Specify modeling assumptions — sewer

Specify model assumptions such as the generation time distribution or shedding load distribution. This is a convenience function to collect all assumptions in one object.

Usage

sewer_assumptions(
  generation_dist = NULL,
  shedding_dist = NULL,
  shedding_reference = NULL,
  incubation_dist = NULL,
  min_cases = 10,
  load_per_case = NULL,
  residence_dist = c(1),
  ...
)

Arguments

generation_dist: Generation time distribution. The intrinsic distribution of the time between infection of a primary case and infection of its secondary cases. Will be automatically passed to generation_dist_assume().
shedding_dist: Shedding load distribution. Describes how the total load shed by an individual is distributed over time (and therefore sums to 1). Will be automatically passed to shedding_dist_assume().
shedding_reference: Is the shedding load distribution relative to the day of "infection" or the day of "symptom_onset"? This is important because shedding load distributions provided in the literature are sometimes by days since infection and sometimes by days since symptom onset. If shedding_reference="symptom_onset", EpiSewer also needs information about the incubation period distribution. Will be automatically passed to shedding_dist_assume().
incubation_dist: Incubation period distribution. The incubation period is the time between infection and symptom onset. This assumption is used when shedding_reference="symptom_onset", i.e. to support shedding load distributions referenced by days since symptom onset. Will be automatically passed to incubation_dist_assume().
min_cases: The minimum incidence (new cases per day) during the modeled time period (default is 10). This assumption is used to calibrate the load_per_case factor (a scaling factor that describes how many pathogen particles are shed by the average infected individual overall and how much of this is detectable at the sampling site). If min_cases is specified, load_per_case is chosen such that the estimated time series of infections does not go significantly below min_cases. Will be automatically passed to load_per_case_calibrate().
load_per_case: This argument allows to directly specify the average total load per case, instead of calibrating it to case data. Note that the load_per_case depends both on biological factors as well as on the specific sewage system and laboratory quantification. Important: To actually use this assumption, the model option load_per_case_assume() must be specified in EpiSewer() via model_shedding(). If you want to use this option to do a manual calibration to case data, the helper function suggest_load_per_case() might also be useful.
residence_dist: Sewer residence time distribution for pathogen particles. By default, EpiSewer assumes that particles arrive at the sampling site within the day of shedding. However, for larger sewage systems, particles may travel longer than a day depending on where and when they were shed into the wastewater. Will be automatically passed to residence_dist_assume().
...: Further assumptions to be passed to EpiSewer().

Value

A list with all assumptions supplied. Can be passed to the assumptions argument in EpiSewer().

Details

Note that if case data is supplied via sewer_data, the min_cases assumption is overwritten and the supplied case data is used for a more accurate calibration instead.