Files in covid-19-Re/estimateR
Reproductive number estimation from delayed observations of infections

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DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/bootstrap.R R/data.R R/deconvolve.R R/estimateR.R R/estimate_Re.R R/pipe.R R/simulate.R R/smooth.R R/utils-arguments.R R/utils-convolution.R R/utils-distribution.R R/utils-empirical_delays.R R/utils-general.R R/utils-input.R R/utils-nowcast.R R/utils-output.R R/utils-simulate.R R/utils-testing.R R/utils-uncertainty.R R/utils-validation.R README.Rmd README.md

_pkgdown.yml

data-raw/EST_incidence_data.R data-raw/HK_delay_data.R data-raw/HK_incidence_data.R

data/CH_simulated_linelist.rda

data/EST_incidence_data.rda

data/HK_delay_data.rda

data/HK_incidence_data.rda

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/adding_methods.html

docs/articles/adding_methods_files/header-attrs-2.11/header-attrs.js

docs/articles/comparison_levels_input_details.html

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docs/articles/comparison_levels_input_details_files/header-attrs-2.11/header-attrs.js

docs/articles/comparison_levels_input_details_files/header-attrs-2.6/header-attrs.js

docs/articles/empirical-delay-data.html

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docs/articles/empirical-delay-data_files/header-attrs-2.6/header-attrs.js

docs/articles/estimateR.html

docs/articles/estimateR_files/figure-html/unnamed-chunk-9-1.png

docs/articles/estimateR_files/header-attrs-2.11/header-attrs.js

docs/articles/estimateR_files/header-attrs-2.6/header-attrs.js

docs/articles/estimation_of_uncertainty.html

docs/articles/estimation_of_uncertainty_files/header-attrs-2.6/header-attrs.js

docs/articles/incidence_data_workflow_example.html

docs/articles/incidence_data_workflow_example_files/figure-html/unnamed-chunk-8-1.png

docs/articles/incidence_data_workflow_example_files/figure-html/unnamed-chunk-9-1.png

docs/articles/incidence_data_workflow_example_files/header-attrs-2.11/header-attrs.js

docs/articles/incidence_data_workflow_example_files/header-attrs-2.6/header-attrs.js

docs/articles/index.html

docs/articles/linelist_workflow_example.html

docs/articles/linelist_workflow_example_files/figure-html/unnamed-chunk-10-1.png

docs/articles/linelist_workflow_example_files/header-attrs-2.11/header-attrs.js

docs/articles/linelist_workflow_example_files/header-attrs-2.6/header-attrs.js

docs/articles/simulating_data.html

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docs/articles/simulating_data_files/header-attrs-2.11/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/CH_simulated_linelist.html

docs/reference/EST_incidence_data.html

docs/reference/EpiEstim_wrapper.html

docs/reference/HK_delay_data.html

docs/reference/HK_incidence_data.html

docs/reference/Rplot001.png

docs/reference/bootstrap_params.html

docs/reference/bootstrap_return.html

docs/reference/build_delay_distribution.html

docs/reference/combining_observations.html

docs/reference/convolve_delays.html

docs/reference/dating.html

docs/reference/deconvolve_incidence.html

docs/reference/delay_empirical.html

docs/reference/delay_high.html

docs/reference/distribution.html

docs/reference/do_uncertainty_summary.html

docs/reference/dot-add_date_column.html

docs/reference/dot-add_noise.html

docs/reference/dot-are_valid_argument_values.html

docs/reference/dot-block_bootstrap.html

docs/reference/dot-block_bootstrap_overlap_func.html

docs/reference/dot-build_list_of_gradually_changing_delays.html

docs/reference/dot-check_class.html

docs/reference/dot-check_class_parameter_name.html

docs/reference/dot-check_if_integer_value.html

docs/reference/dot-check_if_integer_vector.html

docs/reference/dot-check_if_noise.html

docs/reference/dot-check_if_non_neg_integer_vector.html

docs/reference/dot-check_if_non_negative_number.html

docs/reference/dot-check_if_null_or_belongs_to_class.html

docs/reference/dot-check_if_null_or_integer.html

docs/reference/dot-check_if_number.html

docs/reference/dot-check_if_positive_integer.html

docs/reference/dot-check_if_positive_number.html

docs/reference/dot-check_is_bootstrap_estimate.html

docs/reference/dot-check_is_delay_distribution_matrix.html

docs/reference/dot-check_is_empirical_delay_data.html

docs/reference/dot-check_is_estimate.html

docs/reference/dot-check_is_numeric_in_interval.html

docs/reference/dot-check_is_probability_distr_vector.html

docs/reference/dot-compute_Ot.html

docs/reference/dot-compute_discretized_infectiousness.html

docs/reference/dot-convolve_delay_distribution_matrices.html

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docs/reference/dot-convolve_delay_distribution_vectors.html

docs/reference/dot-convolve_delay_distributions.html

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docs/reference/dot-convove_delay_distribution_matrices.html

