+
-Other
+
Other
- Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
@@ -2119,9 +2126,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Functions
as.rsi and as.mic now add the package name and version as attributes
-
+
-Other
+
Other
- Expanded
README.md with more examples
- Added ORCID of authors to DESCRIPTION file
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index f0c65a8b..bfcafffb 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-13T21:04Z
+last_built: 2021-05-15T19:35Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 0996b8d7..04e8ee42 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9030
+ 1.6.0.9031
diff --git a/docs/survey.html b/docs/survey.html
index f52d7b9b..bb803e31 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9030
+ 1.6.0.9031
diff --git a/inst/tinytest/test-_deprecated.R b/inst/tinytest/test-_deprecated.R
new file mode 100644
index 00000000..80c01cce
--- /dev/null
+++ b/inst/tinytest/test-_deprecated.R
@@ -0,0 +1,39 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_identical(suppressWarnings(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3))),
+ c("***", "**", "*", ".", " ", NA, NA))
+
+expect_warning(key_antibiotics(example_isolates))
+expect_identical(suppressWarnings(key_antibiotics(example_isolates)),
+ key_antimicrobials(example_isolates, antifungal = NULL))
+
+expect_warning(key_antibiotics_equal("S", "S"))
+expect_identical(suppressWarnings(key_antibiotics_equal("S", "S")),
+ antimicrobials_equal("S", "S", type = "keyantimicrobials"))
+
+expect_warning(filter_first_weighted_isolate(example_isolates))
+expect_identical(suppressWarnings(filter_first_weighted_isolate(example_isolates)),
+ filter_first_isolate(example_isolates))
diff --git a/tests/testthat/test-_misc.R b/inst/tinytest/test-_misc.R
similarity index 57%
rename from tests/testthat/test-_misc.R
rename to inst/tinytest/test-_misc.R
index 5561429e..af898a51 100755
--- a/tests/testthat/test-_misc.R
+++ b/inst/tinytest/test-_misc.R
@@ -22,47 +22,34 @@
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-
-context("aa_helper_functions.R")
-
-test_that("percentages works", {
- skip_on_cran()
- expect_equal(percentage(0.25), "25%")
- expect_equal(percentage(0.5), "50%")
- expect_equal(percentage(0.500, digits = 1), "50.0%")
- expect_equal(percentage(0.1234), "12.3%")
+
+expect_equal(percentage(0.25), "25%")
+expect_equal(percentage(0.5), "50%")
+expect_equal(percentage(0.500, digits = 1), "50.0%")
+expect_equal(percentage(0.1234), "12.3%")
# round up 0.5
- expect_equal(percentage(0.0054), "0.5%")
- expect_equal(percentage(0.0055), "0.6%")
-})
-
-test_that("functions missing in older R versions work", {
- skip_on_cran()
- expect_equal(strrep("A", 5), "AAAAA")
- expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
- expect_equal(trimws(" test "), "test")
- expect_equal(trimws(" test ", "l"), "test ")
- expect_equal(trimws(" test ", "r"), " test")
-})
-
-test_that("looking up ab columns works", {
- skip_on_cran()
- expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
- expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
- expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
- expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
+expect_equal(percentage(0.0054), "0.5%")
+expect_equal(percentage(0.0055), "0.6%")
+
+expect_equal(strrep("A", 5), "AAAAA")
+expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
+expect_equal(trimws(" test "), "test")
+expect_equal(trimws(" test ", "l"), "test ")
+expect_equal(trimws(" test ", "r"), " test")
+
+expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
+expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
+expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
+expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
if (suppressWarnings(require("dplyr"))) {
- expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
- expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
+ expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
+ expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
}
-})
-
-test_that("looking up ab columns works", {
- skip_on_cran()
+
# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
if (suppressWarnings(require("dplyr"))) {
- expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
+ expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
}
-})
+
diff --git a/tests/testthat/test-join_microorganisms.R b/inst/tinytest/test-ab.R
similarity index 52%
rename from tests/testthat/test-join_microorganisms.R
rename to inst/tinytest/test-ab.R
index 9e0512b2..effe6b8d 100755
--- a/tests/testthat/test-join_microorganisms.R
+++ b/inst/tinytest/test-ab.R
@@ -23,41 +23,50 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("join_microorganisms.R")
+expect_equal(as.character(as.ab(c("J01FA01",
+ "J 01 FA 01",
+ "Erythromycin",
+ "eryt",
+ " eryt 123",
+ "ERYT",
+ "ERY",
+ "erytromicine",
+ "Erythrocin",
+ "Romycin"))),
+ rep("ERY", 10))
-test_that("joins work", {
- skip_on_cran()
- unjoined <- example_isolates
- inner <- example_isolates %>% inner_join_microorganisms()
- left <- example_isolates %>% left_join_microorganisms()
- semi <- example_isolates %>% semi_join_microorganisms()
- anti <- example_isolates %>% anti_join_microorganisms()
- suppressWarnings(right <- example_isolates %>% right_join_microorganisms())
- suppressWarnings(full <- example_isolates %>% full_join_microorganisms())
+expect_identical(class(as.ab("amox")), c("ab", "character"))
+expect_identical(class(antibiotics$ab), c("ab", "character"))
+expect_true(is.ab(as.ab("amox")))
+expect_stdout(print(as.ab("amox")))
+expect_stdout(print(data.frame(a = as.ab("amox"))))
- expect_true(ncol(unjoined) < ncol(inner))
- expect_true(nrow(unjoined) == nrow(inner))
+expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
+expect_warning(as.ab("UNKNOWN"))
+expect_warning(as.ab(""))
- expect_true(ncol(unjoined) < ncol(left))
- expect_true(nrow(unjoined) == nrow(left))
+expect_stdout(print(as.ab("amox")))
- expect_true(ncol(semi) == ncol(semi))
- expect_true(nrow(semi) == nrow(semi))
+expect_equal(as.character(as.ab("Phloxapen")),
+ "FLC")
- expect_true(nrow(anti) == 0)
+expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
+ c(NA, "TMP"))
- expect_true(nrow(unjoined) < nrow(right))
- expect_true(nrow(unjoined) < nrow(full))
+expect_equal(as.character(as.ab("Amoxy + clavulaanzuur")),
+ "AMC")
- expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
- expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
+expect_equal(as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
+ c("MEM", "AMC"))
- expect_equal(nrow(left_join_microorganisms("B_ESCHR_COLI")), 1)
+expect_message(as.ab("cipro mero"))
- expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COLI")), 1)
- expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COLI")), 0)
-
- expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
- expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
-
-})
+# assigning and subsetting
+x <- antibiotics$ab
+expect_inherits(x[1], "ab")
+expect_inherits(x[[1]], "ab")
+expect_inherits(c(x[1], x[9]), "ab")
+expect_inherits(unique(x[1], x[9]), "ab")
+expect_warning(x[1] <- "invalid code")
+expect_warning(x[[1]] <- "invalid code")
+expect_warning(c(x[1], "test"))
diff --git a/tests/testthat/test-ab_from_text.R b/inst/tinytest/test-ab_class_selectors.R
similarity index 55%
rename from tests/testthat/test-ab_from_text.R
rename to inst/tinytest/test-ab_class_selectors.R
index d8c22e89..56327f57 100644
--- a/tests/testthat/test-ab_from_text.R
+++ b/inst/tinytest/test-ab_class_selectors.R
@@ -23,24 +23,20 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("ab_from_text.R")
+if (suppressWarnings(require("dplyr"))) {
+expect_true(example_isolates %>% select(aminoglycosides()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(carbapenems()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(cephalosporins()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(cephalosporins_1st()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(cephalosporins_2nd()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(cephalosporins_3rd()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(cephalosporins_4th()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(cephalosporins_5th()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(fluoroquinolones()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(glycopeptides()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(macrolides()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(oxazolidinones()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(penicillins()) %>% ncol() < ncol(example_isolates))
+expect_true(example_isolates %>% select(tetracyclines()) %>% ncol() < ncol(example_isolates))
+}
-test_that("ab_from_text works", {
- skip_on_cran()
-
- expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")[[1]],
- as.ab("Amoxicillin"))
- expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = TRUE)[[1]],
- as.ab("Amoxicillin"))
- expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = FALSE)[[1]],
- as.ab("Amoxicillin"))
- expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", translate_ab = TRUE)[[1]],
- "Amoxicillin")
- expect_identical(ab_from_text("administered amoxi/clav and cipro", collapse = ", ")[[1]],
- "AMC, CIP")
-
- expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "dose")[[1]],
- 500)
- expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "admin")[[1]],
- "oral")
-})
diff --git a/tests/testthat/test-_deprecated.R b/inst/tinytest/test-ab_from_text.R
similarity index 65%
rename from tests/testthat/test-_deprecated.R
rename to inst/tinytest/test-ab_from_text.R
index be465b59..aaed893b 100644
--- a/tests/testthat/test-_deprecated.R
+++ b/inst/tinytest/test-ab_from_text.R
@@ -23,23 +23,18 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("deprecated.R")
+expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")[[1]],
+ as.ab("Amoxicillin"))
+expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = TRUE)[[1]],
+ as.ab("Amoxicillin"))
+expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = FALSE)[[1]],
+ as.ab("Amoxicillin"))
+expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", translate_ab = TRUE)[[1]],
+ "Amoxicillin")
+expect_identical(ab_from_text("administered amoxi/clav and cipro", collapse = ", ")[[1]],
+ "AMC, CIP")
-test_that("deprecated functions work", {
- skip_on_cran()
- expect_identical(suppressWarnings(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3))),
- c("***", "**", "*", ".", " ", NA, NA))
-
- expect_warning(key_antibiotics(example_isolates))
- expect_identical(suppressWarnings(key_antibiotics(example_isolates)),
- key_antimicrobials(example_isolates, antifungal = NULL))
-
- expect_warning(key_antibiotics_equal("S", "S"))
- expect_identical(suppressWarnings(key_antibiotics_equal("S", "S")),
- antimicrobials_equal("S", "S", type = "keyantimicrobials"))
-
- expect_warning(filter_first_weighted_isolate(example_isolates))
- expect_identical(suppressWarnings(filter_first_weighted_isolate(example_isolates)),
- filter_first_isolate(example_isolates))
-
-})
+expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "dose")[[1]],
+ 500)
+expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "admin")[[1]],
+ "oral")
diff --git a/inst/tinytest/test-ab_property.R b/inst/tinytest/test-ab_property.R
new file mode 100644
index 00000000..dd3f255b
--- /dev/null
+++ b/inst/tinytest/test-ab_property.R
@@ -0,0 +1,63 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
+expect_identical(as.character(ab_atc("AMX")), "J01CA04")
+expect_identical(ab_cid("AMX"), as.integer(33613))
+
+expect_inherits(ab_tradenames("AMX"), "character")
+expect_inherits(ab_tradenames(c("AMX", "AMX")), "list")
+
+expect_identical(ab_group("AMX", language = NULL), "Beta-lactams/penicillins")
+expect_identical(ab_atc_group1("AMX", language = NULL), "Beta-lactam antibacterials, penicillins")
+expect_identical(ab_atc_group2("AMX", language = NULL), "Penicillins with extended spectrum")
+
+expect_identical(ab_name("Fluclox", language = NULL), "Flucloxacillin")
+expect_identical(ab_name("fluklox", language = NULL), "Flucloxacillin")
+expect_identical(ab_name("floxapen", language = NULL), "Flucloxacillin")
+expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
+expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
+
