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Represent infection parameters for DAEDALUS

Source: R/class_infection.R
class_infection.Rd

Helper functions to create and work with S3 class <daedalus_infection> objects for use with daedalus(). These objects store infection parameters for reuse and have methods for easy parameter access and editing, as well as processing raw infection characteristics for the DAEDALUS model.

Usage

daedalus_infection(name, ...)

is_daedalus_infection(x)

# S3 method for class 'daedalus_infection'
print(x, ...)

Arguments

name

An epidemic name from among daedalus.data::epidemic_names. Selecting an epidemic automatically pulls in infection parameters associated with the epidemic; these are stored as packaged data in daedalus.data::infection_data. Default infection parameters for epidemics can be over-ridden by passing them as a named list to ....

...

Other parameters passed to print().

x

An object of the <daedalus_infection> class.

Value

  • daedalus_infection() returns an object of the S3 class <daedalus_infection>.

  • is_daedalus_infection() returns a logical for whether an object is a <daedalus_infection>.

  • print.daedalus_infection() invisibly returns the <daedalus_infection> object x. Called for printing side-effects.

Details

Included epidemics

Epidemics for which data are available are given below (pathogen in parentheses). The string indicates the name that must be passed to the name argument.

  • "sars_cov_1": SARS 2004 (SARS-CoV-1),

  • "influenza_2009": influenza 2009 (influenza A H1N1),

  • "influenza_1957": influenza 1957 (influenza A H2N2),

  • "influenza_1918": influenza 1918 (influenza A H1N1),

  • "sars_cov_2_pre_alpha": Covid-19 wild type (SARS-Cov-2 wild type),

  • "sars_cov_2_omicron": Covid-19 Omicron (SARS-CoV-2 omicron),

  • "sars_cov_2_pre_delta": (SARS-CoV-2 delta).

Infection parameters

All infections have the following parameters, which take default values stored in the package under daedalus.data::infection_data. Users can pass custom values for these parameters as arguments via ....

  • r0: A single numeric value for the basic reproduction value of the infection \(R_0\).

  • sigma: A single numeric value > 0.0 for the rate of transition from the exposed compartment to one of two infectious compartments.

  • p_sigma: A single numeric value in the range \([0.0, 1.0]\) for the proportion of infectious individuals who are also symptomatic. Asymptomatic individuals can have a different contribution to the force of infection from symptomatic individuals.

  • epsilon: A single numeric value for the relative contribution of asymptomatic infectious individuals to the force of infection (compared to symptomatic individuals).

  • gamma_Is: A single numeric value for the recovery rate of infectious individuals who are not hospitalised.

  • gamma_Ia: A single numeric value for the recovery rate from asymptomatic infection.

  • ifr: A numeric vector of length N_AGE_GROUPS (4) for the age-specific infection fatality risk.

  • eta: A numeric vector of length N_AGE_GROUPS (4) for the age-specific hospitalisation rate for individuals who are infectious and symptomatic.

  • hfr: A numeric vector of length N_AGE_GROUPS (4) for the age-specific probability of death conditional on hospitalisation.

  • gamma_H_recovery: A single numeric value for the recovery rate of hospitalised individuals.

  • gamma_H_death: A single numeric value for the death rate of hospitalised individuals.

  • rho: A single numeric value for the rate at which infection-derived immunity wanes, returning individuals in the 'recovered' compartment to the 'susceptible' compartment.

Examples

# make a <daedalus_infection> object with default parameter values
daedalus_infection("sars_cov_1")
#> <daedalus_infection>
#> • Epidemic name: sars_cov_1
#> • R0: 1.75
#> • sigma: 0.217
#> • p_sigma: 0.867
#> • epsilon: 0.58
#> • rho: 0.003
#> • eta: 0.018, 0.082, 0.018, and 0.246
#> • hfr: 0.255, 0.255, 0.255, and 0.255
#> • gamma_Ia: 0.476
#> • gamma_Is: 0.25
#> • gamma_H_recovery: 0.044
#> • gamma_H_death: 0.05

# modify infection parameters R0 and immunity waning rate
daedalus_infection("influenza_1918", r0 = 2.5, rho = 0.01)
#> <daedalus_infection>
#> • Epidemic name: influenza_1918
#> • R0: 2.5
#> • sigma: 0.909
#> • p_sigma: 0.669
#> • epsilon: 0.58
#> • rho: 0.01
#> • eta: 0.073, 0.064, 0.02, and 0.152
#> • hfr: 0.125, 0.125, 0.125, and 0.125
#> • gamma_Ia: 0.4
#> • gamma_Is: 0.4
#> • gamma_H_recovery: 0.2
#> • gamma_H_death: 0.2