covid19_control: COVID19 Parameters Control Data Structure

In SPARSEMODr: SPAtial Resolution-SEnsitive Models of Outbreak Dynamics

COVID19 Parameters Control Data Structure

Description

The COVID19 model uses parameters which are specific to the COVID19 model. This data structure affirms that required parameters are supplied, provides default values for optional parameters, and validates the data of each parameter.

Usage

    covid19_control(
        input_N_pops=NULL,
        input_S_pops=NULL,
        input_E_pops=NULL,
        input_I_asym_pops=NULL,
        input_I_presym_pops=NULL,
        input_I_sym_pops=NULL,
        input_I_home_pops=NULL,
        input_I_hosp_pops=NULL,
        input_I_icu1_pops=NULL,
        input_I_icu2_pops=NULL,
        input_R_pops=NULL,
        input_D_pops=NULL,
        frac_beta_asym=0.55,
        frac_beta_hosp=0.05,
        delta=1/3.0,
        recov_a=1/6.0,
        recov_p=1/2.0,
        recov_s=1/6.0,
        recov_home=1/3.0,
        recov_icu1=1/8.0,
        recov_icu2=1/4.0,
        asym_rate=0.40,
        sym_to_icu_rate=0.015
    )

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_asym_pops	Integer Vector representing the asymptomatic infected population for each county.
input_I_presym_pops	Integer Vector representing the presymptomatic infected population for each county.
input_I_sym_pops	Integer Vector representing the symptomatic infected population for each county.
input_I_home_pops	Integer Vector representing the infected and isolated at home population for each county.
input_I_hosp_pops	Integer Vector representing the hospitalized population for each county.
input_I_icu1_pops	Integer Vector representing the population for each county in ICU.
input_I_icu2_pops	Integer Vector representing the population for each county in ICU recovery.
input_R_pops	Integer Vector representing the recovered population for each county.
input_D_pops	Integer Vector representing the deaths for each county.
frac_beta_asym	An adjustment to beta accounting for asymptomatic individuals being less likely to transmit than symptomatic individuals. Default value is 0.55. Must be greater than zero and less than or equal to one.
frac_beta_hosp	An adjustment to beta accounting for hospitalized individuals being less likely to transmit than non-hospitalized individuals. Default value is 0.05. Must be greater than zero and less than or equal to one.
delta	Incubation period. Default value is 1/3.0. Must be greater than or equal to zero. Values above one are unusual.
recov_a	Recovery rate of asymptomatic individuals. Default value is 1/6.0. Must be greater than or equal to zero. Values above one are unusual.
recov_p	Recovery rate of presymptomatic individuals. Default value is 1/2.0. Must be greater than or equal to zero. Values above one are unusual.
recov_s	Recovery rate of symptomatic individuals. Default value is 1/6.0. Must be greater than or equal to zero. Values above one are unusual.
recov_home	Recovery rate of infected individuals in home isolation. Default value is 1/3.0. Must be greater than or equal to zero. Values above one are unusual.
recov_icu1	Recovery rate of individuals in ICU. Default value is 1/8.0. Must be greater than or equal to zero. Values above one are unusual.
recov_icu2	Recovery rate of individuals in ICU recovery. Default value is 1/4.0. Must be greater than or equal to zero. Values above one are unusual.
asym_rate	Proportion of presymtomatic individuals entering the asymptomatic stage. Default value is 0.40. Must be greater than zero and less than or equal to one.
sym_to_icu_rate	Proportion of symptomatic individuals entering ICU. Default value is 0.015. Must be greater than zero and less than or equal to one.

Details

Defines a set of parameters specific to the COVID19 model. Adjustments to the model calculations can be made by specifying any or all of the optional parameters. 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, input_I_asym_pops, input_I_presym_pops, input_I_sym_pops, input_I_home_pops, input_I_hosp_pops, input_I_icu1_pops, and input_I_icu2_pops must be supplied with a nonzero population. Any of these population parameters not supplied 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

seir_control

Examples

## Data set for the examples:
N_pops <- rep(100000, 10)
E_pops <- c(0, 1, 0, 3, 2, 0, 14, 3, 0, 0)
S_pops <- N_pops - E_pops
I_asym_pops <- rep(0, 10)
I_presym_pops <- rep(0, 10)
I_sym_pops <- c(1, 0, 11, 0, 0, 5, 0, 0, 9, 0)
I_home_pops <- rep(0, 10)
I_hosp_pops <- rep(0, 10)
I_icu1_pops <- rep(0, 10)
I_icu2_pops <- rep(0, 10)
R_pops <- rep(0, 10)
D_pops <- rep(0, 10)

## Example using the default parameters:
covid19_control <- covid19_control(input_S_pops         = S_pops,
                                   input_E_pops         = E_pops)

## Example specifying some parameters:
covid19_control <- covid19_control(input_N_pops         = N_pops,
                                   input_I_sym_pops     = I_sym_pops,
                                   input_I_home_pops    = I_home_pops,
                                   input_I_hosp_pops    = I_hosp_pops,
                                   input_I_icu2_pops    = I_icu2_pops,
                                   input_D_pops         = D_pops,
                                   frac_beta_hosp       = 0.03)

## Example specifying all possible parameters:
covid19_control <- covid19_control(input_S_pops         = S_pops,
                                   input_E_pops         = E_pops,
                                   input_I_asym_pops    = I_asym_pops,
                                   input_I_presym_pops  = I_presym_pops,
                                   input_I_sym_pops     = I_sym_pops,
                                   input_I_home_pops    = I_home_pops,
                                   input_I_hosp_pops    = I_hosp_pops,
                                   input_I_icu1_pops    = I_icu1_pops,
                                   input_I_icu2_pops    = I_icu2_pops,
                                   input_R_pops         = R_pops,
                                   input_D_pops         = D_pops,
                                   frac_beta_asym       = 0.50,
                                   frac_beta_hosp       = 0.06,
                                   delta                = 0.25,
                                   recov_a              = 0.57,
                                   recov_p              = 0.62,
                                   recov_s              = 0.11,
                                   recov_home           = 0.28,
                                   recov_icu1           = 0.12,
                                   recov_icu2           = 0.29,
                                   asym_rate            = 0.65,
                                   sym_to_icu_rate      = 0.122)

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