+expect_identical(ab_ddd("AMX", "oral"), 1.5)
+expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g")
+expect_identical(ab_ddd("AMX", "iv"), 3)
+expect_identical(ab_ddd("AMX", "iv", units = TRUE), "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_inherits(ab_info("AMX"), "list")
+
+expect_error(ab_property("amox", "invalid property"))
+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_true(ab_url("AMX") %like% "whocc.no")
+expect_warning(ab_url("ASP"))
diff --git a/tests/testthat/test-g.test.R b/inst/tinytest/test-age.R
similarity index 55%
rename from tests/testthat/test-g.test.R
rename to inst/tinytest/test-age.R
index dfc1c70b..114ef28a 100644
--- a/tests/testthat/test-g.test.R
+++ b/inst/tinytest/test-age.R
@@ -23,49 +23,46 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("g.test.R")
+expect_equal(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
+ reference = "2019-01-01"),
+ c(39, 34, 29))
-test_that("G-test works", {
- skip_on_cran()
+expect_equal(age(x = c("2019-01-01", "2019-04-01", "2019-07-01"),
+ reference = "2019-09-01",
+ exact = TRUE),
+ c(0.6656393, 0.4191781, 0.1698630),
+ tolerance = 0.001)
- # GOODNESS-OF-FIT
+expect_error(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
+ reference = c("2019-01-01", "2019-01-01")))
- # example 1: clearfield rice vs. red rice
- x <- c(772, 1611, 737)
- expect_equal(g.test(x, p = c(0.25, 0.50, 0.25))$p.value,
- expected = 0.12574,
- tolerance = 0.00001)
+expect_warning(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
+ reference = "1975-01-01"))
- # example 2: red crossbills
- x <- c(1752, 1895)
- expect_equal(g.test(x)$p.value,
- expected = 0.01787343,
- tolerance = 0.00000001)
+expect_warning(age(x = c("1800-01-01", "1805-01-01", "1810-01-01"),
+ reference = "2019-01-01"))
- expect_error(g.test(0))
- expect_error(g.test(c(0, 1), 0))
- expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25)))
- expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24)))
- expect_warning(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24), rescale.p = TRUE))
+expect_equal(length(age(x = c("2019-01-01", NA), na.rm = TRUE)),
+ 1)
- # INDEPENDENCE
- x <- as.data.frame(
- matrix(data = round(runif(4) * 100000, 0),
- ncol = 2,
- byrow = TRUE)
- )
-
- # fisher.test() is always better for 2x2 tables:
- expect_warning(g.test(x))
- expect_lt(suppressWarnings(g.test(x)$p.value),
- 1)
+ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
- expect_warning(g.test(x = c(772, 1611, 737),
- y = c(780, 1560, 780),
- rescale.p = TRUE))
+expect_equal(length(unique(age_groups(ages, 50))),
+ 2)
+expect_equal(length(unique(age_groups(ages, c(50, 60)))),
+ 3)
+expect_identical(class(age_groups(ages, "child")),
+ c("ordered", "factor"))
- expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
- expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))
+expect_identical(class(age_groups(ages, "elderly")),
+ c("ordered", "factor"))
-})
+expect_identical(class(age_groups(ages, "tens")),
+ c("ordered", "factor"))
+
+expect_identical(class(age_groups(ages, "fives")),
+ c("ordered", "factor"))
+
+expect_equal(length(age_groups(c(10, 20, 30, NA), na.rm = TRUE)),
+ 3)
diff --git a/tests/testthat/test-atc_online.R b/inst/tinytest/test-atc_online.R
similarity index 90%
rename from tests/testthat/test-atc_online.R
rename to inst/tinytest/test-atc_online.R
index f014c0bf..bd390e1a 100644
--- a/tests/testthat/test-atc_online.R
+++ b/inst/tinytest/test-atc_online.R
@@ -23,15 +23,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("atc_online.R")
-
-test_that("atc_online works", {
- skip_on_cran()
- skip_if_not_installed("curl")
- skip_if_not(curl::has_internet())
-
- expect_gte(length(atc_online_groups(ab_atc("AMX"))), 1)
+if (tryCatch(curl::has_internet(), error = function(e) FALSE)) {
+ expect_true(length(atc_online_groups(ab_atc("AMX"))) >= 1)
expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "O"), 1.5)
expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "P"), 3)
expect_warning(atc_online_ddd(ab_atc("Novobiocin"), administration = "P"))
-})
+}
diff --git a/tests/testthat/test-availability.R b/inst/tinytest/test-availability.R
similarity index 92%
rename from tests/testthat/test-availability.R
rename to inst/tinytest/test-availability.R
index 171da6fd..79a97f06 100644
--- a/tests/testthat/test-availability.R
+++ b/inst/tinytest/test-availability.R
@@ -22,10 +22,5 @@
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-
-context("availability.R")
-
-test_that("availability works", {
- skip_on_cran()
- expect_equal(class(availability(example_isolates)), "data.frame")
-})
+
+expect_inherits(availability(example_isolates), "data.frame")
diff --git a/tests/testthat/test-bug_drug_combinations.R b/inst/tinytest/test-bug_drug_combinations.R
similarity index 82%
rename from tests/testthat/test-bug_drug_combinations.R
rename to inst/tinytest/test-bug_drug_combinations.R
index 80b83886..50ae048c 100644
--- a/tests/testthat/test-bug_drug_combinations.R
+++ b/inst/tinytest/test-bug_drug_combinations.R
@@ -23,14 +23,8 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("bug_drug_combinations.R")
-
-test_that("bug_drug_combinations works", {
- skip_on_cran()
-
- b <- suppressWarnings(bug_drug_combinations(example_isolates))
- expect_s3_class(b, "bug_drug_combinations")
- expect_output(print(b))
- expect_true(is.data.frame(format(b)))
- expect_true(is.data.frame(format(b, combine_IR = TRUE, add_ab_group = FALSE)))
-})
+b <- suppressWarnings(bug_drug_combinations(example_isolates))
+expect_inherits(b, "bug_drug_combinations")
+expect_stdout(print(b))
+expect_true(is.data.frame(format(b)))
+expect_true(is.data.frame(format(b, combine_IR = TRUE, add_ab_group = FALSE)))
diff --git a/inst/tinytest/test-count.R b/inst/tinytest/test-count.R
new file mode 100644
index 00000000..38cbcd93
--- /dev/null
+++ b/inst/tinytest/test-count.R
@@ -0,0 +1,99 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
+expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
+expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
+
+# AMX resistance in `example_isolates`
+expect_equal(count_R(example_isolates$AMX), 804)
+expect_equal(count_I(example_isolates$AMX), 3)
+expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
+expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
+ suppressWarnings(count_IR(example_isolates$AMX)))
+expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
+ count_SI(example_isolates$AMX))
+
+
+# warning for speed loss
+reset_all_thrown_messages()
+expect_warning(count_resistant(as.character(example_isolates$AMC)))
+reset_all_thrown_messages()
+expect_warning(count_resistant(example_isolates$AMC,
+ as.character(example_isolates$GEN)))
+
+# check for errors
+expect_error(count_resistant("test", minimum = "test"))
+expect_error(count_resistant("test", as_percent = "test"))
+expect_error(count_susceptible("test", minimum = "test"))
+expect_error(count_susceptible("test", as_percent = "test"))
+
+expect_error(count_df(c("A", "B", "C")))
+expect_error(count_df(example_isolates[, "date"]))
+
+if (suppressWarnings(require("dplyr"))) {
+ expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
+ expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
+ expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
+ expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
+ expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
+ expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
+ example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
+ example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE))
+
+ # count of cases
+ expect_equal(example_isolates %>%
+ group_by(hospital_id) %>%
+ summarise(cipro = count_susceptible(CIP),
+ genta = count_susceptible(GEN),
+ combination = count_susceptible(CIP, GEN)) %>%
+ pull(combination),
+ c(253, 465, 192, 558))
+
+ # count_df
+ expect_equal(
+ example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
+ c(example_isolates$AMX %>% count_susceptible(),
+ example_isolates$AMX %>% count_resistant())
+ )
+ expect_equal(
+ example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
+ c(suppressWarnings(example_isolates$AMX %>% count_S()),
+ suppressWarnings(example_isolates$AMX %>% count_IR()))
+ )
+ expect_equal(
+ example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
+ c(suppressWarnings(example_isolates$AMX %>% count_S()),
+ example_isolates$AMX %>% count_I(),
+ example_isolates$AMX %>% count_R())
+ )
+
+ # grouping in rsi_calc_df() (= backbone of rsi_df())
+ expect_true("hospital_id" %in% (example_isolates %>%
+ group_by(hospital_id) %>%
+ select(hospital_id, AMX, CIP, gender) %>%
+ rsi_df() %>%
+ colnames()))
+}
diff --git a/inst/tinytest/test-data.R b/inst/tinytest/test-data.R
new file mode 100644
index 00000000..76be3511
--- /dev/null
+++ b/inst/tinytest/test-data.R
@@ -0,0 +1,84 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_true(check_dataset_integrity()) # in misc.R
+
+# IDs should always be unique
+expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
+expect_identical(class(microorganisms$mo), c("mo", "character"))
+expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
+expect_identical(class(antibiotics$ab), c("ab", "character"))
+
+# check cross table reference
+expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
+expect_true(all(example_isolates$mo %in% microorganisms$mo))
+expect_true(all(microorganisms.translation$mo_new %in% microorganisms$mo))
+expect_true(all(rsi_translation$mo %in% microorganisms$mo))
+expect_true(all(rsi_translation$ab %in% antibiotics$ab))
+expect_true(all(intrinsic_resistant$microorganism %in% microorganisms$fullname)) # also important for mo_is_intrinsic_resistant()
+expect_true(all(intrinsic_resistant$antibiotic %in% antibiotics$name))
+expect_false(any(is.na(microorganisms.codes$code)))
+expect_false(any(is.na(microorganisms.codes$mo)))
+expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))
+expect_true(all(dosage$ab %in% antibiotics$ab))
+expect_true(all(dosage$name %in% antibiotics$name))
+
+# antibiotic names must always be coercible to their original AB code
+expect_identical(as.ab(antibiotics$name), antibiotics$ab)
+
+# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
+datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
+for (i in seq_len(length(datasets))) {
+ dataset <- get(datasets[i], envir = asNamespace("AMR"))
+ expect_identical(dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
+}
+
+df <- AMR:::MO_lookup
+expect_true(nrow(df[which(df$prevalence == 1), ]) < nrow(df[which(df$prevalence == 2), ]))
+expect_true(nrow(df[which(df$prevalence == 2), ]) < nrow(df[which(df$prevalence == 3), ]))
+expect_true(all(c("mo", "fullname",
+ "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
+ "rank", "ref", "species_id", "source", "prevalence", "snomed",
+ "kingdom_index", "fullname_lower", "g_species") %in% colnames(df)))
+
+expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
+ "fullname_lower", "g_species") %in% colnames(AMR:::MO.old_lookup)))
+
+expect_inherits(AMR:::MO_CONS, "mo")
+
+expect_identical(class(catalogue_of_life_version()),
+ c("catalogue_of_life_version", "list"))
+
+expect_stdout(print(catalogue_of_life_version()))
+
+uncategorised <- subset(microorganisms,
+ genus == "Staphylococcus" &
+ !species %in% c("", "aureus") &
+ !mo %in% c(MO_CONS, MO_COPS))
+expect_true(NROW(uncategorised) == 0,
+ info = ifelse(NROW(uncategorised) == 0,
+ "All staphylococcal species categorised as CoNS/CoPS.",
+ paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
+ uncategorised$species, " (", uncategorised$mo, ")")))
diff --git a/tests/testthat/test-disk.R b/inst/tinytest/test-disk.R
similarity index 59%
rename from tests/testthat/test-disk.R
rename to inst/tinytest/test-disk.R
index 15bb359d..5187bd7c 100755
--- a/tests/testthat/test-disk.R
+++ b/inst/tinytest/test-disk.R
@@ -23,39 +23,33 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("disk.R")
+expect_true(as.disk(8) == as.disk("8"))
+expect_true(is.disk(as.disk(8)))
-test_that("disk works", {
- skip_on_cran()
- expect_true(as.disk(8) == as.disk("8"))
- expect_true(is.disk(as.disk(8)))
+expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)
- expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)
+# all levels should be valid disks
+x <- as.disk(c(20, 40))
+expect_inherits(x[1], "disk")
+expect_inherits(x[[1]], "disk")
