seir_control: SEIR Parameters Control Data Structure

In SPARSEMODr: SPAtial Resolution-SEnsitive Models of Outbreak Dynamics

SEIR Parameters Control Data Structure

Description

The SEIR model uses parameters which are specific to the SEIR model. This data structure affirms that required parameters are supplied, provides default values for optional parameters, and validates the data of each parameter.

Usage

    seir_control(
        input_N_pops=NULL,
        input_S_pops=NULL,
        input_E_pops=NULL,
        input_I_pops=NULL,
        input_R_pops=NULL,
        birth=1/(75*365),
        incubate=1/8.0,
        recov=1/3.0
    )

Arguments

input_N_pops	Integer Vector representing the total population for each county.
input_S_pops	Integer Vector representing the susceptible population for each county.
input_E_pops	Integer Vector representing the exposed population for each county.
input_I_pops	Integer Vector representing the infected population for each county.
input_R_pops	Integer Vector representing the recovered population for each county.
birth	Default value is 1/(75*365). Must be greater than or equal to zero. Values above one are unusual.
incubate	Default value is 1/8.0. Must be greater than or equal to zero. Values above one are unusual.
recov	Default value is 1/3.0. Must be greater than or equal to zero. Values above one are unusual.

Details

Defines a set of parameters specific to the SEIR model. If an optional parameter is not set, it will use the default value as specified above. If a parameter is outside the specified limits, execution will stop and an error message will be displayed. Some parameters may have values greater than one. While these situations may be unusual, execution will not stop but a warning message will be displayed.

Note: At least one of input_N_pops or input_S_pops must be supplied. If one is not supplied, it will be calculated within the class.

Note: At least one of input_E_pops and input_I_pops must be supplied with a nonzero population. If either of these population parameters or input_R_pops is not supplied, it will be assumed to be a vector of zeroes.

Value

Returns a named list of vectors that must be supplied to model_interface.

Author(s)

Seth Borkovec, [e-mail]; Joseph Mihaljevic, [e-mail]

See Also

covid19_control

Examples

## Data set for the examples:
S_pops <- rep(100000, 10)
E_pops <- c(0, 1, 0, 3, 2, 0, 13, 3, 0, 0)
I_pops <- c(0, 0, 0, 0, 0, 0, 1, 0, 0, 0)
R_pops <- rep(0, 10)
N_pops <- S_pops + E_pops + I_pops + R_pops

## Example using the default parameters:
seir_control <- seir_control(input_S_pops = S_pops,
                             input_E_pops = E_pops,
                             input_I_pops = I_pops)

## Example specifying one optional parameter:
seir_control <- seir_control(input_N_pops = N_pops,
                             input_I_pops = I_pops,
                             input_R_pops = R_pops,
                             recov          = 1/4.0)

## Example specifying all possible parameters:
seir_control <- seir_control(input_N_pops = N_pops,
                             input_S_pops = S_pops,
                             input_E_pops = E_pops,
                             input_I_pops = I_pops,
                             input_R_pops = R_pops,
                             birth          = 1/(65*365),
                             incubate       = 0.12,
                             recov          = 0.25)

SPARSEMODr documentation built on July 20, 2022, 1:09 a.m.