convolve_delays: Convolve delay distributions

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

Convolve delay distributions

Description

Take a list of delay distributions and return their convolution. The convolution of a delay A -> B and a delay B -> C corresponds to the delay distribution of A -> C. Delays are assumed to happen in the same chronological order as the order they are given in in the delays list.

Usage

convolve_delays(delays, n_report_time_steps = NULL, ...)

Arguments

delays	List of delays, with flexible structure. Each delay in the delays list can be one of: a list representing a distribution object a discretized delay distribution vector a discretized delay distribution matrix a dataframe containing empirical delay data
n_report_time_steps	integer. Length of incidence time series. Use only when providing empirical delay data.
...	Arguments passed on to get_matrix_from_empirical_delay_distr, build_delay_distribution min_number_cases integer. Minimal number of cases to build the empirical distribution from. If num_steps_in_a_unit is NULL, for any time step T, the min_number_cases records prior to T are used. If less than min_number_cases delays were recorded before T, then T is ignored and the min_number_cases earliest-recorded delays are used. If num_steps_in_a_unit is given a value, a similar same procedure is applied, except that, now at least min_number_cases must be taken over a round number of time units. For example, if num_steps_in_a_unit = 7, and time steps represent consecutive days, to build the distribution for time step T, we find the smallest number of weeks starting from T and going in the past, for which at least min_number_cases delays were recorded. We then use all the delays recorded during these weeks. Weeks are not meant as necessarily being Monday to Sunday, but simply 7 days in a row, e.g. it can be Thursday-Wednesday. Again, if less than min_number_cases delays were recorded before T, then T is ignored. We then find the minimum number of weeks, starting from the first recorded delay that contains at least min_number_cases. upper_quantile_threshold numeric. Between 0 and 1. Argument for internal use. min_number_cases_fraction numeric. Between 0 and 1. If min_number_cases is not provided (kept to NULL), the number of most-recent cases used to build the instant delay distribution is min_number_cases_fraction times the total number of reported delays. min_min_number_cases numeric. Lower bound for number of cases used to build an instant delay distribution. fit string. One of "gamma" or "none". Specifies the type of fit that is applied to the columns of the delay matrix num_steps_in_a_unit Optional argument. Number of time steps in a full time unit (e.g. 7 if looking at weeks). If set, the delays used to build a particular delay distribution will span over a round number of such time units. This option is included for comparison with legacy code. ref_date Date. Optional. Date of the first data entry in incidence_data time_step string. Time between two consecutive incidence datapoints. "day", "2 days", "week", "year"... (see seq.Date for details) max_quantile numeric value between 0 and 1. Upper quantile reached by the last element in the discretized distribution vector. offset_by_one boolean. Set to TRUE if distribution represents the fit of data that was offset by one (fitted_data = original_data + 1) to accommodate zeroes in original_data.

Details

This function is flexible in the type of delay inputs it can handle. Each delay in the delays list can be one of:

• a list representing a distribution object

• a discretized delay distribution vector

• a discretized delay distribution matrix

• a dataframe containing empirical delay data

see get_matrix_from_empirical_delay_distr for details on the format expected for the empirical delay data.

Value

a discretized delay distribution vector or matrix. A vector is returned when input delay distributions are constant through time: either they are vectors already or in the form of a list-specified distribution. A matrix is returned when at least one of the delays has a delay distribution that can change through time. This is the case with empirical delay data or if any of the input is already a delay distribution matrix.

Examples

## Convolving the delay between infection and onset of symptoms with the delay
# between onset of symptoms and case report to obtain the final delay between
# infection and case report. Using the resulting delay distribution to recover
# the original infection events

smoothed_incidence <- smooth_incidence(HK_incidence_data$case_incidence)

shape_incubation = 3.2
scale_incubation = 1.3
delay_incubation <- list(name="gamma", shape = shape_incubation, scale = scale_incubation)

shape_onset_to_report = 2.7
scale_onset_to_report = 1.6
delay_onset_to_report <- list(name="gamma",
                              shape = shape_onset_to_report,
                              scale = scale_onset_to_report)

total_delay_1 <- convolve_delays(list(delay_incubation, delay_onset_to_report))

deconvolved_incidence <- deconvolve_incidence(
  incidence_data = smoothed_incidence,
  delay = total_delay_1
)

## Convolving multiple delays
# In this example it is assumed that the delay between infection and case report
# is composed of three delays; the delay between infection and symptom onset,
# the delay between symptom onset and case testing

shape_incubation = 3.2
scale_incubation = 1.3
delay_incubation <- list(name="gamma", shape = shape_incubation, scale = scale_incubation)

delay_onset_to_test_taken <- list(name = "norm", mean = 5, sd = 2)

delay_test_to_report <- list(name="norm", mean = 2, sd = 0.5)

total_delay_2 <- convolve_delays(list(delay_incubation,
                                      delay_onset_to_test_taken,
                                      delay_test_to_report))

## Convolving delays of multiple types
# Defining the incubation period as a probability vector, and the delay between
# symptom onset and case observation as a delay matrix

delay_incubation <- c(0.01, 0.1, 0.15, 0.18, 0.17, 0.14, 0.11, 0.07, 0.035, 0.020, 0.015)

delay_matrix <- get_matrix_from_empirical_delay_distr(
  HK_delay_data,
  n_report_time_steps = 50
)

total_delay_3 <- convolve_delays(list(delay_incubation, delay_matrix))

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