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Infection characteristics for model epidemics

Source: R/infection_data.R
epidemic_data.Rd

Infection parameters used in DAEDALUS to simulate epidemics of interest.

epidemic_names provides the tags by which epidemics are known for users' convenience.

Usage

infection_data

infection_parameter_names

epidemic_names

Format

infection_data

A list with 7 elements, each corresponding to an epidemic (see Details), and providing 10 infection parameters:

  • 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.

  • gamma_H: A numeric vector of length 4 for the age-specific recovery rate for individuals who are hospitalised.

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

  • omega: A numeric vector of length N_AGE_GROUPS (4) for the age-specific mortality rate for individuals who are hospitalised.

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

infection_parameter_names

A character vector with 10 names for the infection parameters in infection_data. Mainly for internal use.

epidemic_names

A character vector with 7 elements.

Source

See processing details in `data-raw/infection_data.R

Details

Epidemics for which data are available are (pathogen in parentheses):

  • SARS 2004 (SARS-CoV-1)

  • Influenza 2009 (influenza A H1N1)

  • Influenza 1957 (influenza A H2N2)

  • Influenza 1918 (influenza A H1N1)

  • Covid-19 wild type (SARS-Cov-2 wild type)

  • Covid-19 Omicron (SARS-CoV-2 omicron)

  • Covid-19 Delta (SARS-CoV-2 delta).

Examples

# check available epidemics
epidemic_names
#> [1] "sars_cov_1"           "influenza_2009"       "influenza_1957"      
#> [4] "influenza_1918"       "sars_cov_2_pre_alpha" "sars_cov_2_omicron"  
#> [7] "sars_cov_2_delta"