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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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50
inst/tinytest/test-ab_property.R
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@@ -9,7 +9,7 @@
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
@@ -47,8 +47,10 @@ expect_identical(ab_ddd("AMX", "iv"), 3)
expect_identical(ab_ddd_units("AMX", "iv"), "g")
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
expect_identical(ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL),
c("amoxicillin/clavulanic acid", "polymyxin B"))
expect_identical(
ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL),
c("amoxicillin/clavulanic acid", "polymyxin B")
)
expect_inherits(ab_info("AMX"), "list")
@@ -57,25 +59,37 @@ expect_error(ab_name("amox", language = "INVALID"))
expect_stdout(print(ab_name("amox", language = NULL)))
expect_equal(ab_name("21066-6", language = NULL), "Ampicillin")
expect_equal(ab_loinc("ampicillin"),
c("21066-6", "3355-5", "33562-0", "33919-2", "43883-8", "43884-6", "87604-5"))
expect_equal(
ab_loinc("ampicillin"),
c("21066-6", "3355-5", "33562-0", "33919-2", "43883-8", "43884-6", "87604-5")
)
expect_true(ab_url("AMX") %like% "whocc.no")
expect_warning(ab_url("ASP"))
expect_identical(colnames(set_ab_names(example_isolates[, 20:25])),
c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin"))
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine"))
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01"))
expect_identical(
colnames(set_ab_names(example_isolates[, 20:25])),
c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
)
expect_identical(
colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
)
expect_identical(
colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_identical(example_isolates %>% set_ab_names(),
example_isolates %>% rename_with(set_ab_names))
expect_true(all(c("SXT", "nitrofurantoin", "fosfomycin", "linezolid", "ciprofloxacin",
"moxifloxacin", "vancomycin", "TEC") %in%
(example_isolates %>%
set_ab_names(NIT:VAN) %>%
colnames())))
expect_identical(
example_isolates %>% set_ab_names(),
example_isolates %>% rename_with(set_ab_names)
)
expect_true(all(c(
"SXT", "nitrofurantoin", "fosfomycin", "linezolid", "ciprofloxacin",
"moxifloxacin", "vancomycin", "TEC"
) %in%
(example_isolates %>%
set_ab_names(NIT:VAN) %>%
colnames())))
}