get_infection_density: Dataframe with dates and probability of infection

In smidm: Statistical Modelling for Infectious Disease Management

Dataframe with dates and probability of infection

Description

Creates a dataframe containing probability of infection occurring at a particular date/time, given the symptom_begin_date.

Usage

get_infection_density(
  symptom_begin_date,
  max_incubation_days = 14,
  meanlog = 1.69,
  sdlog = 0.55
)

Arguments

symptom_begin_date	Date, when the person gets symptoms.
max_incubation_days	Number of incubation days.
meanlog	Number, the parameter of mean from the log-normal distribution.
sdlog	Number, the parameter of sd from the log-normal distribution.

Details

meanlog and sdlog are the log-normal distribution parameters derived from the incubation period characteristics described in Xin et al. (2021).

Value

Dataframe with dates and probability of infection.

References

Xin H, Wong JY, Murphy C et al. (2021) "The Incubation Period Distribution of Coronavirus Disease 2019: A Systematic Review and Meta-Analysis". Clinical Infectious Diseases, 73(12): 2344-2352.

Examples

get_infection_density(as.Date("2022-03-22"))
get_infection_density(as.Date("2022-03-22"), max_incubation_days = 14, meanlog = 1.69, sdlog = 0.55)

smidm documentation built on Aug. 27, 2022, 9:06 a.m.