In ffinger/followup: Evidence based prioritisation of contacts to follow-up during infectious disease outbreaks

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width=7,
  fig.height=5,
  fig.path="figs-overview/")

Load environment:

library(dplyr)
library(epitrix)
library(distcrete)
library(followup)

Set up the incubation period distribution:

incubation_days <- 0:3
incubation_frequency <- c(1,3,2,1)
incubation_frequency <- incubation_frequency/sum(incubation_frequency)

plot(incubation_days, incubation_frequency, type = "h")

The integrate_incubation function

Make a list of example contacts each having just one exposure date in dates_exposure.

contact_list <- data.frame(
  id_contact = c("a", "b", "c", "d"),
  type_exposure = c("hospital", "funeral", "family", "restaurant"),
  dates_exposure = as.Date(c("2021-01-15", "2021-01-14", "2021-01-10", "2021-01-16"))
)

contact_list

date_analysis <- as.Date("2021-01-16")

res <- purrr::map(contact_list$dates_exposure, function(x) integrate_incubation(incubation_frequency, date_low = x, date_high = date_analysis))
res <- unlist(res)

res

We can compute the results by hand and compare:

expected <- c(4/7, 6/7, 1, 1/7)
testthat::expect_equal(res, expected)

Should get exactly the same result using the function including a followup when 1) last follow-up is NA 2) last follow-up is in before exposure

testthat::expect_equal(
  expected,
  integrate_incubation_followup(incubation_frequency, date_exposure = contact_list$dates_exposure, date_analysis = date_analysis, date_last_followup = NA)
  )

testthat::expect_equal(
  expected,
  integrate_incubation_followup(incubation_frequency, date_exposure = contact_list$dates_exposure, date_analysis = date_analysis, date_last_followup = as.Date("2021-01-01"))
  )

Check the integrate_incubation_followup function

Now add a date of last follow-up for each contact:

contact_list$dates_last_followup <- as.Date(c("2021-01-15", "2021-01-15", "2021-01-12", "2021-01-16"))

contact_list

res <- integrate_incubation_followup(incubation_frequency, date_exposure = contact_list$dates_exposure, date_analysis = date_analysis, date_last_followup = contact_list$dates_last_followup)

expected <- c((3/7) / (1-1/7), (2/7) / (1-1/7-3/7), 1, 0)
testthat::expect_equal(res, expected)

there is a few more special cases here that should be illustrated here, see code

ffinger/followup documentation built on Jan. 28, 2021, 3:20 a.m.