get_infectiousness_density {smidm}

Dataframe with dates and infectiousness probability

Description

Creates a dataframe containing infectiousness at a particular date/time, given the symptom_begin_date.

Usage

get_infectiousness_density(
  symptom_begin_date,
  infectiousness_shift = 12.272481,
  max_infectious_days = 24,
  shape_infectiousness_gamma = 20.516508,
  rate_infectiousness_gamma = 1.592124
)

Arguments

symptom_begin_date

Date, when the person gets symptoms.

infectiousness_shift

Number of days with the largest contagions before the first symptoms.

max_infectious_days

Number of the infectious days.

shape_infectiousness_gamma

Number, the shape parameter for the gamma distribution.

rate_infectiousness_gamma

Number, the rate parameter for the gamma distribution.

Details

infectiousness_shift, shape_infectiousness_gamma and rate_infectiousness_gamma are the distribution parameters for the infectious period from He et al. (2020).

Value

Dataframe with dates and infectiousness probability.

References

He, X et al. (2020) "Temporal dynamics in viral shedding and transmissibility of COVID-19". Nature Medicine, 26: 672–675.

Examples

get_infectiousness_density(as.Date("2022-03-22"))
get_infectiousness_density(as.Date("2022-03-22"), infectiousness_shift = 12.272481,
                           max_infectious_days = 24, shape_infectiousness_gamma = 20.516508,
                           rate_infectiousness_gamma = 1.592124)