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  "Description": "Implements statistical methods for estimating disease\npenetrance in family-based studies. Penetrance refers to the\nprobability of disease manifestation in individuals carrying\nspecific genetic variants. The package provides tools for\nage-specific penetrance estimation, handling missing data, and\naccounting for ascertainment bias in family studies. Cite as:\nKubista, N., Braun, D. & Parmigiani, G. (2025)\n<doi:10.1093/bioadv/vbaf154>.",
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    "generate_summary_noSex",
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    "makePriors",
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    "mhLogLikelihood_clipp",
    "penetrance",
    "plot_acf",
    "plot_loglikelihood",
    "plot_pdf",
    "plot_penetrance",
    "plot_trace",
    "printRejectionRates",
    "prior_params_default",
    "risk_proportion_default",
    "transformDF",
    "validate_allele_freq",
    "validate_baseline_data",
    "validate_weibull_parameters"
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      "title": "Simulated Output Data",
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      "class": [
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      ],
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      "table": false,
      "tojson": true
    },
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      "title": "Processed Family Data",
      "object": "simulated_families",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "test_fam2",
      "title": "Processed Family Data",
      "object": "test_fam2",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
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      "page": "absValue",
      "title": "Function to return absolute values",
      "topics": [
        "absValue"
      ]
    },
    {
      "page": "apply_burn_in",
      "title": "Apply Burn-In",
      "topics": [
        "apply_burn_in"
      ]
    },
    {
      "page": "apply_thinning",
      "title": "Apply Thinning",
      "topics": [
        "apply_thinning"
      ]
    },
    {
      "page": "baseline_data_default",
      "title": "Default Baseline Data",
      "topics": [
        "baseline_data_default"
      ]
    },
    {
      "page": "calculate_weibull_parameters",
      "title": "Calculate Weibull Parameters",
      "topics": [
        "calculate_weibull_parameters"
      ]
    },
    {
      "page": "calculateBaseline",
      "title": "Calculate Baseline Risk",
      "topics": [
        "calculateBaseline"
      ]
    },
    {
      "page": "calculateEmpiricalDensity",
      "title": "Calculate Empirical Age Density",
      "topics": [
        "calculateEmpiricalDensity"
      ]
    },
    {
      "page": "calculateNCPen",
      "title": "Calculate Age-Specific Non-Carrier Penetrance",
      "topics": [
        "calculateNCPen"
      ]
    },
    {
      "page": "combine_chains",
      "title": "Combine Chains Function to combine the posterior samples from the multiple chains.",
      "topics": [
        "combine_chains"
      ]
    },
    {
      "page": "combine_chains_noSex",
      "title": "Combine Chains for Non-Sex-Specific Estimation",
      "topics": [
        "combine_chains_noSex"
      ]
    },
    {
      "page": "distribution_data_default",
      "title": "Default Distribution Data",
      "topics": [
        "distribution_data_default"
      ]
    },
    {
      "page": "drawBaseline",
      "title": "Draw Ages Using the Inverse CDF Method from the baseline data",
      "topics": [
        "drawBaseline"
      ]
    },
    {
      "page": "drawEmpirical",
      "title": "Draw Ages Using the Inverse CDF Method from Empirical Density",
      "topics": [
        "drawEmpirical"
      ]
    },
    {
      "page": "generate_density_plots",
      "title": "Generate Posterior Density Plots",
      "topics": [
        "generate_density_plots"
      ]
    },
    {
      "page": "generate_summary",
      "title": "Generate Summary",
      "topics": [
        "generate_summary"
      ]
    },
    {
      "page": "generate_summary_noSex",
      "title": "Generate Summary for Non-Sex-Specific Estimation",
      "topics": [
        "generate_summary_noSex"
      ]
    },
    {
      "page": "imputeAges",
      "title": "Impute Missing Ages in Family-Based Data",
      "topics": [
        "imputeAges"
      ]
    },
    {
      "page": "imputeAgesInit",
      "title": "Initialize Age Imputation",
      "topics": [
        "imputeAgesInit"
      ]
    },
    {
      "page": "imputeUnaffectedAges",
      "title": "Impute Ages for Unaffected Individuals",
      "topics": [
        "imputeUnaffectedAges"
      ]
    },
    {
      "page": "lik_noSex",
      "title": "Likelihood Calculation without Sex Differentiation",
      "topics": [
        "lik_noSex"
      ]
    },
    {
      "page": "lik.fn",
      "title": "Penetrance Function",
      "topics": [
        "lik.fn"
      ]
    },
    {
      "page": "makePriors",
      "title": "Make Priors",
      "topics": [
        "makePriors"
      ]
    },
    {
      "page": "mhChain",
      "title": "Execution of a Single Chain in Metropolis-Hastings for Cancer Risk Estimation",
      "topics": [
        "mhChain"
      ]
    },
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      "title": "Calculate Log Likelihood using clipp Package",
      "topics": [
        "mhLogLikelihood_clipp"
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    },
    {
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      "title": "Calculate Log Likelihood without Sex Differentiation",
      "topics": [
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      ]
    },
    {
      "page": "out_sim",
      "title": "Simulated Output Data",
      "topics": [
        "out_sim"
      ]
    },
    {
      "page": "penetrance",
      "title": "penetrance: A Package for Penetrance Estimation",
      "topics": [
        "penetrance-package",
        "penetrance"
      ]
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      "page": "plot_acf",
      "title": "Plot Autocorrelation for Multiple MCMC Chains (Posterior Samples)",
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    },
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      "page": "plot_loglikelihood",
      "title": "Plot Log-Likelihood for Multiple MCMC Chains",
      "topics": [
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      ]
    },
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      "title": "Plot Weibull Probability Density Function with Credible Intervals",
      "topics": [
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      ]
    },
    {
      "page": "plot_penetrance",
      "title": "Plot Weibull Distribution with Credible Intervals",
      "topics": [
        "plot_penetrance"
      ]
    },
    {
      "page": "plot_trace",
      "title": "Plot MCMC Trace Plots",
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