+expect_inherits(c(x[1], x[9]), "disk")
+expect_inherits(unique(x[1], x[9]), "disk")
+expect_warning(as.disk("INVALID VALUE"))
+x[2] <- 32
+expect_inherits(x, "disk")
- # all levels should be valid disks
- x <- as.disk(c(20, 40))
- expect_s3_class(x[1], "disk")
- expect_s3_class(x[[1]], "disk")
- expect_s3_class(c(x[1], x[9]), "disk")
- expect_s3_class(unique(x[1], x[9]), "disk")
- expect_warning(as.disk("INVALID VALUE"))
- x[2] <- 32
- expect_s3_class(x, "disk")
-
- pdf(NULL) # prevent Rplots.pdf being created
- expect_silent(barplot(as.disk(c(10, 20, 40))))
- expect_silent(plot(as.disk(c(10, 20, 40))))
- expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
- expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"))
- if (suppressWarnings(require("ggplot2"))) {
- expect_s3_class(ggplot(as.disk(c(10, 20, 40))), "gg")
- expect_s3_class(ggplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
- expect_s3_class(ggplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
- }
- expect_output(print(as.disk(12)))
-
- if (suppressWarnings(require("dplyr"))) {
- expect_output(print(tibble(d = as.disk(12))))
- }
+pdf(NULL) # prevent Rplots.pdf being created
+expect_silent(barplot(as.disk(c(10, 20, 40))))
+expect_silent(plot(as.disk(c(10, 20, 40))))
+expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
+expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"))
+if (suppressWarnings(require("ggplot2"))) {
+ expect_inherits(ggplot(as.disk(c(10, 20, 40))), "gg")
+ expect_inherits(ggplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
+ expect_inherits(ggplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
+}
+expect_stdout(print(as.disk(12)))
-})
+if (suppressWarnings(require("dplyr"))) {
+ expect_stdout(print(tibble(d = as.disk(12))))
+}
diff --git a/tests/testthat/test-random.R b/inst/tinytest/test-episode.R
similarity index 63%
rename from tests/testthat/test-random.R
rename to inst/tinytest/test-episode.R
index 637683e8..618963f5 100644
--- a/tests/testthat/test-random.R
+++ b/inst/tinytest/test-episode.R
@@ -23,22 +23,30 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("random.R")
+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"
+ ))
-test_that("random works", {
- skip_on_cran()
+expect_equal(get_episode(test_df$date, 365),
+ c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3))
+
+if (suppressWarnings(require("dplyr"))) {
+ 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))
- expect_s3_class(random_mic(100), "mic")
- expect_s3_class(random_mic(100, mo = "Klebsiella pneumoniae"), "mic")
- expect_s3_class(random_mic(100, mo = "Klebsiella pneumoniae", ab = "meropenem"), "mic")
- expect_s3_class(random_mic(100, ab = "meropenem"), "mic")
- # no normal factors of 2
- expect_s3_class(random_mic(100, "Haemophilus influenzae", "ceftaroline"), "mic")
+ suppressMessages(
+ x <- example_isolates %>%
+ mutate(out = first_isolate(., include_unknown = TRUE, method = "episode-based", info = FALSE))
+ )
+ y <- example_isolates %>%
+ group_by(patient_id, mo) %>%
+ mutate(out = is_new_episode(date, 365))
- expect_s3_class(random_disk(100), "disk")
- expect_s3_class(random_disk(100, mo = "Klebsiella pneumoniae"), "disk")
- expect_s3_class(random_disk(100, mo = "Klebsiella pneumoniae", ab = "meropenem"), "disk")
- expect_s3_class(random_disk(100, ab = "meropenem"), "disk")
-
- expect_s3_class(random_rsi(100), "rsi")
-})
+ expect_identical(which(x$out), which(y$out))
+}
diff --git a/inst/tinytest/test-eucast_rules.R b/inst/tinytest/test-eucast_rules.R
new file mode 100755
index 00000000..014f073f
--- /dev/null
+++ b/inst/tinytest/test-eucast_rules.R
@@ -0,0 +1,158 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+# thoroughly check input table
+expect_equal(colnames(eucast_rules_file),
+ c("if_mo_property", "like.is.one_of", "this_value",
+ "and_these_antibiotics", "have_these_values",
+ "then_change_these_antibiotics", "to_value",
+ "reference.rule", "reference.rule_group",
+ "reference.version",
+ "note"))
+MOs_mentioned <- unique(eucast_rules_file$this_value)
+MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
+MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
+expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
+
+expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
+expect_error(eucast_rules(x = "text"))
+expect_error(eucast_rules(data.frame(a = "test")))
+expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
+
+expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE)))
+
+expect_identical(colnames(example_isolates),
+ colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
+expect_stdout(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
+
+a <- data.frame(mo = c("Klebsiella pneumoniae",
+ "Pseudomonas aeruginosa",
+ "Enterobacter cloacae"),
+ amox = "-", # Amoxicillin
+ stringsAsFactors = FALSE)
+b <- data.frame(mo = c("Klebsiella pneumoniae",
+ "Pseudomonas aeruginosa",
+ "Enterobacter cloacae"),
+ amox = "R", # Amoxicillin
+ stringsAsFactors = FALSE)
+expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
+expect_stdout(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE))))
+
+a <- data.frame(mo = c("Staphylococcus aureus",
+ "Streptococcus group A"),
+ COL = "-", # Colistin
+ stringsAsFactors = FALSE)
+b <- data.frame(mo = c("Staphylococcus aureus",
+ "Streptococcus group A"),
+ COL = "R", # Colistin
+ stringsAsFactors = FALSE)
+expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
+
+# piperacillin must be R in Enterobacteriaceae when tica is R
+if (suppressWarnings(require("dplyr"))) {
+ expect_equal(suppressWarnings(
+ example_isolates %>%
+ filter(mo_family(mo) == "Enterobacteriaceae") %>%
+ mutate(TIC = as.rsi("R"),
+ PIP = as.rsi("S")) %>%
+ eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
+ pull(PIP) %>%
+ unique() %>%
+ as.character()),
+ "R")
+}
+
+# Azithromycin and Clarythromycin must be equal to Erythromycin
+a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
+ ERY = example_isolates$ERY,
+ AZM = as.rsi("R"),
+ CLR = factor("R"),
+ stringsAsFactors = FALSE),
+ version_expertrules = 3.1,
+ only_rsi_columns = FALSE)$CLR))
+b <- example_isolates$ERY
+expect_identical(a[!is.na(b)],
+ b[!is.na(b)])
+
+# amox is inferred by benzylpenicillin in Kingella kingae
+expect_equal(
+ suppressWarnings(
+ as.list(eucast_rules(
+ data.frame(mo = as.mo("Kingella kingae"),
+ PEN = "S",
+ AMX = "-",
+ stringsAsFactors = FALSE)
+ , info = FALSE))$AMX
+ ),
+ "S")
+
+# also test norf
+if (suppressWarnings(require("dplyr"))) {
+ expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
+}
+
+# check verbose output
+expect_stdout(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
+
+# AmpC de-repressed cephalo mutants
+expect_identical(
+ eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
+ cefotax = as.rsi(c("S", "S"))),
+ ampc_cephalosporin_resistance = TRUE,
+ info = FALSE)$cefotax,
+ as.rsi(c("S", "R")))
+expect_identical(
+ eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
+ cefotax = as.rsi(c("S", "S"))),
+ ampc_cephalosporin_resistance = NA,
+ info = FALSE)$cefotax,
+ as.rsi(c("S", NA)))
+expect_identical(
+ eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
+ cefotax = as.rsi(c("S", "S"))),
+ ampc_cephalosporin_resistance = NULL,
+ info = FALSE)$cefotax,
+ as.rsi(c("S", "S")))
+
+# EUCAST dosage -----------------------------------------------------------
+expect_equal(nrow(eucast_dosage(c("tobra", "genta", "cipro"))), 3)
+expect_inherits(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
+
+
+
+x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
+ AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I",
+ AMX == "S" ~ AMC == "S")
+expect_stdout(print(x))
+expect_stdout(print(c(x, x)))
+expect_stdout(print(as.list(x, x)))
+
+# this custom rules makes 8 changes
+expect_equal(nrow(eucast_rules(example_isolates,
+ rules = "custom",
+ custom_rules = x,
+ info = FALSE,
+ verbose = TRUE)),
+ 8)
diff --git a/inst/tinytest/test-filter_ab_class.R b/inst/tinytest/test-filter_ab_class.R
new file mode 100644
index 00000000..1476933d
--- /dev/null
+++ b/inst/tinytest/test-filter_ab_class.R
@@ -0,0 +1,48 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+if (suppressWarnings(require("dplyr"))) {
+ expect_true(example_isolates %>% filter_ab_class("carbapenem") %>% nrow() > 0)
+ expect_true(example_isolates %>% filter_aminoglycosides() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_carbapenems() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_cephalosporins() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_1st_cephalosporins() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_2nd_cephalosporins() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_3rd_cephalosporins() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_4th_cephalosporins() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_5th_cephalosporins() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_fluoroquinolones() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_glycopeptides() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_macrolides() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_oxazolidinones() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_penicillins() %>% ncol() > 0)
+ expect_true(example_isolates %>% filter_tetracyclines() %>% ncol() > 0)
+
+ expect_true(example_isolates %>% filter_carbapenems("R", "all") %>% nrow() > 0)
+
+ expect_error(example_isolates %>% filter_carbapenems(result = "test"))
+ expect_error(example_isolates %>% filter_carbapenems(scope = "test"))
+ expect_message(example_isolates %>% select(1:3) %>% filter_carbapenems())
+}
diff --git a/inst/tinytest/test-first_isolate.R b/inst/tinytest/test-first_isolate.R
new file mode 100755
index 00000000..fa591837
--- /dev/null
+++ b/inst/tinytest/test-first_isolate.R
@@ -0,0 +1,182 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+# all four methods
+expect_equal(sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE),
+ 1984)
+expect_equal(sum(first_isolate(x = example_isolates, method = "patient-based", info = TRUE), na.rm = TRUE),
+ 1265)
+expect_equal(sum(first_isolate(x = example_isolates, method = "episode-based", info = TRUE), na.rm = TRUE),
+ 1300)
+expect_equal(sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
+ 1379)
+
+# Phenotype-based, using key antimicrobials
+expect_equal(sum(first_isolate(x = example_isolates,
+ method = "phenotype-based",
+ type = "keyantimicrobials",
+ antifungal = NULL, info = TRUE), na.rm = TRUE),
+ 1395)
+expect_equal(sum(first_isolate(x = example_isolates,
+ method = "phenotype-based",
+ type = "keyantimicrobials",
+ antifungal = NULL, info = TRUE, ignore_I = FALSE), na.rm = TRUE),
+ 1418)
+
+
+# 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),
+ 941)
+
+# set 1500 random observations to be of specimen type 'Urine'
+random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
+x <- example_isolates
+x$specimen <- "Other"
+x[random_rows, "specimen"] <- "Urine"
+expect_true(
+ sum(first_isolate(x = x,
+ 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_true(
+ sum(first_isolate(x = x,
+ 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"
+test_iso <- example_isolates
+test_iso$specimen <- "test"
+expect_message(first_isolate(test_iso,
+ "date",
+ "patient_id",
+ col_mo = "mo",
+ col_specimen = "specimen",
+ filter_specimen = "something_unexisting",
+ info = TRUE))
+
+# printing of exclusion message
+expect_message(first_isolate(example_isolates,
+ col_date = "date",
+ col_mo = "mo",
+ col_patient_id = "patient_id",
+ col_testcode = "gender",
+ testcodes_exclude = "M",
+ info = TRUE))
+
+# errors
+expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
+expect_error(first_isolate(example_isolates,
+ col_date = "non-existing col",
+ col_mo = "mo"))
+
+if (suppressWarnings(require("dplyr"))) {
+ # if mo is not an mo class, result should be the same
+ expect_identical(example_isolates %>%
+ mutate(mo = as.character(mo)) %>%
+ first_isolate(col_date = "date",
+ col_mo = "mo",
+ col_patient_id = "patient_id",
+ info = FALSE),
+ example_isolates %>%
+ first_isolate(col_date = "date",
+ col_mo = "mo",
+ col_patient_id = "patient_id",
+ info = FALSE))
+
+ # support for WHONET
+ expect_message(example_isolates %>%
+ select(-patient_id) %>%
+ mutate(`First name` = "test",
+ `Last name` = "test",
+ Sex = "Female") %>%
+ first_isolate(info = TRUE))
