",
      "title": "Plot Case-Control Minimum Sample Size Necessary",
      "topics": [
        "plot_cc_mssn"
      ]
    },
    {
      "page": "plot_cc_power",
      "title": "Plot Case-Control Power",
      "topics": [
        "plot_cc_power"
      ]
    },
    {
      "page": "plot_ngs_mssn",
      "title": "Plot MSSN Sensitivity for Sequencing Designs",
      "topics": [
        "plot_ngs_mssn"
      ]
    },
    {
      "page": "plot_ngs_power",
      "title": "Plot Power Sensitivity for Sequencing Designs",
      "topics": [
        "plot_ngs_power"
      ]
    },
    {
      "page": "plot_qtl_anova_mssn",
      "title": "Plot One-Way ANOVA Minimum Sample Size Under the Falconer Model",
      "topics": [
        "plot_qtl_anova_mssn"
      ]
    },
    {
      "page": "plot_qtl_anova_power",
      "title": "Plot One-Way ANOVA Power Under the Falconer Model",
      "topics": [
        "plot_qtl_anova_power"
      ]
    },
    {
      "page": "plot_qtl_genotype_distribution",
      "title": "Plot Falconer Genotype-Specific Quantitative-Trait Distributions",
      "topics": [
        "plot_qtl_genotype_distribution"
      ]
    },
    {
      "page": "plot_qtl_threshold_chisq_mssn",
      "title": "Plot Threshold-Selected Genotype Chi-Square Minimum Sample Size",
      "topics": [
        "plot_qtl_threshold_chisq_mssn"
      ]
    },
    {
      "page": "plot_qtl_threshold_chisq_power",
      "title": "Plot Threshold-Selected Genotype Chi-Square Power",
      "topics": [
        "plot_qtl_threshold_chisq_power"
      ]
    },
    {
      "page": "plot_tdt_mssn",
      "title": "Plot TDT Minimum Sample Size Necessary",
      "topics": [
        "plot_tdt_mssn"
      ]
    },
    {
      "page": "plot_tdt_mssn_locus_heterogeneity",
      "title": "Plot TDT MSSN Sensitivity to Locus Heterogeneity",
      "topics": [
        "plot_tdt_mssn_locus_heterogeneity"
      ]
    },
    {
      "page": "plot_tdt_mssn_phenotype_misclassification",
      "title": "Plot TDT MSSN Sensitivity to Phenotype Misclassification",
      "topics": [
        "plot_tdt_mssn_phenotype_misclassification"
      ]
    },
    {
      "page": "plot_tdt_power",
      "title": "Plot TDT Power",
      "topics": [
        "plot_tdt_power"
      ]
    },
    {
      "page": "plot_tdt_power_locus_heterogeneity",
      "title": "Plot TDT Power Sensitivity to Locus Heterogeneity",
      "topics": [
        "plot_tdt_power_locus_heterogeneity"
      ]
    },
    {
      "page": "plot_tdt_power_phenotype_misclassification",
      "title": "Plot TDT Power Sensitivity to Phenotype Misclassification",
      "topics": [
        "plot_tdt_power_phenotype_misclassification"
      ]
    },
    {
      "page": "plot_tdt_surface3d",
      "title": "Plot a Generalized 3D TDT Sensitivity Surface",
      "topics": [
        "plot_tdt_surface3d"
      ]
    },
    {
      "page": "qtl_anova_mssn",
      "title": "Minimum Sample Size for One-Way ANOVA Under the Falconer Model",
      "topics": [
        "qtl_anova_mssn"
      ]
    },
    {
      "page": "qtl_anova_power",
      "title": "Power for One-Way ANOVA Under the Falconer Model",
      "topics": [
        "qtl_anova_power"
      ]
    },
    {
      "page": "qtl_falconer_parameters",
      "title": "Falconer Parameters for a Single Quantitative Trait",
      "topics": [
        "qtl_falconer_parameters"
      ]
    },
    {
      "page": "qtl_falconer_threshold_parameters",
      "title": "Threshold-Selected Parameters Under the Falconer Model",
      "topics": [
        "qtl_falconer_threshold_parameters"
      ]
    },
    {
      "page": "qtl_multivariate_mssn_full",
      "title": "Multivariate Falconer Minimum Sample Size",
      "topics": [
        "qtl_multivariate_mssn_full"
      ]
    },
    {
      "page": "qtl_multivariate_power_full",
      "title": "Multivariate Falconer Power",
      "topics": [
        "qtl_multivariate_power_full"
      ]
    },
    {
      "page": "qtl_threshold_chisq_mssn",
      "title": "Minimum Sample Size for a Threshold-Selected Genotype Chi-Square Test",
      "topics": [
        "qtl_threshold_chisq_mssn"
      ]
    },
    {
      "page": "qtl_threshold_chisq_power",
      "title": "Power for a Threshold-Selected Genotype Chi-Square Test",
      "topics": [
        "qtl_threshold_chisq_power"
      ]
    },
    {
      "page": "tdt_expected_nontransmission_probability",
      "title": "Expected Non-Transmission Probability (gNT*) in the Transmission Disequilibrium Test (TDT)",
      "topics": [
        "tdt_expected_nontransmission_probability"
      ]
    },
    {
      "page": "tdt_expected_transmission_counts",
      "title": "Expected Transmissions (ET*) and Non-Transmissions (ENT*) in the Transmission Disequilibrium Test (TDT)",
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        "tdt_expected_transmission_counts"
      ]
    },
    {
      "page": "tdt_expected_transmission_probability",
      "title": "Expected Transmission Probability (gT*) in the Transmission Disequilibrium Test (TDT)",
      "topics": [
        "tdt_expected_transmission_probability"
      ]
    },
    {
      "page": "tdt_mssn",
      "title": "Family-Based (TDT) Minimum Sample Size Necessary",
      "topics": [
        "tdt_mssn"
      ]
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    {
      "page": "tdt_mssn_from_model",
      "title": "TDT Minimum Sample Size Necessary from Genetic Model Parameters",
      "topics": [
        "tdt_mssn_from_model"
      ]
    },
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      "page": "tdt_mssn_phenotype_misclassification_from_ncp",
      "title": "TDT Minimum Sample Size Necessary from an NCP under Phenotype Misclassification",
      "topics": [
        "tdt_mssn_phenotype_misclassification_from_ncp"
      ]
    },
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      "topics": [
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      ]
    },
    {
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      "title": "Analytic Power for a TDT1-NGS Sequencing Study",
      "topics": [
        "tdt_ngs_power"
      ]
    },
    {
      "page": "tdt_power",
      "title": "Family-Based (TDT) Power",
      "topics": [
        "tdt_power"
      ]
    },
    {
      "page": "tdt_power_from_expected_counts",
      "title": "Transmission Disequilibrium Test (TDT) Power from Expected Transmissions and Non-Transmissions",
      "topics": [
        "tdt_power_from_expected_counts"
      ]
    },
    {
      "page": "tdt_power_from_model",
      "title": "Transmission Disequilibrium Test (TDT) Power from Genetic Model Parameters",
      "topics": [
        "tdt_power_from_model"
      ]
    }
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