AMR/tests/testthat/test-first_isolate.R

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R
Executable File

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# #
# We created this package for both routine data analysis and academic #
# research and it 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.gitlab.io/AMR. #
# ==================================================================== #
context("first_isolate.R")
test_that("first isolates work", {
skip_on_cran()
# first isolates
expect_equal(
sum(
first_isolate(x = example_isolates,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1317)
# first weighted isolates
expect_equal(
suppressWarnings(
sum(
first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
# let syntax determine arguments automatically
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
# should be same for tibbles
expect_equal(
suppressWarnings(
sum(
first_isolate(x = example_isolates %>% 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)
# when not ignoring I
expect_equal(
suppressWarnings(
sum(
first_isolate(x = example_isolates %>% 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)
# when using points
expect_equal(
suppressWarnings(
sum(
first_isolate(x = example_isolates %>% 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)
# first non-ICU isolates
expect_equal(
sum(
first_isolate(example_isolates,
col_mo = "mo",
col_date = "date",
col_patient_id = "patient_id",
col_icu = "ward_icu",
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
906)
# 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(x = mutate(example_isolates,
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(x = mutate(example_isolates,
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(example_isolates %>%
mutate(specimen = "test") %>%
mutate(first = first_isolate(., "date", "patient_id",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "something_unexisting",
info = TRUE)))
# printing of exclusion message
expect_message(example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
col_testcode = "gender",
testcodes_exclude = "M",
info = TRUE))
# errors
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate(example_isolates,
col_date = "non-existing col",
col_mo = "mo"))
# look for columns itself
expect_message(first_isolate(example_isolates))
expect_message(first_isolate(example_isolates %>%
mutate(mo = as.character(mo)) %>%
left_join_microorganisms()))
# if mo is not an mo class, result should be the same
expect_identical(example_isolates %>%
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"),
example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"))
# missing dates should be no problem
df <- example_isolates
df[1:100, "date"] <- NA
expect_equal(
sum(
first_isolate(x = df,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1322)
# unknown MOs
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = FALSE)) %>%
.$first %>%
sum(),
1062)
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = TRUE)) %>%
.$first %>%
sum(),
1529)
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", NA, mo)) %>%
mutate(first = first_isolate(.)) %>%
.$first %>%
sum(),
1062)
})