+
+ # groups
+ x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
+ y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
+ expect_identical(x, y)
+
+}
+
+# missing dates should be no problem
+df <- example_isolates
+df[1:100, "date"] <- NA
+expect_equal(
+ sum(
+ first_isolate(x = df,
+ col_date = "date",
+ col_patient_id = "patient_id",
+ col_mo = "mo",
+ info = TRUE),
+ na.rm = TRUE),
+ 1382)
+
+# unknown MOs
+test_unknown <- example_isolates
+test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
+expect_equal(sum(first_isolate(test_unknown, include_unknown = FALSE)),
+ 1108)
+expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)),
+ 1591)
+
+test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
+expect_equal(sum(first_isolate(test_unknown)),
+ 1108)
+
+# empty rsi results
+expect_equal(sum(first_isolate(example_isolates, include_untested_rsi = FALSE)),
+ 1366)
+
+# shortcuts
+expect_identical(filter_first_isolate(example_isolates),
+ subset(example_isolates, first_isolate(example_isolates)))
+
+
+# notice that all mo's are distinct, so all are TRUE
+expect_true(all(example_isolates %pm>%
+ pm_distinct(mo, .keep_all = TRUE) %pm>%
+ first_isolate(info = TRUE) == TRUE))
+
+# only one isolate, so return fast
+expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
diff --git a/tests/testthat/test-key_antimicrobials.R b/inst/tinytest/test-g.test.R
similarity index 60%
rename from tests/testthat/test-key_antimicrobials.R
rename to inst/tinytest/test-g.test.R
index 2a5910e4..aed6f20a 100644
--- a/tests/testthat/test-key_antimicrobials.R
+++ b/inst/tinytest/test-g.test.R
@@ -23,19 +23,41 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("key_antimcrobials.R")
+# GOODNESS-OF-FIT
-test_that("key_antimcrobials work", {
- skip_on_cran()
- expect_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
- expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
- expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))
- expect_false(antimicrobials_equal("SSS", "SRS", type = "keyantimicrobials"))
- expect_true(antimicrobials_equal("SSS", "SRS", type = "points"))
- expect_true(antimicrobials_equal("SSS", "SIS", ignore_I = TRUE, type = "keyantimicrobials"))
- expect_false(antimicrobials_equal("SSS", "SIS", ignore_I = FALSE, type = "keyantimicrobials"))
- expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials"))
- expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials"))
-
- expect_warning(key_antimicrobials(example_isolates[rep(1, 10), ]))
-})
+# example 1: clearfield rice vs. red rice
+x <- c(772, 1611, 737)
+expect_equal(g.test(x, p = c(0.25, 0.50, 0.25))$p.value,
+ 0.12574,
+ tolerance = 0.0001)
+
+# example 2: red crossbills
+x <- c(1752, 1895)
+expect_equal(g.test(x)$p.value,
+ 0.017873,
+ tolerance = 0.0001)
+
+expect_error(g.test(0))
+expect_error(g.test(c(0, 1), 0))
+expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25)))
+expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24)))
+expect_warning(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24), rescale.p = TRUE))
+
+# INDEPENDENCE
+
+x <- as.data.frame(
+ matrix(data = round(runif(4) * 100000, 0),
+ ncol = 2,
+ byrow = TRUE)
+)
+
+# fisher.test() is always better for 2x2 tables:
+expect_warning(g.test(x))
+expect_true(suppressWarnings(g.test(x)$p.value) < 1)
+
+expect_warning(g.test(x = c(772, 1611, 737),
+ y = c(780, 1560, 780),
+ rescale.p = TRUE))
+
+expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
+expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))
diff --git a/tests/testthat/test-kurtosis.R b/inst/tinytest/test-get_locale.R
similarity index 71%
rename from tests/testthat/test-kurtosis.R
rename to inst/tinytest/test-get_locale.R
index e4f6848f..758e83a5 100644
--- a/tests/testthat/test-kurtosis.R
+++ b/inst/tinytest/test-get_locale.R
@@ -23,25 +23,12 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("kurtosis.R")
+expect_identical(mo_genus("B_GRAMP", language = "pt"),
+ "(Gram positivos desconhecidos)")
-test_that("kurtosis works", {
- skip_on_cran()
- expect_equal(kurtosis(example_isolates$age),
- 5.227999,
- tolerance = 0.00001)
-
- expect_equal(unname(kurtosis(data.frame(example_isolates$age))),
- 5.227999,
- tolerance = 0.00001)
- expect_equal(unname(kurtosis(data.frame(example_isolates$age), excess = TRUE)),
- 2.227999,
- tolerance = 0.00001)
-
- expect_equal(kurtosis(matrix(example_isolates$age)),
- 5.227999,
- tolerance = 0.00001)
- expect_equal(kurtosis(matrix(example_isolates$age), excess = TRUE),
- 2.227999,
- tolerance = 0.00001)
-})
+expect_identical(mo_fullname("CoNS", "en"), "Coagulase-negative Staphylococcus (CoNS)")
+expect_identical(mo_fullname("CoNS", "de"), "Koagulase-negative Staphylococcus (KNS)")
+expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
+expect_identical(mo_fullname("CoNS", "es"), "Staphylococcus coagulasa negativo (SCN)")
+expect_identical(mo_fullname("CoNS", "it"), "Staphylococcus negativo coagulasi (CoNS)")
+expect_identical(mo_fullname("CoNS", "pt"), "Staphylococcus coagulase negativo (CoNS)")
diff --git a/inst/tinytest/test-ggplot_rsi.R b/inst/tinytest/test-ggplot_rsi.R
new file mode 100644
index 00000000..b328ce12
--- /dev/null
+++ b/inst/tinytest/test-ggplot_rsi.R
@@ -0,0 +1,112 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+if (suppressWarnings(require("dplyr")) & suppressWarnings(require("ggplot2"))) {
+
+ pdf(NULL) # prevent Rplots.pdf being created
+
+ # data should be equal
+ expect_equal(
+ (example_isolates %>%
+ select(AMC, CIP) %>%
+ ggplot_rsi())$data %>%
+ summarise_all(resistance) %>%
+ as.double(),
+ example_isolates %>%
+ select(AMC, CIP) %>%
+ summarise_all(resistance) %>%
+ as.double()
+ )
+
+ expect_stdout(print(example_isolates %>%
+ select(AMC, CIP) %>%
+ ggplot_rsi(x = "interpretation", facet = "antibiotic")))
+ expect_stdout(print(example_isolates %>%
+ select(AMC, CIP) %>%
+ ggplot_rsi(x = "antibiotic", facet = "interpretation")))
+
+ expect_equal(
+ (example_isolates %>%
+ select(AMC, CIP) %>%
+ ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>%
+ summarise_all(resistance) %>%
+ as.double(),
+ example_isolates %>%
+ select(AMC, CIP) %>%
+ summarise_all(resistance) %>%
+ as.double()
+ )
+
+ expect_equal(
+ (example_isolates %>%
+ select(AMC, CIP) %>%
+ ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>%
+ summarise_all(resistance) %>%
+ as.double(),
+ example_isolates %>%
+ select(AMC, CIP) %>%
+ summarise_all(resistance) %>%
+ as.double()
+ )
+
+ expect_equal(
+ (example_isolates %>%
+ select(AMC, CIP) %>%
+ ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>%
+ summarise_all(count_resistant) %>%
+ as.double(),
+ example_isolates %>%
+ select(AMC, CIP) %>%
+ summarise_all(count_resistant) %>%
+ as.double()
+ )
+
+ # support for scale_type ab and mo
+ expect_inherits((data.frame(mo = as.mo(c("e. coli", "s aureus")),
+ n = c(40, 100)) %>%
+ ggplot(aes(x = mo, y = n)) +
+ geom_col())$data,
+ "data.frame")
+ expect_inherits((data.frame(ab = as.ab(c("amx", "amc")),
+ n = c(40, 100)) %>%
+ ggplot(aes(x = ab, y = n)) +
+ geom_col())$data,
+ "data.frame")
+
+ expect_inherits((data.frame(ab = as.ab(c("amx", "amc")),
+ n = c(40, 100)) %>%
+ ggplot(aes(x = ab, y = n)) +
+ geom_col())$data,
+ "data.frame")
+
+ # support for manual colours
+ expect_inherits((ggplot(data.frame(x = c("Value1", "Value2", "Value3"),
+ y = c(1, 2, 3),
+ z = c("Value4", "Value5", "Value6"))) +
+ geom_col(aes(x = x, y = y, fill = z)) +
+ scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R"))$data,
+ "data.frame")
+
+}
diff --git a/inst/tinytest/test-guess_ab_col.R b/inst/tinytest/test-guess_ab_col.R
new file mode 100644
index 00000000..afd1f356
--- /dev/null
+++ b/inst/tinytest/test-guess_ab_col.R
@@ -0,0 +1,42 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_equal(guess_ab_col(example_isolates, "amox"),
+ "AMX")
+expect_equal(guess_ab_col(example_isolates, "amoxicillin"),
+ "AMX")
+expect_equal(guess_ab_col(example_isolates, "J01AA07"),
+ "TCY")
+expect_equal(guess_ab_col(example_isolates, "tetracycline"),
+ "TCY")
+expect_equal(guess_ab_col(example_isolates, "TETR"),
+ "TCY")
+
+df <- data.frame(AMP_ND10 = "R",
+ AMC_ED20 = "S")
+expect_equal(guess_ab_col(df, "ampicillin"),
+ "AMP_ND10")
+expect_equal(guess_ab_col(df, "J01CR02"),
+ "AMC_ED20")
diff --git a/tests/testthat/test-italicise_taxonomy.R b/inst/tinytest/test-italicise_taxonomy.R
similarity index 78%
rename from tests/testthat/test-italicise_taxonomy.R
rename to inst/tinytest/test-italicise_taxonomy.R
index 859e84fa..5d88a775 100644
--- a/tests/testthat/test-italicise_taxonomy.R
+++ b/inst/tinytest/test-italicise_taxonomy.R
@@ -23,17 +23,11 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("italicise_taxonomy.R")
-
-test_that("italic taxonomy works", {
- skip_on_cran()
-
- expect_identical(italicise_taxonomy("test for E. coli"),
- "test for *E. coli*")
- expect_identical(italicise_taxonomy("test for E. coli"),
- italicize_taxonomy("test for E. coli"))
- if (has_colour()) {
- expect_identical(italicise_taxonomy("test for E. coli", type = "ansi"),
- "test for \033[3mE. coli\033[23m")
- }
-})
+expect_identical(italicise_taxonomy("test for E. coli"),
+ "test for *E. coli*")
+expect_identical(italicise_taxonomy("test for E. coli"),
+ italicize_taxonomy("test for E. coli"))
+if (has_colour()) {
+ expect_identical(italicise_taxonomy("test for E. coli", type = "ansi"),
+ "test for \033[3mE. coli\033[23m")
+}
diff --git a/tests/testthat/test-episode.R b/inst/tinytest/test-join_microorganisms.R
old mode 100644
new mode 100755
similarity index 58%
rename from tests/testthat/test-episode.R
rename to inst/tinytest/test-join_microorganisms.R
index c7005393..c79aed5f
--- a/tests/testthat/test-episode.R
+++ b/inst/tinytest/test-join_microorganisms.R
@@ -23,36 +23,35 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("episode.R")
+unjoined <- example_isolates
+inner <- example_isolates %>% inner_join_microorganisms()
+left <- example_isolates %>% left_join_microorganisms()
+semi <- example_isolates %>% semi_join_microorganisms()
+anti <- example_isolates %>% anti_join_microorganisms()
+suppressWarnings(right <- example_isolates %>% right_join_microorganisms())
+suppressWarnings(full <- example_isolates %>% full_join_microorganisms())
-test_that("episodes work", {
- skip_on_cran()
-
- 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))
-
- if (suppressWarnings(require("dplyr"))) {
- 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_id, mo) %>%
- mutate(out = is_new_episode(date, 365))
-
- expect_identical(which(x$out), which(y$out))
- }
-})
+expect_true(ncol(unjoined) < ncol(inner))
+expect_true(nrow(unjoined) == nrow(inner))
+
+expect_true(ncol(unjoined) < ncol(left))
+expect_true(nrow(unjoined) == nrow(left))
+
+expect_true(ncol(semi) == ncol(semi))
+expect_true(nrow(semi) == nrow(semi))
+
+expect_true(nrow(anti) == 0)
+
+expect_true(nrow(unjoined) < nrow(right))
+expect_true(nrow(unjoined) < nrow(full))
+
+expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
+expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
+
+expect_equal(nrow(left_join_microorganisms("B_ESCHR_COLI")), 1)
+
+expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COLI")), 1)
+expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COLI")), 0)
+
+expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
+expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
diff --git a/inst/tinytest/test-key_antimicrobials.R b/inst/tinytest/test-key_antimicrobials.R
new file mode 100644
index 00000000..fc648956
--- /dev/null
+++ b/inst/tinytest/test-key_antimicrobials.R
@@ -0,0 +1,36 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
+expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
+expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))
+expect_false(antimicrobials_equal("SSS", "SRS", type = "keyantimicrobials"))
+expect_true(antimicrobials_equal("SSS", "SRS", type = "points"))
+expect_true(antimicrobials_equal("SSS", "SIS", ignore_I = TRUE, type = "keyantimicrobials"))
+expect_false(antimicrobials_equal("SSS", "SIS", ignore_I = FALSE, type = "keyantimicrobials"))
+expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials"))
+expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials"))
+
+expect_warning(key_antimicrobials(example_isolates[rep(1, 10), ]))
diff --git a/tests/testthat/test-guess_ab_col.R b/inst/tinytest/test-kurtosis.R
