mirror of https://github.com/msberends/AMR.git
176 lines
7.1 KiB
R
Executable File
176 lines
7.1 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This package is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This R package is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License version 2.0 for more details. #
|
|
# ==================================================================== #
|
|
|
|
context("first_isolate.R")
|
|
|
|
test_that("first isolates work", {
|
|
# septic_patients contains 1317 out of 2000 first isolates
|
|
expect_equal(
|
|
sum(
|
|
first_isolate(tbl = septic_patients,
|
|
col_date = "date",
|
|
col_patient_id = "patient_id",
|
|
col_mo = "mo",
|
|
info = TRUE),
|
|
na.rm = TRUE),
|
|
1317)
|
|
|
|
# septic_patients contains 1413 out of 2000 first *weighted* isolates
|
|
expect_equal(
|
|
suppressWarnings(
|
|
sum(
|
|
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
|
|
# 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)
|
|
# should be same for tibbles
|
|
expect_equal(
|
|
suppressWarnings(
|
|
sum(
|
|
first_isolate(tbl = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
|
|
# 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)
|
|
# 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",
|
|
col_mo = "mo",
|
|
col_keyantibiotics = "keyab",
|
|
ignore_I = FALSE,
|
|
type = "keyantibiotics",
|
|
info = TRUE),
|
|
na.rm = TRUE)),
|
|
1436)
|
|
# and 1417 when using points
|
|
expect_equal(
|
|
suppressWarnings(
|
|
sum(
|
|
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
|
|
col_date = "date",
|
|
col_patient_id = "patient_id",
|
|
col_mo = "mo",
|
|
col_keyantibiotics = "keyab",
|
|
type = "points",
|
|
info = TRUE),
|
|
na.rm = TRUE)),
|
|
1417)
|
|
|
|
# septic_patients contains 1163 out of 2000 first non-ICU isolates
|
|
expect_equal(
|
|
sum(
|
|
first_isolate(septic_patients,
|
|
col_mo = "mo",
|
|
col_date = "date",
|
|
col_patient_id = "patient_id",
|
|
col_icu = "ward_icu",
|
|
info = TRUE,
|
|
icu_exclude = TRUE),
|
|
na.rm = TRUE),
|
|
1163)
|
|
|
|
# set 1500 random observations to be of specimen type 'Urine'
|
|
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
|
|
expect_lt(
|
|
sum(
|
|
first_isolate(tbl = mutate(septic_patients,
|
|
specimen = if_else(row_number() %in% random_rows,
|
|
"Urine",
|
|
"Other")),
|
|
col_date = "date",
|
|
col_patient_id = "patient_id",
|
|
col_mo = "mo",
|
|
col_specimen = "specimen",
|
|
filter_specimen = "Urine",
|
|
info = TRUE),
|
|
na.rm = TRUE),
|
|
1501)
|
|
# same, but now exclude ICU
|
|
expect_lt(
|
|
sum(
|
|
first_isolate(tbl = mutate(septic_patients,
|
|
specimen = if_else(row_number() %in% random_rows,
|
|
"Urine",
|
|
"Other")),
|
|
col_date = "date",
|
|
col_patient_id = "patient_id",
|
|
col_mo = "mo",
|
|
col_specimen = "specimen",
|
|
filter_specimen = "Urine",
|
|
col_icu = "ward_icu",
|
|
icu_exclude = TRUE,
|
|
info = TRUE),
|
|
na.rm = TRUE),
|
|
1501)
|
|
|
|
# "No isolates found"
|
|
expect_message(septic_patients %>%
|
|
mutate(specimen = "test") %>%
|
|
mutate(first = first_isolate(., "date", "patient_id",
|
|
col_mo = "mo",
|
|
col_specimen = "specimen",
|
|
filter_specimen = "something_unexisting")))
|
|
|
|
# printing of exclusion message
|
|
expect_output(septic_patients %>%
|
|
first_isolate(col_date = "date",
|
|
col_mo = "mo",
|
|
col_patient_id = "patient_id",
|
|
col_testcode = "gender",
|
|
testcodes_exclude = "M"))
|
|
|
|
# errors
|
|
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
|
|
expect_error(first_isolate(septic_patients,
|
|
col_date = "non-existing col",
|
|
col_mo = "mo"))
|
|
|
|
# look for columns itself
|
|
expect_message(first_isolate(septic_patients))
|
|
expect_error(first_isolate(septic_patients %>%
|
|
mutate(mo = as.character(mo)) %>%
|
|
left_join_microorganisms()))
|
|
|
|
# if mo is not an mo class, result should be the same
|
|
expect_identical(septic_patients %>%
|
|
mutate(mo = as.character(mo)) %>%
|
|
first_isolate(col_date = "date",
|
|
col_mo = "mo",
|
|
col_patient_id = "patient_id"),
|
|
septic_patients %>%
|
|
first_isolate(col_date = "date",
|
|
col_mo = "mo",
|
|
col_patient_id = "patient_id"))
|
|
|
|
})
|