secondary_opts: Secondary Reports Options

Description

Returns a list of options defining the secondary model used in estimate_secondary(). This model is a combination of a convolution of previously observed primary reports combined with current primary reports (either additive or subtractive). It can optionally be cumulative. See the documentation of type for sensible options to cover most use cases and the returned values of secondary_opts() for all currently supported options.

Usage

secondary_opts(type = "incidence", ...)

Value

A list of binary options summarising secondary model used in estimate_secondary(). Options returned are cumulative (should the secondary report be cumulative), historic (should a convolution of primary reported cases be used to predict secondary reported cases), primary_hist_additive (should the historic convolution of primary reported cases be additive or subtractive), current (should currently observed primary reported cases contribute to current secondary reported cases), primary_current_additive (should current primary reported cases be additive or subtractive).

Arguments

type

A character string indicating the type of observation the secondary reports are. Options include:

"incidence": Assumes that secondary reports equal a convolution of previously observed primary reported cases. An example application is deaths from an infectious disease predicted by reported cases of that disease (or estimated infections).
"prevalence": Assumes that secondary reports are cumulative and are defined by currently observed primary reports minus a convolution of secondary reports. An example application is hospital bed usage predicted by hospital admissions.

...

Overwrite options defined by type. See the returned values for all options that can be passed.

Author

Sam Abbott

Examples

Run this code

# incidence model
secondary_opts("incidence")

# prevalence model
secondary_opts("prevalence")