Man pages for covid-19-Re/estimateR
Reproductive number estimation from delayed observations of infections
| bootstrap_params | Bootstrapping parameters |
| bootstrap_return | Bootstrapping pipe |
| build_delay_distribution | Build a discretized probability distribution vector |
| CH_simulated_linelist | Synthetic linelist of COVID-19 patients |
| combining_observations | Details on combining observations |
| convolve_delays | Convolve delay distributions |
| dating | Dating parameters |
| deconvolve_incidence | Infer infection events dates from delayed observations |
| delay_empirical | Empirical delays parameters |
| delay_high | High-level delay parameters |
| distribution | Distribution |
| dot-add_date_column | Add dates column to dataframe. |
| dot-add_noise | Add noise to a series of observations. |
| dot-are_valid_argument_values | Utility functions for input validity. |
| dot-block_bootstrap | Apply block-bootstrapping procedure to module input |
| dot-block_bootstrap_overlap_func | Helper function for block-bootstrapping |
| dot-build_list_of_gradually_changing_delays | Generate a list of delay distributions with a gradual... |
| dot-check_class | Check whether the class of an object is as expected |
| dot-check_class_parameter_name | Utility functions for input validity. |
| dot-check_if_integer_value | Utility functions for input validity. |
| dot-check_if_integer_vector | Utility functions for input validity. |
| dot-check_if_noise | Utility functions for input validity. |
| dot-check_if_non_negative_number | Utility functions for input validity. |
| dot-check_if_non_neg_integer_vector | Utility functions for input validity. |
| dot-check_if_null_or_belongs_to_class | Utility functions for input validity. |
| dot-check_if_null_or_integer | Utility functions for input validity. |
| dot-check_if_number | Utility functions for input validity. |
| dot-check_if_positive_integer | Utility functions for input validity. |
| dot-check_if_positive_number | Utility functions for input validity. |
| dot-check_is_bootstrap_estimate | Utility functions for input validity. |
| dot-check_is_delay_distribution_matrix | Utility functions for input validity. |
| dot-check_is_empirical_delay_data | Check if input is in the proper empirical delay data format |
| dot-check_is_estimate | Utility functions for input validity. |
| dot-check_is_numeric_in_interval | Utility functions for input validity. |
| dot-check_is_probability_distr_vector | Check that an object represents a probability distribution. |
| dot-compute_discretized_infectiousness | Compute the discretized infectiousness for a particular time... |
| dot-compute_Ot | Compute the number of delayed observations of infections at... |
| dot-convolve_delay_distribution_matrices | Convolve two delay distribution matrices |
| dot-convolve_delay_distributions | Convolve a list of delay vectors or matrices |
| dot-convolve_delay_distribution_vectors | Convolve two discretized probability distribution vectors. |
| dot-convolve_delay_distribution_vector_with_matrix | Convolve a delay distribution vector with a delay... |
| dot-convolve_two_delay_distributions | Convolve two delay vectors or matrices |
| dot-deconvolve_incidence_Richardson_Lucy | Deconvolve the incidence input with the Richardson-Lucy (R-L)... |
| dot-delay_distribution_matrix_rmse_compute | Utility function that generates delay data, assuming a... |
| dot-draw_It | Draw the number of infections for a particular time step. |
| dot-estimate_Re_EpiEstim_piecewise_constant | Estimate Re with EpiEstim in a piecewise-constant fashion |
| dot-estimate_Re_EpiEstim_sliding_window | Estimate Re with EpiEstim using a sliding window |
| dot-generate_delay_data | Generate artificial delay data. |
| dot-get_arg_names | Get the names of the arguments of a function |
| dot-get_delay_distribution | Return probability distribution vector or matrix |
| dot-get_delay_matrix_column | Build a specific column of the delay distribution matrix |
| dot-get_delay_matrix_from_delay_distributions | Build delay distribution matrix from a single delay or a list... |
| dot-get_delays_over_full_time_units | Get delay entries corresponding to a round number of weeks... |
| dot-get_discretized_distribution | Discretize a probability distribution. |
| dot-get_distribution_function | Get distribution function |
| dot-get_distribution_parms | Get relevant parameters from distribution |
| dot-get_dots_as_list | Return dots arguments as list. |
| dot-get_infectiousness_profile | Compute a discretized infectiousness profile from a serial... |
