get_misc_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 dates/times, given the symptom_begin_dates and number_of_persons per date.

Usage

get_misc_infection_density(
  symptom_begin_dates,
  number_of_persons,
  max_incubation_days = 17,
  meanlog = 1.69,
  sdlog = 0.55
)

Arguments

symptom_begin_dates	Dates, when the persons get symptoms.
number_of_persons	Number of persons who get symptoms on each date.
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

symptom_begin_dates <- c(as.Date("2022-03-22"), as.Date("2022-03-26"))
number_of_persons <- c(3,1)
get_misc_infection_density(symptom_begin_dates, number_of_persons)

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