similarity index 71%
rename from tests/testthat/test-guess_ab_col.R
rename to inst/tinytest/test-kurtosis.R
index ebcf728d..e2d0419f 100644
--- a/tests/testthat/test-guess_ab_col.R
+++ b/inst/tinytest/test-kurtosis.R
@@ -23,27 +23,20 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("guess_ab_col.R")
+expect_equal(kurtosis(example_isolates$age),
+ 5.227999,
+ tolerance = 0.00001)
-test_that("guess_ab_col works", {
- skip_on_cran()
+expect_equal(unname(kurtosis(data.frame(example_isolates$age))),
+ 5.227999,
+ tolerance = 0.00001)
+expect_equal(unname(kurtosis(data.frame(example_isolates$age), excess = TRUE)),
+ 2.227999,
+ tolerance = 0.00001)
- expect_equal(guess_ab_col(example_isolates, "amox"),
- "AMX")
- expect_equal(guess_ab_col(example_isolates, "amoxicillin"),
- "AMX")
- expect_equal(guess_ab_col(example_isolates, "J01AA07"),
- "TCY")
- expect_equal(guess_ab_col(example_isolates, "tetracycline"),
- "TCY")
- expect_equal(guess_ab_col(example_isolates, "TETR"),
- "TCY")
-
- df <- data.frame(AMP_ND10 = "R",
- AMC_ED20 = "S")
- expect_equal(guess_ab_col(df, "ampicillin"),
- "AMP_ND10")
- expect_equal(guess_ab_col(df, "J01CR02"),
- "AMC_ED20")
-
-})
+expect_equal(kurtosis(matrix(example_isolates$age)),
+ 5.227999,
+ tolerance = 0.00001)
+expect_equal(kurtosis(matrix(example_isolates$age), excess = TRUE),
+ 2.227999,
+ tolerance = 0.00001)
diff --git a/tests/testthat/test-get_locale.R b/inst/tinytest/test-like.R
similarity index 70%
rename from tests/testthat/test-get_locale.R
rename to inst/tinytest/test-like.R
index 938eef21..cf3f7e73 100644
--- a/tests/testthat/test-get_locale.R
+++ b/inst/tinytest/test-like.R
@@ -23,18 +23,18 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("get_locale.R")
+expect_true(sum("test" %like% c("^t", "^s")) == 1)
-test_that("get_locale works", {
- skip_on_cran()
- expect_identical(mo_genus("B_GRAMP", language = "pt"),
- "(Gram positivos desconhecidos)")
+expect_true("test" %like% "test")
+expect_false("test" %like_case% "TEST")
+expect_true(factor("test") %like% factor("t"))
+expect_true(factor("test") %like% "t")
+expect_true("test" %like% factor("t"))
- expect_identical(mo_fullname("CoNS", "en"), "Coagulase-negative Staphylococcus (CoNS)")
- expect_identical(mo_fullname("CoNS", "de"), "Koagulase-negative Staphylococcus (KNS)")
- expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
- expect_identical(mo_fullname("CoNS", "es"), "Staphylococcus coagulasa negativo (SCN)")
- expect_identical(mo_fullname("CoNS", "it"), "Staphylococcus negativo coagulasi (CoNS)")
- expect_identical(mo_fullname("CoNS", "pt"), "Staphylococcus coagulase negativo (CoNS)")
-
-})
+expect_true(as.factor("test") %like% "TEST")
+expect_identical(factor(c("Test case", "Something different", "Yet another thing")) %like% c("case", "diff", "yet"),
+ c(TRUE, TRUE, TRUE))
+expect_identical("test" %like% c("t", "e", "s", "t"),
+ c(TRUE, TRUE, TRUE, TRUE))
+expect_identical(factor("test") %like% factor(c("t", "e", "s", "t")),
+ c(TRUE, TRUE, TRUE, TRUE))
diff --git a/inst/tinytest/test-mdro.R b/inst/tinytest/test-mdro.R
new file mode 100755
index 00000000..38644726
--- /dev/null
+++ b/inst/tinytest/test-mdro.R
@@ -0,0 +1,238 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
+expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
+expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
+expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
+
+expect_stdout(suppressMessages(suppressWarnings(mdro(example_isolates, info = TRUE))))
+expect_stdout(suppressMessages(suppressWarnings(mdro(example_isolates, "eucast3.1", info = TRUE))))
+expect_stdout(outcome <- suppressMessages(suppressWarnings(eucast_exceptional_phenotypes(example_isolates, info = TRUE))))
+# check class
+expect_identical(class(outcome), c("ordered", "factor"))
+
+expect_stdout(outcome <- mdro(example_isolates, "nl", info = TRUE))
+# check class
+expect_identical(class(outcome), c("ordered", "factor"))
+
+# example_isolates should have these finding using Dutch guidelines
+expect_equal(as.double(table(outcome)),
+ c(1970, 24, 6)) # 1970 neg, 24 unconfirmed, 6 pos
+
+expect_equal(brmo(example_isolates, info = FALSE),
+ mdro(example_isolates, guideline = "BRMO", info = FALSE))
+
+# test Dutch P. aeruginosa MDRO
+expect_equal(
+ as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
+ cfta = "S",
+ cipr = "S",
+ mero = "S",
+ imip = "S",
+ gent = "S",
+ tobr = "S",
+ pita = "S"),
+ guideline = "BRMO",
+ col_mo = "mo",
+ info = FALSE)),
+ "Negative")
+expect_equal(
+ as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
+ cefta = "R",
+ cipr = "R",
+ mero = "R",
+ imip = "R",
+ gent = "R",
+ tobr = "R",
+ pita = "R"),
+ guideline = "BRMO",
+ col_mo = "mo",
+ info = FALSE)),
+ "Positive")
+
+# German 3MRGN and 4MRGN
+expect_equal(as.character(mrgn(
+ data.frame(mo = c("E. coli", "E. coli", "K. pneumoniae", "E. coli",
+ "A. baumannii", "A. baumannii", "A. baumannii",
+ "P. aeruginosa", "P. aeruginosa", "P. aeruginosa"),
+ PIP = c("S", "R", "R", "S",
+ "S", "R", "R",
+ "S", "R", "R"),
+ CTX = c("S", "R", "R", "S",
+ "R", "R", "R",
+ "R", "R", "R"),
+ IPM = c("S", "R", "S", "R",
+ "R", "R", "S",
+ "S", "R", "R"),
+ CIP = c("S", "R", "R", "S",
+ "R", "R", "R",
+ "R", "S", "R"),
+ stringsAsFactors = FALSE))),
+ c("Negative", "4MRGN", "3MRGN", "4MRGN", "4MRGN", "4MRGN", "3MRGN", "Negative", "3MRGN", "4MRGN"))
+
+# MDR TB
+expect_equal(
+ # select only rifampicine, mo will be determined automatically (as M. tuberculosis),
+ # number of mono-resistant strains should be equal to number of rifampicine-resistant strains
+ as.double(table(mdr_tb(example_isolates[, "RIF", drop = FALSE])))[2],
+ count_R(example_isolates$RIF))
+
+x <- data.frame(rifampicin = random_rsi(5000, prob_RSI = c(0.4, 0.1, 0.5)),
+ inh = random_rsi(5000, prob_RSI = c(0.4, 0.1, 0.5)),
+ gatifloxacin = random_rsi(5000, prob_RSI = c(0.4, 0.1, 0.5)),
+ eth = random_rsi(5000, prob_RSI = c(0.4, 0.1, 0.5)),
+ pza = random_rsi(5000, prob_RSI = c(0.4, 0.1, 0.5)),
+ MFX = random_rsi(5000, prob_RSI = c(0.4, 0.1, 0.5)),
+ KAN = random_rsi(5000, prob_RSI = c(0.4, 0.1, 0.5)))
+expect_true(length(unique(mdr_tb(x))) > 2)
+
+# check the guideline by Magiorakos et al. (2012), the default guideline
+stau <- data.frame(mo = c("S. aureus", "S. aureus", "S. aureus", "S. aureus"),
+ GEN = c("R", "R", "S", "R"),
+ RIF = c("S", "R", "S", "R"),
+ CPT = c("S", "R", "R", "R"),
+ OXA = c("S", "R", "R", "R"),
+ CIP = c("S", "S", "R", "R"),
+ MFX = c("S", "S", "R", "R"),
+ SXT = c("S", "S", "R", "R"),
+ FUS = c("S", "S", "R", "R"),
+ VAN = c("S", "S", "R", "R"),
+ TEC = c("S", "S", "R", "R"),
+ TLV = c("S", "S", "R", "R"),
+ TGC = c("S", "S", "R", "R"),
+ CLI = c("S", "S", "R", "R"),
+ DAP = c("S", "S", "R", "R"),
+ ERY = c("S", "S", "R", "R"),
+ LNZ = c("S", "S", "R", "R"),
+ CHL = c("S", "S", "R", "R"),
+ FOS = c("S", "S", "R", "R"),
+ QDA = c("S", "S", "R", "R"),
+ TCY = c("S", "S", "R", "R"),
+ DOX = c("S", "S", "R", "R"),
+ MNO = c("S", "S", "R", "R"),
+ stringsAsFactors = FALSE)
+expect_equal(as.integer(mdro(stau)), c(1:4))
+expect_inherits(mdro(stau, verbose = TRUE), "data.frame")
+
+ente <- data.frame(mo = c("Enterococcus", "Enterococcus", "Enterococcus", "Enterococcus"),
+ GEH = c("R", "R", "S", "R"),
+ STH = c("S", "R", "S", "R"),
+ IPM = c("S", "R", "R", "R"),
+ MEM = c("S", "R", "R", "R"),
+ DOR = c("S", "S", "R", "R"),
+ CIP = c("S", "S", "R", "R"),
+ LVX = c("S", "S", "R", "R"),
+ MFX = c("S", "S", "R", "R"),
+ VAN = c("S", "S", "R", "R"),
+ TEC = c("S", "S", "R", "R"),
+ TGC = c("S", "S", "R", "R"),
+ DAP = c("S", "S", "R", "R"),
+ LNZ = c("S", "S", "R", "R"),
+ AMP = c("S", "S", "R", "R"),
+ QDA = c("S", "S", "R", "R"),
+ DOX = c("S", "S", "R", "R"),
+ MNO = c("S", "S", "R", "R"),
+ stringsAsFactors = FALSE)
+expect_equal(as.integer(mdro(ente)), c(1:4))
+expect_inherits(mdro(ente, verbose = TRUE), "data.frame")
+
+entero <- data.frame(mo = c("E. coli", "E. coli", "E. coli", "E. coli"),
+ GEN = c("R", "R", "S", "R"), TOB = c("S", "R", "S", "R"),
+ AMK = c("S", "R", "R", "R"), NET = c("S", "R", "R", "R"),
+ CPT = c("S", "R", "R", "R"), TCC = c("S", "R", "R", "R"),
+ TZP = c("S", "S", "R", "R"), ETP = c("S", "S", "R", "R"),
+ IPM = c("S", "S", "R", "R"), MEM = c("S", "S", "R", "R"),
+ DOR = c("S", "S", "R", "R"), CZO = c("S", "S", "R", "R"),
+ CXM = c("S", "S", "R", "R"), CTX = c("S", "S", "R", "R"),
+ CAZ = c("S", "S", "R", "R"), FEP = c("S", "S", "R", "R"),
+ FOX = c("S", "S", "R", "R"), CTT = c("S", "S", "R", "R"),
+ CIP = c("S", "S", "R", "R"), SXT = c("S", "S", "R", "R"),
+ TGC = c("S", "S", "R", "R"), ATM = c("S", "S", "R", "R"),
+ AMP = c("S", "S", "R", "R"), AMC = c("S", "S", "R", "R"),
+ SAM = c("S", "S", "R", "R"), CHL = c("S", "S", "R", "R"),
+ FOS = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
+ TCY = c("S", "S", "R", "R"), DOX = c("S", "S", "R", "R"),
+ MNO = c("S", "S", "R", "R"),
+ stringsAsFactors = FALSE)
+expect_equal(as.integer(mdro(entero)), c(1:4))
+expect_inherits(mdro(entero, verbose = TRUE), "data.frame")
+
+pseud <- data.frame(mo = c("P. aeruginosa", "P. aeruginosa", "P. aeruginosa", "P. aeruginosa"),
+ GEN = c("R", "R", "S", "R"), TOB = c("S", "S", "S", "R"),
+ AMK = c("S", "S", "R", "R"), NET = c("S", "S", "R", "R"),
+ IPM = c("S", "R", "R", "R"), MEM = c("S", "S", "R", "R"),
+ DOR = c("S", "S", "R", "R"), CAZ = c("S", "S", "R", "R"),
+ FEP = c("S", "R", "R", "R"), CIP = c("S", "S", "R", "R"),
+ LVX = c("S", "S", "R", "R"), TCC = c("S", "S", "R", "R"),
+ TZP = c("S", "S", "R", "R"), ATM = c("S", "S", "R", "R"),
+ FOS = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
+ PLB = c("S", "S", "R", "R"),
+ stringsAsFactors = FALSE)
+expect_equal(as.integer(mdro(pseud)), c(1:4))
+expect_inherits(mdro(pseud, verbose = TRUE), "data.frame")
+
+acin <- data.frame(mo = c("A. baumannii", "A. baumannii", "A. baumannii", "A. baumannii"),
+ GEN = c("R", "R", "S", "R"), TOB = c("S", "R", "S", "R"),
+ AMK = c("S", "R", "R", "R"), NET = c("S", "R", "R", "R"),
+ IPM = c("S", "S", "R", "R"), MEM = c("S", "R", "R", "R"),
+ DOR = c("S", "S", "R", "R"), CIP = c("S", "S", "R", "R"),
+ LVX = c("S", "S", "R", "R"), TZP = c("S", "S", "R", "R"),
+ TCC = c("S", "S", "R", "R"), CTX = c("S", "S", "R", "R"),
+ CRO = c("S", "S", "R", "R"), CAZ = c("S", "S", "R", "R"),
+ FEP = c("S", "R", "R", "R"), SXT = c("S", "S", "R", "R"),
+ SAM = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
+ PLB = c("S", "S", "R", "R"), TCY = c("S", "S", "R", "R"),
+ DOX = c("S", "S", "R", "R"), MNO = c("S", "S", "R", "R"),
+ stringsAsFactors = FALSE)
+expect_equal(as.integer(mdro(acin)), c(1:4))
+expect_inherits(mdro(acin, verbose = TRUE), "data.frame")
+
+# custom rules
+custom <- custom_mdro_guideline("CIP == 'R' & age > 60" ~ "Elderly Type A",
+ "ERY == 'R' & age > 60" ~ "Elderly Type B",
+ as_factor = TRUE)
+expect_stdout(print(custom))
+expect_stdout(print(c(custom, custom)))
+expect_stdout(print(as.list(custom, custom)))
+
+expect_stdout(x <- mdro(example_isolates, guideline = custom, info = TRUE))
+expect_equal(as.double(table(x)), c(1070, 198, 732))
+
+expect_stdout(print(custom_mdro_guideline(AMX == "R" ~ "test", as_factor = FALSE)))
+expect_error(custom_mdro_guideline())
+expect_error(custom_mdro_guideline("test"))
+expect_error(custom_mdro_guideline("test" ~ c(1:3)))
+expect_error(custom_mdro_guideline("test" ~ A))
+expect_warning(mdro(example_isolates,
+ # since `test` gives an error, it will be ignored with a warning
+ guideline = custom_mdro_guideline(test ~ "A"),
+ info = FALSE))
+
+# print groups
+if (suppressWarnings(require("dplyr"))) {
+ expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
+ expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
+}
diff --git a/inst/tinytest/test-mic.R b/inst/tinytest/test-mic.R
new file mode 100755
index 00000000..acefa5e0
--- /dev/null
+++ b/inst/tinytest/test-mic.R
@@ -0,0 +1,136 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_true(as.mic(8) == as.mic("8"))
+expect_true(as.mic("1") > as.mic("<=0.0625"))
+expect_true(as.mic("1") < as.mic(">=32"))
+expect_true(is.mic(as.mic(8)))
+
+expect_equal(as.double(as.mic(">=32")), 32)
+expect_equal(as.numeric(as.mic(">=32")), 32)
+expect_equal(as.integer(as.mic(">=32")), 32)
+expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
+
+# all levels should be valid MICs
+x <- as.mic(c(2, 4))
+expect_inherits(x[1], "mic")
