Man pages for penetrance
Methods for Penetrance Estimation in Family-Based Studies
| absValue | Function to return absolute values |
| apply_burn_in | Apply Burn-In |
| apply_thinning | Apply Thinning |
| baseline_data_default | Default Baseline Data |
| calculateBaseline | Calculate Baseline Risk |
| calculateEmpiricalDensity | Calculate Empirical Age Density |
| calculateNCPen | Calculate Age-Specific Non-Carrier Penetrance |
| calculate_weibull_parameters | Calculate Weibull Parameters |
| combine_chains | Combine Chains Function to combine the posterior samples from... |
| combine_chains_noSex | Combine Chains for Non-Sex-Specific Estimation |
| distribution_data_default | Default Distribution Data |
| drawBaseline | Draw Ages Using the Inverse CDF Method from the baseline data |
| drawEmpirical | Draw Ages Using the Inverse CDF Method from Empirical Density |
| generate_density_plots | Generate Posterior Density Plots |
| generate_summary | Generate Summary |
| generate_summary_noSex | Generate Summary for Non-Sex-Specific Estimation |
| imputeAges | Impute Missing Ages in Family-Based Data |
| imputeAgesInit | Initialize Age Imputation |
| imputeUnaffectedAges | Impute Ages for Unaffected Individuals |
| lik.fn | Penetrance Function |
| lik_noSex | Likelihood Calculation without Sex Differentiation |
| makePriors | Make Priors |
| mhChain | Execution of a Single Chain in Metropolis-Hastings for Cancer... |
| mhLogLikelihood_clipp | Calculate Log Likelihood using clipp Package |
| mhLogLikelihood_clipp_noSex | Calculate Log Likelihood without Sex Differentiation |
| out_sim | Simulated Output Data |
| penetrance | penetrance: A Package for Penetrance Estimation |
| plot_acf | Plot Autocorrelation for Multiple MCMC Chains (Posterior... |
| plot_loglikelihood | Plot Log-Likelihood for Multiple MCMC Chains |
| plot_pdf | Plot Weibull Probability Density Function with Credible... |
| plot_penetrance | Plot Weibull Distribution with Credible Intervals |
| plot_trace | Plot MCMC Trace Plots |
| printRejectionRates | Print MCMC Rejection Rates |
| prior_params_default | Default Prior Parameters |
| risk_proportion_default | Default Risk Proportions |
| simulated_families | Processed Family Data |
| test_fam2 | Processed Family Data |
| transformDF | Transform Data Frame |
| validate_weibull_parameters | Validate Weibull Parameters |
