itd_distribution {Bernadette}

Distribution of the time between infection and death

Description

Function to discretize the infection-to-death distribution

Usage

itd_distribution(
  ts_length,
  gamma_mean = 24.19231,
  gamma_cv = 0.3987261,
  gamma_shape = 6.29,
  gamma_rate = 0.26
)

Arguments

ts_length

integer; time from infection to death in days.

gamma_mean

numeric; mean of a gamma distribution, for a given shape and rate. See also GammaDist.

gamma_cv

numeric; coefficient of variation of a gamma distribution, for a given shape and rate. See also GammaDist.

gamma_shape

numeric; shape parameter of a gamma distribution. See also GammaDist.

gamma_rate

numeric; rate parameter of a gamma distribution. See also GammaDist.

Value

A vector of length ts_length.

References

Flaxman et al (2020). Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe. Nature, 584, 257-261.

Examples

# Age-specific mortality/incidence count time series:
data(age_specific_mortality_counts)

# Infection-to-death distribution:
ditd <- itd_distribution(ts_length  = nrow(age_specific_mortality_counts),
                         gamma_mean = 24.19231,
                         gamma_cv   = 0.3987261)