docs/reference/dot-deconvolve_incidence_Richardson_Lucy.html

docs/reference/dot-delay_distribution_matrix_rmse_compute.html

docs/reference/dot-draw_It.html

docs/reference/dot-estimate_Re_EpiEstim_piecewise_constant.html

docs/reference/dot-estimate_Re_EpiEstim_sliding_window.html

docs/reference/dot-generate_delay_data.html

docs/reference/dot-get_arg_names.html

docs/reference/dot-get_delay_distribution.html

docs/reference/dot-get_delay_matrix_column.html

docs/reference/dot-get_delay_matrix_from_delay_distribution_parms.html

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docs/reference/dot-get_delays_over_full_time_units.html

docs/reference/dot-get_discretized_distribution.html

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docs/reference/dot-get_distribution_parms.html

docs/reference/dot-get_dots_as_list.html

docs/reference/dot-get_infectiousness_profile.html

docs/reference/dot-get_initial_deconvolution_shift.html

docs/reference/dot-get_input_length.html

docs/reference/dot-get_matrix_from_single_delay_distr.html

docs/reference/dot-get_matrix_from_waiting_time_distributions.html

docs/reference/dot-get_module_input.html

docs/reference/dot-get_module_output.html

docs/reference/dot-get_offset.html

docs/reference/dot-get_quantiles.html

docs/reference/dot-get_right_boundary_for_distribution_vector.html

docs/reference/dot-get_shared_args.html

docs/reference/dot-get_time_steps_quantile.html

docs/reference/dot-get_values.html

docs/reference/dot-is_numeric_vector.html

docs/reference/dot-is_positive_numeric_vector.html

docs/reference/dot-is_single_delay.html

docs/reference/dot-is_valid_computation_ready_delay_object.html

docs/reference/dot-is_valid_delay_object.html

docs/reference/dot-is_valid_delay_single_or_list.html

docs/reference/dot-is_valid_distribution.html

docs/reference/dot-is_valid_module_input.html

docs/reference/dot-is_value_in_accepted_values_vector.html

docs/reference/dot-is_value_valid_time_step.html

docs/reference/dot-left_augment_delay_distribution.html

docs/reference/dot-make_ecdf_from_empirical_data_and_gamma.html

docs/reference/dot-make_empty_module_output.html

docs/reference/dot-make_tibble_from_output.html

docs/reference/dot-prettify_result.html

docs/reference/dot-print_vector.html

docs/reference/dot-random_round.html

docs/reference/dot-sample_from_distribution.html

docs/reference/dot-simplify_output.html

docs/reference/dot-smooth_LOESS.html

docs/reference/dot-summarise_CI_bootstrap.html

docs/reference/dot-summarise_bagged_mean.html

docs/reference/empirical_delay_data_format.html

docs/reference/estimate_Re.html

docs/reference/estimate_Re_from_noisy_delayed_incidence.html

docs/reference/estimate_from_combined_observations.html

docs/reference/expect_delay_matrix_sums_lte_1.html

docs/reference/generate_delay_data.html

docs/reference/get_block_bootstrapped_estimate.html

docs/reference/get_bootstrap_replicate.html

docs/reference/get_bootstrapped_estimates_from_combined_observations.html

docs/reference/get_infections_from_incidence.html

docs/reference/get_matrix_empirical_waiting_time_distr.html

docs/reference/get_matrix_from_empirical_delay_distr.html

docs/reference/index.html

docs/reference/inner_addition.html

docs/reference/inner_module.html

docs/reference/left_addition.html

docs/reference/leftpad_input.html

docs/reference/make_tibble_from_output.html

docs/reference/merge_outputs.html

docs/reference/module_methods.html

docs/reference/module_objects.html

docs/reference/module_structure.html

docs/reference/nowcast.html

docs/reference/pipe_params.html

docs/reference/simulate.html

docs/reference/simulate_combined_observations.html

docs/reference/simulate_delayed_observations.html

docs/reference/simulate_infections.html

docs/reference/smooth_deconvolve_estimate.html

docs/reference/smooth_incidence.html

docs/reference/summarise_uncertainty.html

docs/reference/uncertainty.html

docs/reference/universal_params.html

docs/reference/validation_utility_params.html

inst/CITATION

vignettes/.gitignore

vignettes/adding_methods.Rmd vignettes/comparison_levels_input_details.Rmd vignettes/estimateR.Rmd vignettes/incidence_data_workflow_example.Rmd vignettes/linelist_workflow_example.Rmd vignettes/simulating_data.Rmd

covid-19-Re/estimateR documentation built on Sept. 14, 2024, 5:49 a.m.

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covid-19-Re/estimateR
Reproductive number estimation from delayed observations of infections

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Reproductive number estimation from delayed observations of infections

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covid-19-Re/estimateR Reproductive number estimation from delayed observations of infections

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covid-19-Re/estimateR
Reproductive number estimation from delayed observations of infections

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Reproductive number estimation from delayed observations of infections