+expect_inherits(x[[1]], "mic")
+expect_inherits(c(x[1], x[9]), "mic")
+expect_inherits(unique(x[1], x[9]), "mic")
+expect_inherits(droplevels(c(x[1], x[9])), "mic")
+x[2] <- 32
+expect_inherits(x, "mic")
+expect_warning(as.mic("INVALID VALUE"))
+
+pdf(NULL) # prevent Rplots.pdf being created
+expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
+expect_silent(plot(as.mic(c(1, 2, 4, 8))))
+expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
+expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr"))
+if (suppressWarnings(require("ggplot2"))) {
+ expect_inherits(ggplot(as.mic(c(1, 2, 4, 8))), "gg")
+ expect_inherits(ggplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
+ expect_inherits(ggplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
+}
+expect_stdout(print(as.mic(c(1, 2, 4, 8))))
+
+expect_inherits(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
+
+if (suppressWarnings(require("dplyr"))) {
+ expect_stdout(print(tibble(m = as.mic(2:4))))
+}
+
+# all mathematical operations
+x <- random_mic(50)
+x_double <- as.double(gsub("[<=>]+", "", as.character(x)))
+suppressWarnings(expect_identical(mean(x), mean(x_double)))
+suppressWarnings(expect_identical(median(x), median(x_double)))
+suppressWarnings(expect_identical(quantile(x), quantile(x_double)))
+suppressWarnings(expect_identical(abs(x), abs(x_double)))
+suppressWarnings(expect_identical(sign(x), sign(x_double)))
+suppressWarnings(expect_identical(sqrt(x), sqrt(x_double)))
+suppressWarnings(expect_identical(floor(x), floor(x_double)))
+suppressWarnings(expect_identical(ceiling(x), ceiling(x_double)))
+suppressWarnings(expect_identical(trunc(x), trunc(x_double)))
+suppressWarnings(expect_identical(round(x), round(x_double)))
+suppressWarnings(expect_identical(signif(x), signif(x_double)))
+suppressWarnings(expect_identical(exp(x), exp(x_double)))
+suppressWarnings(expect_identical(log(x), log(x_double)))
+suppressWarnings(expect_identical(log10(x), log10(x_double)))
+suppressWarnings(expect_identical(log2(x), log2(x_double)))
+suppressWarnings(expect_identical(expm1(x), expm1(x_double)))
+suppressWarnings(expect_identical(log1p(x), log1p(x_double)))
+suppressWarnings(expect_identical(cos(x), cos(x_double)))
+suppressWarnings(expect_identical(sin(x), sin(x_double)))
+suppressWarnings(expect_identical(tan(x), tan(x_double)))
+suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
+suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
+suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))
+suppressWarnings(expect_identical(acos(x), acos(x_double)))
+suppressWarnings(expect_identical(asin(x), asin(x_double)))
+suppressWarnings(expect_identical(atan(x), atan(x_double)))
+suppressWarnings(expect_identical(cosh(x), cosh(x_double)))
+suppressWarnings(expect_identical(sinh(x), sinh(x_double)))
+suppressWarnings(expect_identical(tanh(x), tanh(x_double)))
+suppressWarnings(expect_identical(acosh(x), acosh(x_double)))
+suppressWarnings(expect_identical(asinh(x), asinh(x_double)))
+suppressWarnings(expect_identical(atanh(x), atanh(x_double)))
+suppressWarnings(expect_identical(lgamma(x), lgamma(x_double)))
+suppressWarnings(expect_identical(gamma(x), gamma(x_double)))
+suppressWarnings(expect_identical(digamma(x), digamma(x_double)))
+suppressWarnings(expect_identical(trigamma(x), trigamma(x_double)))
+suppressWarnings(expect_identical(cumsum(x), cumsum(x_double)))
+suppressWarnings(expect_identical(cumprod(x), cumprod(x_double)))
+suppressWarnings(expect_identical(cummax(x), cummax(x_double)))
+suppressWarnings(expect_identical(cummin(x), cummin(x_double)))
+suppressWarnings(expect_identical(!x, !(x_double)))
+
+suppressWarnings(expect_identical(all(x), all(x_double)))
+suppressWarnings(expect_identical(any(x), any(x_double)))
+suppressWarnings(expect_identical(sum(x), sum(x_double)))
+suppressWarnings(expect_identical(prod(x), prod(x_double)))
+suppressWarnings(expect_identical(min(x), min(x_double)))
+suppressWarnings(expect_identical(max(x), max(x_double)))
+suppressWarnings(expect_identical(range(x), range(x_double)))
+
+el1 <- random_mic(50)
+el1_double <- as.double(gsub("[<=>]+", "", as.character(el1)))
+el2 <- random_mic(50)
+el2_double <- as.double(gsub("[<=>]+", "", as.character(el2)))
+suppressWarnings(expect_identical(el1 + el2, el1_double + el2_double))
+suppressWarnings(expect_identical(el1 - el2, el1_double - el2_double))
+suppressWarnings(expect_identical(el1 * el2, el1_double * el2_double))
+suppressWarnings(expect_identical(el1 / el2, el1_double / el2_double))
+suppressWarnings(expect_identical(el1 ^ el2, el1_double ^ el2_double))
+suppressWarnings(expect_identical(el1 %% el2, el1_double %% el2_double))
+suppressWarnings(expect_identical(el1 %/% el2, el1_double %/% el2_double))
+suppressWarnings(expect_identical(el1 & el2, el1_double & el2_double))
+suppressWarnings(expect_identical(el1 | el2, el1_double | el2_double))
+suppressWarnings(expect_identical(el1 == el2, el1_double == el2_double))
+suppressWarnings(expect_identical(el1 != el2, el1_double != el2_double))
+suppressWarnings(expect_identical(el1 < el2, el1_double < el2_double))
+suppressWarnings(expect_identical(el1 <= el2, el1_double <= el2_double))
+suppressWarnings(expect_identical(el1 >= el2, el1_double >= el2_double))
+suppressWarnings(expect_identical(el1 > el2, el1_double > el2_double))
diff --git a/inst/tinytest/test-mo.R b/inst/tinytest/test-mo.R
new file mode 100644
index 00000000..fedb479d
--- /dev/null
+++ b/inst/tinytest/test-mo.R
@@ -0,0 +1,297 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
+expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
+
+expect_identical(
+ as.character(as.mo(c("E. coli", "H. influenzae"))),
+ c("B_ESCHR_COLI", "B_HMPHL_INFL"))
+
+expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
+expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
+expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
+expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
+expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
+expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
+expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
+expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
+expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
+expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
+expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
+expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
+expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
+expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
+expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
+expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
+expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
+expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
+expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
+expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
+
+expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
+
+
+expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
+
+# GLIMS
+expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
+
+expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
+expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
+expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AERG")
+expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
+expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
+expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
+expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
+
+expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
+expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
+expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
+expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
+expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
+expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
+
+
+expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
+
+# prevalent MO
+expect_identical(
+ suppressWarnings(as.character(
+ as.mo(c("stau",
+ "STAU",
+ "staaur",
+ "S. aureus",
+ "S aureus",
+ "Sthafilokkockus aureeuzz",
+ "Staphylococcus aureus",
+ "MRSA",
+ "VISA")))),
+ rep("B_STPHY_AURS", 9))
+expect_identical(
+ as.character(
+ as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))),
+ rep("B_ESCHR_COLI", 6))
+# unprevalent MO
+expect_identical(
+ as.character(
+ as.mo(c("parnod",
+ "P. nodosa",
+ "P nodosa",
+ "Paraburkholderia nodosa"))),
+ rep("B_PRBRK_NODS", 4))
+
+# empty values
+expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4))
+expect_identical(as.character(as.mo(" ")), NA_character_)
+# too few characters
+expect_warning(as.mo("ab"))
+
+expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRSM", "K. pneu rhino", "esco")))),
+ c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
+
+# check for Becker classification
+expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
+expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
+expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
+expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
+expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
+expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
+# aureus must only be influenced if Becker = "all"
+expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
+expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
+expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
+
+# check for Lancefield classification
+expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
+expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
+expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
+expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
+expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
+expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
+expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
+expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
+# Enterococci must only be influenced if Lancefield = "all"
+expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
+expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
+expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
+expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
+expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
+expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
+expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
+expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
+expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
+
+if (suppressWarnings(require("dplyr"))) {
+ # select with one column
+ expect_identical(
+ example_isolates[1:10, ] %>%
+ left_join_microorganisms() %>%
+ select(genus) %>%
+ as.mo() %>%
+ as.character(),
+ c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
+ "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"))
+
+ # select with two columns
+ expect_identical(
+ example_isolates[1:10, ] %>%
+ pull(mo),
+ example_isolates[1:10, ] %>%
+ left_join_microorganisms() %>%
+ select(genus, species) %>%
+ as.mo())
+
+ # too many columns
+ expect_error(example_isolates %>% select(1:3) %>% as.mo())
+
+ # test pull
+ expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))),
+ 2000)
+ expect_true(example_isolates %>% pull(mo) %>% is.mo())
+}
+
+# unknown results
+expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
+
+# print
+expect_stdout(print(as.mo(c("B_ESCHR_COLI", NA))))
+
+# test data.frame
+expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
+ 1)
+
+# check empty values
+expect_equal(as.character(suppressWarnings(as.mo(""))),
+ NA_character_)
+
+# check less prevalent MOs
+expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
+expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
+expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
+expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN")
+expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
+expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
+expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
+expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
+
+# check old names
+expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
+print(mo_renamed())
+expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
+
+# check uncertain names
+expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
+expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
+expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
+expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
+expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
+expect_equal(suppressMessages(as.character(as.mo(c("s aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB"))
+
+# predefined reference_df
+expect_equal(as.character(as.mo("TestingOwnID",
+ reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))),
+ "B_ESCHR_COLI")
+expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"),
+ reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))),
+ c("B_ESCHR_COLI", "B_ESCHR_COLI"))
+expect_warning(as.mo("TestingOwnID", reference_df = NULL))
+expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
+
+# combination of existing mo and other code
+expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
+ c("B_ESCHR_COLI", "B_ESCHR_COLI"))
+
+# from different sources
+expect_equal(as.character(as.mo(
+ c("PRTMIR", "bclcer", "B_ESCHR_COLI"))),
+ c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI"))
+
+# hard to find
+expect_equal(as.character(suppressMessages(as.mo(
+ c("Microbacterium paraoxidans",
+ "Streptococcus suis (bovis gr)",
+ "Raoultella (here some text) terrigena")))),
+ c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG"))
+expect_stdout(print(mo_uncertainties()))
+x <- as.mo("S. aur")
+# many hits
+expect_stdout(print(mo_uncertainties()))
+
+# Salmonella (City) are all actually Salmonella enterica spp (City)
+expect_equal(suppressMessages(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
+ c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
+
+# no virusses
+expect_equal(as.character(as.mo("Virus")), NA_character_)
+
+# summary
+expect_equal(length(summary(example_isolates$mo)), 6)
+
+# WHONET codes and NA/NaN
+expect_equal(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
+ rep(NA_character_, 3))
+expect_equal(as.character(as.mo("con")), "UNKNOWN")
+expect_equal(as.character(as.mo("xxx")), NA_character_)
+expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI"))
+expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
+ rep("UNKNOWN", 3))
+
+expect_null(mo_failures())
+
+expect_error(translate_allow_uncertain(5))
+
+# debug mode
+expect_stdout(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
+
+# ..coccus
+expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
+ c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN"))
+# yeasts and fungi
+expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
+ c("F_YEAST", "F_FUNGUS"))
+
+if (suppressWarnings(require("dplyr"))) {
+ # print tibble
+ expect_stdout(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
+}
+
+# assigning and subsetting
+x <- example_isolates$mo
+expect_inherits(x[1], "mo")
+expect_inherits(x[[1]], "mo")
+expect_inherits(c(x[1], x[9]), "mo")
+expect_warning(x[1] <- "invalid code")
+expect_warning(x[[1]] <- "invalid code")
+expect_warning(c(x[1], "test"))
+
+# ignoring patterns
+expect_equal(as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_pattern = "this")),
+ c("B_ESCHR_COLI", NA))
+
+# frequency tables
+if (suppressWarnings(require("cleaner"))) {
+ expect_inherits(cleaner::freq(example_isolates$mo), "freq")
+}
diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R
new file mode 100644
index 00000000..ece3e6bc
--- /dev/null
+++ b/inst/tinytest/test-mo_property.R
@@ -0,0 +1,129 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
+expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
+expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
+expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
+expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
+expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
+expect_equal(mo_genus("Escherichia coli"), "Escherichia")
+expect_equal(mo_species("Escherichia coli"), "coli")
+expect_equal(mo_subspecies("Escherichia coli"), "")
+expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
+expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
+expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
+expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
+expect_inherits(mo_taxonomy("Escherichia coli"), "list")
+expect_equal(names(mo_taxonomy("Escherichia coli")), c("kingdom", "phylum", "class", "order",
+ "family", "genus", "species", "subspecies"))
+expect_equal(mo_synonyms("Escherichia coli"), NULL)
+expect_true(length(mo_synonyms("Candida albicans")) > 1)
+expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
+expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
+ "family", "genus", "species", "subspecies",
+ "synonyms", "gramstain", "url", "ref",
+ "snomed"))
+expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
+
+expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
+expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
+expect_equal(mo_year("Escherichia coli"), 1919)
+
+expect_equal(mo_shortname("Escherichia coli"), "E. coli")
+expect_equal(mo_shortname("Escherichia"), "Escherichia")
+expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
+expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
+expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
+expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
+expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
+
+expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
+expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
+
+# test integrity
+MOs <- microorganisms
+expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
+
+# check languages
+expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
+expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
+
+expect_stdout(print(mo_gramstain("Escherichia coli", language = "en")))
+expect_stdout(print(mo_gramstain("Escherichia coli", language = "de")))
+expect_stdout(print(mo_gramstain("Escherichia coli", language = "nl")))
+expect_stdout(print(mo_gramstain("Escherichia coli", language = "es")))
+expect_stdout(print(mo_gramstain("Escherichia coli", language = "pt")))
+expect_stdout(print(mo_gramstain("Escherichia coli", language = "it")))
+expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
+
+expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
+dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
+expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
+
+# manual property function
+expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
+expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
+expect_identical(mo_property("Escherichia coli", property = "fullname"),
+ mo_fullname("Escherichia coli"))
+expect_identical(mo_property("Escherichia coli", property = "genus"),
+ mo_genus("Escherichia coli"))
+expect_identical(mo_property("Escherichia coli", property = "species"),
+ mo_species("Escherichia coli"))
+
+expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
+expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
+
+expect_true(112283007 %in% mo_snomed("Escherichia coli"))
+# old codes must throw a warning in mo_* family
+expect_message(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
+# outcome of mo_fullname must always return the fullname from the data set
+x <- data.frame(mo = microorganisms$mo,
+ # fullname from the original data:
+ f1 = microorganisms$fullname,
+ # newly created fullname based on MO code:
+ f2 = mo_fullname(microorganisms$mo, language = "en"),
+ stringsAsFactors = FALSE)
+expect_equal(nrow(subset(x, f1 != f2)), 0)
+# is gram pos/neg (also return FALSE for all non-bacteria)
+expect_equal(mo_is_gram_negative(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
+ c(TRUE, FALSE, FALSE))
+expect_equal(mo_is_gram_positive(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
+ c(FALSE, TRUE, FALSE))
+# is intrinsic resistant
+expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans"),
+ "vanco"),
+ c(TRUE, FALSE, FALSE))
+# with reference data
+expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
+ "Escherichia coli")
+if (suppressWarnings(require("dplyr"))) {
+ expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
+ 730)
+ expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),
+ 1238)
+ expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(),
+ 710)
+}
diff --git a/inst/tinytest/test-pca.R b/inst/tinytest/test-pca.R
new file mode 100644
index 00000000..d0868094
--- /dev/null
+++ b/inst/tinytest/test-pca.R
@@ -0,0 +1,63 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+resistance_data <- structure(list(order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
+ genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
+ AMC = c(0.00425, 0.13062, 0.10344),
+ CXM = c(0.00425, 0.05376, 0.10344),
+ CTX = c(0.00000, 0.02396, 0.05172),
+ TOB = c(0.02325, 0.02597, 0.10344),
+ TMP = c(0.08387, 0.39141, 0.18367)),
+ class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
+ row.names = c(NA, -3L),
+ groups = structure(list(order = c("Bacillales", "Enterobacterales"),
+ .rows = list(1L, 2:3)),
+ row.names = c(NA, -2L),
+ class = c("tbl_df", "tbl", "data.frame"),
+ .drop = TRUE))
+pca_model <- pca(resistance_data)
+expect_inherits(pca_model, "pca")
+
+pdf(NULL) # prevent Rplots.pdf being created
+
+if (suppressWarnings(require("ggplot2"))) {
+ ggplot_pca(pca_model, ellipse = TRUE)
+ ggplot_pca(pca_model, arrows_textangled = FALSE)
+}
+
+if (suppressWarnings(require("dplyr"))) {
+ resistance_data <- example_isolates %>%
+ group_by(order = mo_order(mo),
+ genus = mo_genus(mo)) %>%
+ summarise_if(is.rsi, resistance, minimum = 0)
+ pca_result <- resistance_data %>%
+ pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT")
+ expect_inherits(pca_result, "prcomp")
+
+ if (suppressWarnings(require("ggplot2"))) {
+ ggplot_pca(pca_result, ellipse = TRUE)
+ ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
+ }
+}
diff --git a/inst/tinytest/test-proportion.R b/inst/tinytest/test-proportion.R
new file mode 100755
index 00000000..6de6476d
--- /dev/null
+++ b/inst/tinytest/test-proportion.R
@@ -0,0 +1,130 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_equal(proportion_R(example_isolates$AMX), resistance(example_isolates$AMX))
+expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX))
+# AMX resistance in `example_isolates`
+expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001)
+expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001)
+expect_equal(1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX),
+ proportion_S(example_isolates$AMX))
+expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$AMX),
+ proportion_IR(example_isolates$AMX))
+expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
+ proportion_SI(example_isolates$AMX))
+
+expect_equal(example_isolates %>% proportion_SI(AMC),
+ 0.7626397,
+ tolerance = 0.0001)
+expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
+ 0.9408,
+ tolerance = 0.0001)
+expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
+ 0.9382647,
+ tolerance = 0.0001)
+
+if (suppressWarnings(require("dplyr"))) {
+ # percentages
+ expect_equal(example_isolates %>%
+ group_by(hospital_id) %>%
+ summarise(R = proportion_R(CIP, as_percent = TRUE),
+ I = proportion_I(CIP, as_percent = TRUE),
+ S = proportion_S(CIP, as_percent = TRUE),
+ n = n_rsi(CIP),
+ total = n()) %>%
+ pull(n) %>%
+ sum(),
+ 1409)
+
+ # count of cases
+ expect_equal(example_isolates %>%
+ group_by(hospital_id) %>%
+ summarise(cipro_p = proportion_SI(CIP, as_percent = TRUE),
+ cipro_n = n_rsi(CIP),
+ genta_p = proportion_SI(GEN, as_percent = TRUE),
+ genta_n = n_rsi(GEN),
+ combination_p = proportion_SI(CIP, GEN, as_percent = TRUE),
+ combination_n = n_rsi(CIP, GEN)) %>%
+ pull(combination_n),
+ c(305, 617, 241, 711))
+
+ # proportion_df
+ expect_equal(
+ example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value),
+ c(example_isolates$AMX %>% proportion_SI(),
+ example_isolates$AMX %>% proportion_R())
+ )
+ expect_equal(
+ example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value),
+ c(example_isolates$AMX %>% proportion_S(),
+ example_isolates$AMX %>% proportion_IR())
+ )
+ expect_equal(
+ example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
+ c(example_isolates$AMX %>% proportion_S(),
+ example_isolates$AMX %>% proportion_I(),
+ example_isolates$AMX %>% proportion_R())
+ )
+}
+reset_all_thrown_messages()
+expect_warning(proportion_R(as.character(example_isolates$AMC)))
+reset_all_thrown_messages()
+expect_warning(proportion_S(as.character(example_isolates$AMC)))
