get_serial_interval_density {smidm}

Dataframe with dates and contact symptom begin probability

Description

Creates a dataframe containing probability that a contact will start showing symptoms (serial interval) at a particular date/time, given the symptom_begin_date.

Usage

get_serial_interval_density(
  symptom_begin_date,
  max_serial_interval_days = 20,
  shape_serial = 2.154631545,
  rate_serial = 0.377343528
)

Arguments

symptom_begin_date

Date, when the index person got symptoms.

max_serial_interval_days

Number of serial interval days.

shape_serial

Number, the shape parameter for the gamma distribution.

rate_serial

Number, the rate parameter for the gamma distribution.

Details

shape_serial and rate_serial are the parameters of the gamma distribution for the serial interval derived from Najafi et al. (2020).

Value

Dataframe with dates and contact symptom begin probability.

References

Najafi F et al. (2020) "Serial interval and time-varying reproduction number estimation for COVID-19 in western Iran.". New Microbes and New Infections, 36: 100715.

Examples

get_serial_interval_density(as.Date("2022-03-22"))
get_serial_interval_density(as.Date("2022-03-22"), max_serial_interval_days = 20,
                            shape_serial = 2.15, rate_serial = 0.38)