Files in ben18785/incidenceinflation

Estimate R0 Given Case Reporting Delays

LICENSE.md R/convergence_checking.R R/data.R R/probabilities.R R/sampling.R R/simulated-data.R R/utils.R README.Rmd README.md man/ILI_2014.Rd man/accept_reject.Rd man/combine_chains.Rd man/conditional_cases_logp.Rd man/construct_w_matrix.Rd man/convert_df_to_posterior_format.Rd man/convert_results_to_posterior_format.Rd man/create_reporting_from_single_parameters_df.Rd man/detected_after_unobserved_prob.Rd man/dgamma_mean_sd.Rd man/expected_cases.Rd man/gamma_discrete_pmf.Rd man/generate_snapshots.Rd man/max_uncertain_days.Rd man/maximise_reporting_logp.Rd man/mcmc.Rd man/mcmc_single.Rd man/measles_NL_2013.Rd man/metropolis_step.Rd man/metropolis_step_overdispersion.Rd man/metropolis_steps.Rd man/nb_log_likelihood_Rt_piece.Rd man/observation_process_all_times_logp.Rd man/observation_process_logp.Rd man/observation_process_single_logp.Rd man/observed_cases.Rd man/observed_cases_single.Rd man/observed_cases_trajectory.Rd man/pgamma_mean_sd.Rd man/prior_reporting_parameters.Rd man/propose_overdispersion_parameter.Rd man/propose_reporting_parameters.Rd man/qgamma_mean_sd.Rd man/sample_Rt.Rd man/sample_Rt_single_piece.Rd man/sample_cases_history.Rd man/sample_nb_Rt_piece.Rd man/sample_or_maximise_gamma.Rd man/sample_reporting.Rd man/sample_true_cases_single_onset.Rd man/state_process_logp.Rd man/state_process_nb_logp_all_onsets.Rd man/thin_series.Rd man/thin_single_series.Rd man/true_cases.Rd man/true_cases_single.Rd man/undetected_prob.Rd man/weights_series.Rd tests/testthat.R tests/testthat/test-convergence_checking.R tests/testthat/test-probabilities.R tests/testthat/test-sampling.R tests/testthat/test-simulated-data.R tests/testthat/test-utils.R vignettes/negative_binomial_sampling.Rmd vignettes/simulating_data_and_model_fit.Rmd vignettes/temporal_variation_in_reporting.Rmd