tests/testthat/test-flag_low_counts.R

In reconhub/i2extras: Functions to Work with 'incidence2' Objects

library(incidence2)
library(outbreaks)

context("flag_low_counts")

test_that("flag_low_counts: true positives", {
    skip_on_cran()

    dat <- dplyr::filter(ebola_sim_clean$linelist,
                         date_of_onset >= as.Date("2014-09-01"),
                         date_of_onset < as.Date("2015-01-01"))

    target_hosp <- levels(dat$hospital)[1:2]
    target_date <- as_period(as.Date("2014-09-29"), n = 7L)

    i <- incidence(dat,
                   date_index = "date_of_onset",
                   interval = 7,
                   groups = "hospital")
    i <- dplyr::mutate(i, count =
                           dplyr::if_else(
                               date_index ==  target_date &
                                   hospital %in% target_hosp,
                               0L,
                               count))


    ## check with set_missing TRUE
    res <- flag_low_counts(i, set_missing = TRUE, threshold = 0.05)
    expect_equal(sum(is.na(res$count)), length(target_hosp))
    expect_true(all(as.Date(i$date_index[is.na(res$count)]) == as.Date(target_date)))
    expect_true(all(i$hospital[is.na(res$count)] %in% target_hosp))

    ## check with set_missing FALSE
    expect_identical(
        is.na(flag_low_counts(i, set_missing = TRUE)$count),
        flag_low_counts(i, set_missing = FALSE)$count_flag_low
    )

})



test_that("flag_low_counts: true negatives ", {
    skip_on_cran()

    set.seed(1)
    df <- data.frame(
        dates = 1:100,
        counts = round(rnorm(100, 1000, 200))
    )

    x <- incidence(df, date_index = "dates", counts = "counts")
    expect_true(!any(is.na(flag_low_counts(x, set_missing = TRUE)$counts)))

})



test_that("flag_low_counts errors as it should", {
    msg <- "`letters` is not an incidence object"
    expect_error(flag_low_counts(letters), msg)
})