AMR/tests/testthat/test-first_isolate.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
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# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
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context("first_isolate.R")
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test_that("first isolates work", {
# septic_patients contains 1317 out of 2000 first isolates
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expect_equal(
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sum(
first_isolate(tbl = septic_patients,
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col_date = "date",
col_patient_id = "patient_id",
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col_mo = "mo",
info = TRUE),
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na.rm = TRUE),
1317)
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# septic_patients contains 1413 out of 2000 first *weighted* isolates
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expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
# col_mo = "mo",
# col_keyantibiotics = "keyab",
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
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# should be same for tibbles
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
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# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
# col_mo = "mo",
# col_keyantibiotics = "keyab",
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type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
# and 1436 when not ignoring I
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
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col_mo = "mo",
col_keyantibiotics = "keyab",
ignore_I = FALSE,
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1436)
# and 1417 when using points
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expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
type = "points",
info = TRUE),
na.rm = TRUE)),
1417)
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# septic_patients contains 1163 out of 2000 first non-ICU isolates
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expect_equal(
sum(
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first_isolate(septic_patients,
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col_mo = "mo",
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col_date = "date",
col_patient_id = "patient_id",
col_icu = "ward_icu",
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1163)
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# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
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expect_lt(
sum(
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
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col_date = "date",
col_patient_id = "patient_id",
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col_mo = "mo",
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col_specimen = "specimen",
filter_specimen = "Urine",
info = TRUE),
na.rm = TRUE),
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1501)
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# same, but now exclude ICU
expect_lt(
sum(
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
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col_date = "date",
col_patient_id = "patient_id",
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col_mo = "mo",
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col_specimen = "specimen",
filter_specimen = "Urine",
col_icu = "ward_icu",
icu_exclude = TRUE,
info = TRUE),
na.rm = TRUE),
1501)
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# "No isolates found"
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expect_message(septic_patients %>%
mutate(specimen = "test") %>%
mutate(first = first_isolate(., "date", "patient_id",
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col_mo = "mo",
col_specimen = "specimen",
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filter_specimen = "something_unexisting")))
# printing of exclusion message
expect_output(septic_patients %>%
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first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
col_testcode = "gender",
testcodes_exclude = "M"))
# errors
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expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate(septic_patients,
col_date = "non-existing col",
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col_mo = "mo"))
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# look for columns itself
expect_message(first_isolate(septic_patients))
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expect_error(first_isolate(septic_patients %>%
mutate(mo = as.character(mo)) %>%
left_join_microorganisms()))
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# if mo is not an mo class, result should be the same
expect_identical(septic_patients %>%
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mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"),
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septic_patients %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"))
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})