├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── bootstrap.R ├── data.R ├── deconvolve.R ├── estimateR.R ├── estimate_Re.R ├── pipe.R ├── simulate.R ├── smooth.R ├── utils-arguments.R ├── utils-convolution.R ├── utils-distribution.R ├── utils-empirical_delays.R ├── utils-general.R ├── utils-input.R ├── utils-nowcast.R ├── utils-output.R ├── utils-simulate.R ├── utils-testing.R ├── utils-uncertainty.R └── utils-validation.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data-raw ├── EST_incidence_data.R ├── HK_delay_data.R └── HK_incidence_data.R ├── data ├── CH_simulated_linelist.rda ├── EST_incidence_data.rda ├── HK_delay_data.rda └── HK_incidence_data.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── articles │ ├── adding_methods.html │ ├── adding_methods_files │ │ └── header-attrs-2.11 │ │ │ └── header-attrs.js │ ├── comparison_levels_input_details.html │ ├── comparison_levels_input_details_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-15-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── empirical-delay-data.html │ ├── empirical-delay-data_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── estimateR.html │ ├── estimateR_files │ │ ├── figure-html │ │ │ └── unnamed-chunk-9-1.png │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── estimation_of_uncertainty.html │ ├── estimation_of_uncertainty_files │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── incidence_data_workflow_example.html │ ├── incidence_data_workflow_example_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── index.html │ ├── linelist_workflow_example.html │ ├── linelist_workflow_example_files │ │ ├── figure-html │ │ │ └── unnamed-chunk-10-1.png │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── simulating_data.html │ └── simulating_data_files │ │ ├── figure-html │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-5-1.png │ │ ├── unnamed-chunk-6-1.png │ │ └── unnamed-chunk-7-1.png │ │ └── header-attrs-2.11 │ │ └── header-attrs.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── CH_simulated_linelist.html │ ├── EST_incidence_data.html │ ├── EpiEstim_wrapper.html │ ├── HK_delay_data.html │ ├── HK_incidence_data.html │ ├── Rplot001.png │ ├── bootstrap_params.html │ ├── bootstrap_return.html │ ├── build_delay_distribution.html │ ├── combining_observations.html │ ├── convolve_delays.html │ ├── dating.html │ ├── deconvolve_incidence.html │ ├── delay_empirical.html │ ├── delay_high.html │ ├── distribution.html │ ├── do_uncertainty_summary.html │ ├── dot-add_date_column.html │ ├── dot-add_noise.html │ ├── dot-are_valid_argument_values.html │ ├── dot-block_bootstrap.html │ ├── dot-block_bootstrap_overlap_func.html │ ├── dot-build_list_of_gradually_changing_delays.html │ ├── dot-check_class.html │ ├── dot-check_class_parameter_name.html │ ├── dot-check_if_integer_value.html │ ├── dot-check_if_integer_vector.html │ ├── dot-check_if_noise.html │ ├── dot-check_if_non_neg_integer_vector.html │ ├── dot-check_if_non_negative_number.html │ ├── dot-check_if_null_or_belongs_to_class.html │ ├── dot-check_if_null_or_integer.html │ ├── dot-check_if_number.html │ ├── dot-check_if_positive_integer.html │ ├── dot-check_if_positive_number.html │ ├── dot-check_is_bootstrap_estimate.html │ ├── dot-check_is_delay_distribution_matrix.html │ ├── dot-check_is_empirical_delay_data.html │ ├── dot-check_is_estimate.html │ ├── dot-check_is_numeric_in_interval.html │ ├── dot-check_is_probability_distr_vector.html │ ├── dot-compute_Ot.html │ ├── dot-compute_discretized_infectiousness.html │ ├── dot-convolve_delay_distribution_matrices.html │ ├── dot-convolve_delay_distribution_vector_with_matrix.html │ ├── dot-convolve_delay_distribution_vectors.html │ ├── dot-convolve_delay_distributions.html │ ├── dot-convolve_two_delay_distributions.html │ ├── dot-convove_delay_distribution_matrices.html │ ├── dot-deconvolve_incidence_Richardson_Lucy.html │ ├── dot-delay_distribution_matrix_rmse_compute.html │ ├── dot-draw_It.html │ ├── dot-estimate_Re_EpiEstim_piecewise_constant.html │ ├── dot-estimate_Re_EpiEstim_sliding_window.html │ ├── dot-generate_delay_data.html │ ├── dot-get_arg_names.html │ ├── dot-get_delay_distribution.html │ ├── dot-get_delay_matrix_column.html │ ├── dot-get_delay_matrix_from_delay_distribution_parms.html │ ├── dot-get_delay_matrix_from_delay_distributions.html │ ├── dot-get_delays_over_full_time_units.html │ ├── dot-get_discretized_distribution.html │ ├── dot-get_distribution_function.html │ ├── dot-get_distribution_parms.html │ ├── dot-get_dots_as_list.html │ ├── dot-get_infectiousness_profile.html │ ├── dot-get_initial_deconvolution_shift.html │ ├── dot-get_input_length.html │ ├── dot-get_matrix_from_single_delay_distr.html │ ├── dot-get_matrix_from_waiting_time_distributions.html │ ├── dot-get_module_input.html │ ├── dot-get_module_output.html │ ├── dot-get_offset.html │ ├── dot-get_quantiles.html │ ├── dot-get_right_boundary_for_distribution_vector.html │ ├── dot-get_shared_args.html │ ├── dot-get_time_steps_quantile.html │ ├── dot-get_values.html │ ├── dot-is_numeric_vector.html │ ├── dot-is_positive_numeric_vector.html │ ├── dot-is_single_delay.html │ ├── dot-is_valid_computation_ready_delay_object.html │ ├── dot-is_valid_delay_object.html │ ├── dot-is_valid_delay_single_or_list.html │ ├── dot-is_valid_distribution.html │ ├── dot-is_valid_module_input.html │ ├── dot-is_value_in_accepted_values_vector.html │ ├── dot-is_value_valid_time_step.html │ ├── dot-left_augment_delay_distribution.html │ ├── dot-make_ecdf_from_empirical_data_and_gamma.html │ ├── dot-make_empty_module_output.html │ ├── dot-make_tibble_from_output.html │ ├── dot-prettify_result.html │ ├── dot-print_vector.html │ ├── dot-random_round.html │ ├── dot-sample_from_distribution.html │ ├── dot-simplify_output.html │ ├── dot-smooth_LOESS.html │ ├── dot-summarise_CI_bootstrap.html │ ├── dot-summarise_bagged_mean.html │ ├── empirical_delay_data_format.html │ ├── estimate_Re.html │ ├── estimate_Re_from_noisy_delayed_incidence.html │ ├── estimate_from_combined_observations.html │ ├── expect_delay_matrix_sums_lte_1.html │ ├── generate_delay_data.html │ ├── get_block_bootstrapped_estimate.html │ ├── get_bootstrap_replicate.html │ ├── get_bootstrapped_estimates_from_combined_observations.html │ ├── get_infections_from_incidence.html │ ├── get_matrix_empirical_waiting_time_distr.html │ ├── get_matrix_from_empirical_delay_distr.html │ ├── index.html │ ├── inner_addition.html │ ├── inner_module.html │ ├── left_addition.html │ ├── leftpad_input.html │ ├── make_tibble_from_output.html │ ├── merge_outputs.html │ ├── module_methods.html │ ├── module_objects.html │ ├── module_structure.html │ ├── nowcast.html │ ├── pipe_params.html │ ├── simulate.html │ ├── simulate_combined_observations.html │ ├── simulate_delayed_observations.html │ ├── simulate_infections.html │ ├── smooth_deconvolve_estimate.html │ ├── smooth_incidence.html │ ├── summarise_uncertainty.html │ ├── uncertainty.html │ ├── universal_params.html │ └── validation_utility_params.html ├── inst └── CITATION ├── man ├── CH_simulated_linelist.Rd ├── EST_incidence_data.Rd ├── EpiEstim_wrapper.Rd ├── HK_delay_data.Rd ├── HK_incidence_data.Rd ├── bootstrap_params.Rd ├── bootstrap_return.Rd ├── build_delay_distribution.Rd ├── combining_observations.Rd ├── convolve_delays.Rd ├── dating.Rd ├── deconvolve_incidence.Rd ├── delay_empirical.Rd ├── delay_high.Rd ├── distribution.Rd ├── do_uncertainty_summary.Rd ├── dot-add_date_column.Rd ├── dot-add_noise.Rd ├── dot-are_valid_argument_values.Rd ├── dot-block_bootstrap.Rd ├── dot-block_bootstrap_overlap_func.Rd ├── dot-build_list_of_gradually_changing_delays.Rd ├── dot-check_class.Rd ├── dot-check_class_parameter_name.Rd ├── dot-check_if_integer_value.Rd ├── dot-check_if_integer_vector.Rd ├── dot-check_if_noise.Rd ├── dot-check_if_non_neg_integer_vector.Rd ├── dot-check_if_non_negative_number.Rd ├── dot-check_if_null_or_belongs_to_class.Rd ├── dot-check_if_null_or_integer.Rd ├── dot-check_if_number.Rd ├── dot-check_if_positive_integer.Rd ├── dot-check_if_positive_number.Rd ├── dot-check_is_bootstrap_estimate.Rd ├── dot-check_is_delay_distribution_matrix.Rd ├── dot-check_is_empirical_delay_data.Rd ├── dot-check_is_estimate.Rd ├── dot-check_is_numeric_in_interval.Rd ├── dot-check_is_probability_distr_vector.Rd ├── dot-compute_Ot.Rd ├── dot-compute_discretized_infectiousness.Rd ├── dot-convolve_delay_distribution_matrices.Rd ├── dot-convolve_delay_distribution_vector_with_matrix.Rd ├── dot-convolve_delay_distribution_vectors.Rd ├── dot-convolve_delay_distributions.Rd ├── dot-convolve_two_delay_distributions.Rd ├── dot-deconvolve_incidence_Richardson_Lucy.Rd ├── dot-delay_distribution_matrix_rmse_compute.Rd ├── dot-draw_It.Rd ├── dot-estimate_Re_EpiEstim_piecewise_constant.Rd ├── dot-estimate_Re_EpiEstim_sliding_window.Rd ├── dot-generate_delay_data.Rd ├── dot-get_arg_names.Rd ├── dot-get_delay_distribution.Rd ├── dot-get_delay_matrix_column.Rd ├── dot-get_delay_matrix_from_delay_distributions.Rd ├── dot-get_delays_over_full_time_units.Rd ├── dot-get_discretized_distribution.Rd ├── dot-get_distribution_function.Rd ├── dot-get_distribution_parms.Rd ├── dot-get_dots_as_list.Rd ├── dot-get_infectiousness_profile.Rd ├── dot-get_input_length.Rd ├── dot-get_module_input.Rd ├── dot-get_module_output.Rd ├── dot-get_offset.Rd ├── dot-get_quantiles.Rd ├── dot-get_right_boundary_for_distribution_vector.Rd ├── dot-get_shared_args.Rd ├── dot-get_time_steps_quantile.Rd ├── dot-get_values.Rd ├── dot-is_numeric_vector.Rd ├── dot-is_positive_numeric_vector.Rd ├── dot-is_single_delay.Rd ├── dot-is_valid_computation_ready_delay_object.Rd ├── dot-is_valid_delay_object.Rd ├── dot-is_valid_delay_single_or_list.Rd ├── dot-is_valid_distribution.Rd ├── dot-is_valid_module_input.Rd ├── dot-is_value_in_accepted_values_vector.Rd ├── dot-is_value_valid_time_step.Rd ├── dot-left_augment_delay_distribution.Rd ├── dot-make_empty_module_output.Rd ├── dot-prettify_result.Rd ├── dot-print_vector.Rd ├── dot-random_round.Rd ├── dot-sample_from_distribution.Rd ├── dot-simplify_output.Rd ├── dot-smooth_LOESS.Rd ├── dot-summarise_CI_bootstrap.Rd ├── dot-summarise_bagged_mean.Rd ├── empirical_delay_data_format.Rd ├── estimate_Re.Rd ├── estimate_Re_from_noisy_delayed_incidence.Rd ├── estimate_from_combined_observations.Rd ├── examples │ ├── build_delay_distribution.R │ ├── convolve_delays.R │ ├── deconvolve_incidence.R │ ├── estimate_Re.R │ ├── estimate_Re_from_noisy_delayed_incidence.R │ ├── estimate_from_combined_observations.R │ ├── get_block_bootstrapped_estimate.R │ ├── get_bootstrap_replicate.R │ ├── get_bootstrapped_estimates_from_combined_observations.R │ ├── get_infections_from_incidence.R │ ├── get_matrix_from_empirical_delay_distr.R │ ├── make_tibble_from_output.R │ ├── merge_outputs.R │ ├── nowcast.R │ ├── simulate_combined_observations.R │ ├── simulate_delayed_observations.R │ ├── simulate_infections.R │ └── smooth_incidence.R ├── expect_delay_matrix_sums_lte_1.Rd ├── get_block_bootstrapped_estimate.Rd ├── get_bootstrap_replicate.Rd ├── get_bootstrapped_estimates_from_combined_observations.Rd ├── get_infections_from_incidence.Rd ├── get_matrix_from_empirical_delay_distr.Rd ├── inner_addition.Rd ├── inner_module.Rd ├── left_addition.Rd ├── leftpad_input.Rd ├── make_tibble_from_output.Rd ├── merge_outputs.Rd ├── module_methods.Rd ├── module_objects.Rd ├── module_structure.Rd ├── nowcast.Rd ├── pipe_params.Rd ├── simulate.Rd ├── simulate_combined_observations.Rd ├── simulate_delayed_observations.Rd ├── simulate_infections.Rd ├── smooth_incidence.Rd ├── summarise_uncertainty.Rd ├── uncertainty.Rd ├── universal_params.Rd └── validation_utility_params.Rd ├── tests ├── testthat.R └── testthat │ ├── test-bootstrap.R │ ├── test-deconvolve.R │ ├── test-estimate_Re.R │ ├── test-pipe.R │ ├── test-smooth.R │ ├── test-utils-convolution.R │ ├── test-utils-distribution.R │ ├── test-utils-empirical_delays.R │ ├── test-utils-input.R │ ├── test-utils-nowcast.R │ └── test-utils-output.R └── vignettes ├── .gitignore ├── adding_methods.Rmd ├── comparison_levels_input_details.Rmd ├── estimateR.Rmd ├── incidence_data_workflow_example.Rmd 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