| dot-get_input_length | Get length of values vector in a module input object. |
| dot-get_module_input | Transform input data into a module input object |
| dot-get_module_output | Transform a result output of a module into a module output... |
| dot-get_offset | Get offset from module object |
| dot-get_quantiles | Obtain quantile values for a distribution |
| dot-get_right_boundary_for_distribution_vector | Get the number of steps before a quantile is reached. |
| dot-get_shared_args | Get the arguments which apply to a function among a given... |
| dot-get_time_steps_quantile | Get initial shift for deconvolution step |
| dot-get_values | Get values from module object |
| dot-is_numeric_vector | Check if object is numeric vector. |
| dot-is_positive_numeric_vector | Utility functions for input validity. |
| dot-is_single_delay | Is input a single delay object? |
| dot-is_valid_computation_ready_delay_object | Utility functions for input validity. |
| dot-is_valid_delay_object | Utility functions for input validity. |
| dot-is_valid_delay_single_or_list | Utility functions for input validity. |
| dot-is_valid_distribution | Check if valid distribution list |
| dot-is_valid_module_input | Utility functions for input validity. |
| dot-is_value_in_accepted_values_vector | Utility functions for input validity. |
| dot-is_value_valid_time_step | Utility functions for input validity. |
| dot-left_augment_delay_distribution | Augment a delay distribution by left padding with new... |
| dot-make_empty_module_output | Make empty module output object |
| dot-prettify_result | Prettify results of pipe functions by removing leading and... |
| dot-print_vector | Utility function to print vectors in a copy-pastable format |
| dot-random_round | Round a value to the integer to either the floor or ceiling... |
| dot-sample_from_distribution | Draw samples from a probability distribution. |
| dot-simplify_output | Simplify output object if possible |
| dot-smooth_LOESS | LOESS smoothing function |
| dot-summarise_bagged_mean | Compute bagged mean from bootstrapped replicates |
| dot-summarise_CI_bootstrap | Build a confidence interval from bootstrapped values |
| do_uncertainty_summary | Utility for summarising uncertainty |
| empirical_delay_data_format | Empirical delay data format |
| EpiEstim_wrapper | EpiEstim wrappers arguments |
| estimate_from_combined_observations | Estimate Re from delayed observations of infection events. |
| estimate_Re | Estimate the effective reproductive number Re through time... |
| estimate_Re_from_noisy_delayed_incidence | Estimate Re from incidence data |
| EST_incidence_data | Incidence data for COVID-19 in Estonia |
| expect_delay_matrix_sums_lte_1 | Test whether a delay matrix columns sum to less than one. |
| get_block_bootstrapped_estimate | Estimate Re from incidence and estimate uncertainty with... |
| get_bootstrapped_estimates_from_combined_observations | Estimate Re from incidence and estimate uncertainty by... |
| get_bootstrap_replicate | Obtain a bootstrap replicate from incidence data |
| get_infections_from_incidence | Infer timeseries of infection events from incidence data of... |
| get_matrix_from_empirical_delay_distr | Build matrix of delay distributions through time from... |
| HK_delay_data | Delay between date of onset of symptoms of COVID-19 and date... |
| HK_incidence_data | Incidence data for COVID-19 in Hong Kong |
| inner_addition | Add values from two module objects |
| inner_module | Inner module option characteristics |
| left_addition | Add values from two module objects |
| leftpad_input | Pad values on the left side of input |
| make_tibble_from_output | Convert module output object into tibble |
| merge_outputs | Merge multiple module outputs into tibble |
| module_methods | Methods available for each module |
| module_objects | Module object utilities |
| module_structure | Module structure characteristics |
| nowcast | Correct incidence data for yet-to-be-observed fraction of... |
| pipe_params | Pipe parameters |
| simulate | Simulation parameters |
| simulate_combined_observations | Simulate a series of observations from a course of... |
| simulate_delayed_observations | Simulate a series of delayed observations from a series of... |
| simulate_infections | Simulate a series of infections |
| smooth_incidence | Smooth noisy incidence data |
| summarise_uncertainty | Summarise the uncertainty obtained from bootstrapping |
| uncertainty | Uncertainty summary |
| universal_params | Universal parameters |
| validation_utility_params | Utility functions for input validity. |
