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Model the shedding process

Source: R/model_shedding.R
model_shedding.Rd

This module function is used to specify the components of the shedding module in EpiSewer.

Each component can be specified using one or several helper functions (see available options below). See the documentation of the individual helper functions to adjust model priors and further settings.

Usage

model_shedding(
  incubation_dist = incubation_dist_assume(),
  shedding_dist = shedding_dist_assume(),
  load_per_case = load_per_case_calibrate(),
  load_variation = load_variation_estimate()
)

Arguments

incubation_dist

Incubation period distribution. EpiSewer uses this as a proxy for the time between infection and the start of shedding, as shedding load distributions in the literature are often given from symptom onset onwards. If the assumed shedding load distribution instead starts from the time of infection, the incubation period should be fixed to 0 days. Modeling options:

shedding_dist

Shedding load distribution. Describes how the total load shed by an individual is distributed over time (and therefore sums to 1). Modeling options:

load_per_case

Average total load per case. This is 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. It depends both on biological factors as well as on the specific sewage system. Modeling options:

load_variation

Individual-level shedding load variation. The strength of shedding may vary between individuals. Modeling this variation can better account for uncertainty especially at low incidence. Modeling options:

Value

A modeldata object containing the data and specifications of the shedding module.

See also

Other module functions: model_forecast(), model_infections(), model_measurements(), model_sampling(), model_sewage()