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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
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88
tests/testthat/test-get_episode.R
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@ -27,51 +27,53 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
x <- data.frame(dates = as.Date(c("2021-01-01", "2021-01-02", "2021-01-05", "2021-01-08", "2021-02-21", "2021-02-22", "2021-02-23", "2021-02-24", "2021-03-01", "2021-03-01")))
x$absolute <- get_episode(x$dates, episode_days = 7)
x$relative <- get_episode(x$dates, case_free_days = 7)
expect_equal(x$absolute, c(1, 1, 1, 2, 3, 3, 3, 3, 4, 4))
expect_equal(x$relative, c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2))
expect_equal(get_episode(as.Date(c("2022-01-01", "2020-01-01")), 365), c(2, 1))
expect_equal(get_episode(as.Date(c("2020-01-01", "2022-01-01")), 365), c(1, 2))
test_that("get_episode works", {
x <- data.frame(dates = as.Date(c("2021-01-01", "2021-01-02", "2021-01-05", "2021-01-08", "2021-02-21", "2021-02-22", "2021-02-23", "2021-02-24", "2021-03-01", "2021-03-01")))
x$absolute <- get_episode(x$dates, episode_days = 7)
x$relative <- get_episode(x$dates, case_free_days = 7)
expect_equal(x$absolute, c(1, 1, 1, 2, 3, 3, 3, 3, 4, 4))
expect_equal(x$relative, c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2))
expect_equal(get_episode(as.Date(c("2022-01-01", "2020-01-01")), 365), c(2, 1))
expect_equal(get_episode(as.Date(c("2020-01-01", "2022-01-01")), 365), c(1, 2))
test_df <- rbind(
data.frame(
date = as.Date(c("2015-01-01", "2015-10-01", "2016-02-04", "2016-12-31", "2017-01-01", "2017-02-01", "2017-02-05", "2020-01-01")),
patient_id = "A"
),
data.frame(
date = as.Date(c("2015-01-01", "2016-02-01", "2016-12-31", "2017-01-01", "2017-02-03")),
patient_id = "B"
)
)
expect_equal(
get_episode(test_df$date, 365),
c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3)
)
expect_equal(
get_episode(test_df$date[which(test_df$patient_id == "A")], 365),
c(1, 1, 2, 2, 2, 2, 3, 4)
)
expect_equal(
get_episode(test_df$date[which(test_df$patient_id == "B")], 365),
c(1, 2, 2, 2, 3)
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_identical(
test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f),
c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE)
test_df <- rbind(
data.frame(
date = as.Date(c("2015-01-01", "2015-10-01", "2016-02-04", "2016-12-31", "2017-01-01", "2017-02-01", "2017-02-05", "2020-01-01")),
patient_id = "A"
),
data.frame(
date = as.Date(c("2015-01-01", "2016-02-01", "2016-12-31", "2017-01-01", "2017-02-03")),
patient_id = "B"
)
)
suppressMessages(
x <- example_isolates %>%
mutate(out = first_isolate(., include_unknown = TRUE, method = "episode-based", info = FALSE))
expect_equal(
get_episode(test_df$date, 365),
c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3)
)
expect_equal(
get_episode(test_df$date[which(test_df$patient_id == "A")], 365),
c(1, 1, 2, 2, 2, 2, 3, 4)
)
expect_equal(
get_episode(test_df$date[which(test_df$patient_id == "B")], 365),
c(1, 2, 2, 2, 3)
)
y <- example_isolates %>%
group_by(patient, mo) %>%
mutate(out = is_new_episode(date, 365))
expect_identical(which(x$out), which(y$out))
}
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_identical(
test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f),
c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE)
)
suppressMessages(
x <- example_isolates %>%
mutate(out = first_isolate(., include_unknown = TRUE, method = "episode-based", info = FALSE))
)
y <- example_isolates %>%
group_by(patient, mo) %>%
mutate(out = is_new_episode(date, 365))
expect_identical(which(x$out), which(y$out))
}
})