+reset_all_thrown_messages()
+expect_warning(proportion_S(as.character(example_isolates$AMC,
+ example_isolates$GEN)))
+reset_all_thrown_messages()
+expect_warning(n_rsi(as.character(example_isolates$AMC,
+ example_isolates$GEN)))
+expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
+ example_isolates$GEN))),
+ 1879)
+
+# check for errors
+expect_error(proportion_IR("test", minimum = "test"))
+expect_error(proportion_IR("test", as_percent = "test"))
+expect_error(proportion_I("test", minimum = "test"))
+expect_error(proportion_I("test", as_percent = "test"))
+expect_error(proportion_S("test", minimum = "test"))
+expect_error(proportion_S("test", as_percent = "test"))
+expect_error(proportion_S("test", also_single_tested = TRUE))
+
+# check too low amount of isolates
+expect_identical(suppressWarnings(proportion_R(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
+ NA_real_)
+expect_identical(suppressWarnings(proportion_I(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
+ NA_real_)
+expect_identical(suppressWarnings(proportion_S(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
+ NA_real_)
+
+# warning for speed loss
+reset_all_thrown_messages()
+expect_warning(proportion_R(as.character(example_isolates$GEN)))
+reset_all_thrown_messages()
+expect_warning(proportion_I(as.character(example_isolates$GEN)))
+reset_all_thrown_messages()
+expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
+expect_error(proportion_df(c("A", "B", "C")))
+expect_error(proportion_df(example_isolates[, "date"]))
diff --git a/tests/testthat/test-like.R b/inst/tinytest/test-random.R
similarity index 72%
rename from tests/testthat/test-like.R
rename to inst/tinytest/test-random.R
index 4bbf4ceb..505beb6f 100644
--- a/tests/testthat/test-like.R
+++ b/inst/tinytest/test-random.R
@@ -23,23 +23,14 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("like.R")
-
-test_that("`like` works", {
- skip_on_cran()
- expect_true(sum("test" %like% c("^t", "^s")) == 1)
-
- expect_true("test" %like% "test")
- expect_false("test" %like_case% "TEST")
- expect_true(factor("test") %like% factor("t"))
- expect_true(factor("test") %like% "t")
- expect_true("test" %like% factor("t"))
-
- expect_true(as.factor("test") %like% "TEST")
- expect_identical(factor(c("Test case", "Something different", "Yet another thing")) %like% c("case", "diff", "yet"),
- c(TRUE, TRUE, TRUE))
- expect_identical("test" %like% c("t", "e", "s", "t"),
- c(TRUE, TRUE, TRUE, TRUE))
- expect_identical(factor("test") %like% factor(c("t", "e", "s", "t")),
- c(TRUE, TRUE, TRUE, TRUE))
-})
+expect_inherits(random_mic(100), "mic")
+expect_inherits(random_mic(100, mo = "Klebsiella pneumoniae"), "mic")
+expect_inherits(random_mic(100, mo = "Klebsiella pneumoniae", ab = "meropenem"), "mic")
+expect_inherits(random_mic(100, ab = "meropenem"), "mic")
+# no normal factors of 2
+expect_inherits(random_mic(100, "Haemophilus influenzae", "ceftaroline"), "mic")
+expect_inherits(random_disk(100), "disk")
+expect_inherits(random_disk(100, mo = "Klebsiella pneumoniae"), "disk")
+expect_inherits(random_disk(100, mo = "Klebsiella pneumoniae", ab = "meropenem"), "disk")
+expect_inherits(random_disk(100, ab = "meropenem"), "disk")
+expect_inherits(random_rsi(100), "rsi")
diff --git a/inst/tinytest/test-resistance_predict.R b/inst/tinytest/test-resistance_predict.R
new file mode 100644
index 00000000..a19584f2
--- /dev/null
+++ b/inst/tinytest/test-resistance_predict.R
@@ -0,0 +1,95 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+if (suppressWarnings(require("dplyr"))) {
+ expect_stdout(AMX_R <- example_isolates %>%
+ filter(mo == "B_ESCHR_COLI") %>%
+ rsi_predict(col_ab = "AMX",
+ col_date = "date",
+ model = "binomial",
+ minimum = 10,
+ info = TRUE) %>%
+ pull("value"))
+ # AMX resistance will increase according to data set `example_isolates`
+ expect_true(AMX_R[3] < AMX_R[20])
+}
+
+expect_stdout(x <- suppressMessages(resistance_predict(example_isolates,
+ col_ab = "AMX",
+ year_min = 2010,
+ model = "binomial",
+ info = TRUE)))
+pdf(NULL) # prevent Rplots.pdf being created
+expect_silent(plot(x))
+if (suppressWarnings(require("ggplot2"))) {
+ expect_silent(ggplot_rsi_predict(x))
+ expect_silent(ggplot(x))
+ expect_error(ggplot_rsi_predict(example_isolates))
+}
+expect_stdout(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ model = "binomial",
+ col_ab = "AMX",
+ col_date = "date",
+ info = TRUE))
+expect_stdout(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ model = "loglin",
+ col_ab = "AMX",
+ col_date = "date",
+ info = TRUE))
+expect_stdout(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ model = "lin",
+ col_ab = "AMX",
+ col_date = "date",
+ info = TRUE))
+
+expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ model = "INVALID MODEL",
+ col_ab = "AMX",
+ col_date = "date",
+ info = TRUE))
+expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ model = "binomial",
+ col_ab = "NOT EXISTING COLUMN",
+ col_date = "date",
+ info = TRUE))
+expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ model = "binomial",
+ col_ab = "AMX",
+ col_date = "NOT EXISTING COLUMN",
+ info = TRUE))
+expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ col_ab = "AMX",
+ col_date = "NOT EXISTING COLUMN",
+ info = TRUE))
+expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ col_ab = "AMX",
+ col_date = "date",
+ info = TRUE))
+# almost all E. coli are MEM S in the Netherlands :)
+expect_error(resistance_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+ model = "binomial",
+ col_ab = "MEM",
+ col_date = "date",
+ info = TRUE))
diff --git a/inst/tinytest/test-rsi.R b/inst/tinytest/test-rsi.R
new file mode 100644
index 00000000..afcac559
--- /dev/null
+++ b/inst/tinytest/test-rsi.R
@@ -0,0 +1,157 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+expect_true(as.rsi("S") < as.rsi("I"))
+expect_true(as.rsi("I") < as.rsi("R"))
+expect_true(is.rsi(as.rsi("S")))
+x <- example_isolates$AMX
+expect_inherits(x[1], "rsi")
+expect_inherits(x[[1]], "rsi")
+expect_inherits(c(x[1], x[9]), "rsi")
+expect_inherits(unique(x[1], x[9]), "rsi")
+pdf(NULL) # prevent Rplots.pdf being created
+expect_silent(barplot(as.rsi(c("S", "I", "R"))))
+expect_silent(plot(as.rsi(c("S", "I", "R"))))
+if (suppressWarnings(require("ggplot2"))) expect_inherits(ggplot(as.rsi(c("S", "I", "R"))), "gg")
+expect_stdout(print(as.rsi(c("S", "I", "R"))))
+expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
+expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
+expect_equal(summary(as.rsi(c("S", "R"))),
+ structure(c("Class" = "rsi",
+ "%R" = "50.0% (n=1)",
+ "%SI" = "50.0% (n=1)",
+ "- %S" = "50.0% (n=1)",
+ "- %I" = " 0.0% (n=0)"), class = c("summaryDefault", "table")))
+expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
+ rep(FALSE, length(example_isolates)))
+expect_error(as.rsi.mic(as.mic(16)))
+expect_error(as.rsi.disk(as.disk(16)))
+expect_error(get_guideline("this one does not exist"))
+if (suppressWarnings(require("dplyr"))) {
+ # 40 rsi columns
+ expect_equal(example_isolates %>%
+ mutate_at(vars(PEN:RIF), as.character) %>%
+ lapply(is.rsi.eligible) %>%
+ as.logical() %>%
+ sum(),
+ 40)
+ expect_equal(sum(is.rsi(example_isolates)), 40)
+
+ expect_stdout(print(tibble(ab = as.rsi("S"))))
+}
+if (suppressWarnings(require("skimr"))) {
+ expect_inherits(skim(example_isolates),
+ "data.frame")
+ if (suppressWarnings(require("dplyr"))) {
+ expect_inherits(example_isolates %>%
+ mutate(m = as.mic(2),
+ d = as.disk(20)) %>%
+ skim(),
+ "data.frame")
+ }
+}
+
+
+# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
+expect_equal(as.character(
+ as.rsi(x = as.mic(c(0.125, 0.5, 1, 2, 4)),
+ mo = "B_STRPT_PNMN",
+ ab = "AMP",
+ guideline = "EUCAST 2020")),
+ c("S", "S", "I", "I", "R"))
+# S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
+expect_equal(as.character(
+ as.rsi(x = as.mic(c(1, 2, 4, 8, 16)),
+ mo = "B_STRPT_PNMN",
+ ab = "AMX",
+ guideline = "CLSI 2019")),
+ c("S", "S", "I", "R", "R"))
+
+# cutoffs at MIC = 8
+expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
+ as.rsi("S"))
+expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
+ as.rsi("R"))
+if (suppressWarnings(require("dplyr"))) {
+ expect_true(suppressWarnings(example_isolates %>%
+ mutate(amox_mic = as.mic(2)) %>%
+ select(mo, amox_mic) %>%
+ as.rsi() %>%
+ pull(amox_mic) %>%
+ is.rsi()))
+}
+
+expect_equal(as.character(
+ as.rsi(x = as.disk(22),
+ mo = "B_STRPT_PNMN",
+ ab = "ERY",
+ guideline = "CLSI")),
+ "S")
+expect_equal(as.character(
+ as.rsi(x = as.disk(18),
+ mo = "B_STRPT_PNMN",
+ ab = "ERY",
+ guideline = "CLSI")),
+ "I")
+expect_equal(as.character(
+ as.rsi(x = as.disk(10),
+ mo = "B_STRPT_PNMN",
+ ab = "ERY",
+ guideline = "CLSI")),
+ "R")
+if (suppressWarnings(require("dplyr"))) {
+ expect_true(example_isolates %>%
+ mutate(amox_disk = as.disk(15)) %>%
+ select(mo, amox_disk) %>%
+ as.rsi(guideline = "CLSI") %>%
+ pull(amox_disk) %>%
+ is.rsi())
+}
+# frequency tables
+if (suppressWarnings(require("cleaner"))) {
+ expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
+}
+
+
+df <- data.frame(microorganism = "Escherichia coli",
+ AMP = as.mic(8),
+ CIP = as.mic(0.256),
+ GEN = as.disk(18),
+ TOB = as.disk(16),
+ ERY = "R", # note about assigning
class
+ CLR = "V") # note about cleaning
+expect_inherits(suppressWarnings(as.rsi(df)),
+ "data.frame")
+expect_inherits(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli",
+ amoxi = c("R", "S", "I", "invalid")))$amoxi),
+ "rsi")
+expect_warning(as.rsi(data.frame(mo = "E. coli",
+ NIT = c("<= 2", 32))))
+expect_message(as.rsi(data.frame(mo = "E. coli",
+ NIT = c("<= 2", 32),
+ uti = TRUE)))
+expect_message(as.rsi(data.frame(mo = "E. coli",
+ NIT = c("<= 2", 32),
+ specimen = c("urine", "blood"))))
diff --git a/tests/testthat/test-skewness.R b/inst/tinytest/test-skewness.R
similarity index 80%
rename from tests/testthat/test-skewness.R
rename to inst/tinytest/test-skewness.R
index 0de83335..1ba333da 100644
--- a/tests/testthat/test-skewness.R
+++ b/inst/tinytest/test-skewness.R
@@ -23,17 +23,12 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-context("skewness.R")
-
-test_that("skewness works", {
- skip_on_cran()
- expect_equal(skewness(example_isolates$age),
- -1.212888,
- tolerance = 0.00001)
- expect_equal(unname(skewness(data.frame(example_isolates$age))),
- -1.212888,
- tolerance = 0.00001)
- expect_equal(skewness(matrix(example_isolates$age)),
- -1.212888,
- tolerance = 0.00001)
-})
+expect_equal(skewness(example_isolates$age),
+ -1.212888,
+ tolerance = 0.00001)
+expect_equal(unname(skewness(data.frame(example_isolates$age))),
+ -1.212888,
+ tolerance = 0.00001)
+expect_equal(skewness(matrix(example_isolates$age)),
+ -1.212888,
+ tolerance = 0.00001)
diff --git a/inst/tinytest/test-zzz.R b/inst/tinytest/test-zzz.R
new file mode 100644
index 00000000..5fa85f89
--- /dev/null
+++ b/inst/tinytest/test-zzz.R
@@ -0,0 +1,112 @@
+# ==================================================================== #
+# TITLE #
+# Antimicrobial Resistance (AMR) Data Analysis for R #
+# #
+# SOURCE #
+# https://github.com/msberends/AMR #
+# #
+# LICENCE #
+# (c) 2018-2021 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. #
+# #
+# 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 the full manual and a complete tutorial about #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
+# ==================================================================== #
+
+# Check if these function still exist in the package (all are in Suggests field)
+# Since GitHub Action runs every night, we will get emailed when a dependency fails based on this unit test
+# functions used by import_fn()
+import_functions <- c(
+ "anti_join" = "dplyr",
+ "cur_column" = "dplyr",
+ "full_join" = "dplyr",
+ "has_internet" = "curl",
+ "html_attr" = "rvest",
+ "html_children" = "rvest",
+ "html_node" = "rvest",
+ "html_nodes" = "rvest",
+ "html_table" = "rvest",
+ "html_text" = "rvest",
+ "inner_join" = "dplyr",
+ "insertText" = "rstudioapi",
+ "left_join" = "dplyr",
+ "new_pillar_shaft_simple" = "pillar",
+ "read_html" = "xml2",
+ "right_join" = "dplyr",
+ "semi_join" = "dplyr",
+ "showQuestion" = "rstudioapi")
+# functions that are called directly
+
+call_functions <- c(
+ # cleaner
+ "freq.default" = "cleaner",
+ # skimr
+ "inline_hist" = "skimr",
+ "sfl" = "skimr",
+ # set_mo_source
+ "read_excel" = "readxl",
+ # ggplot_rsi
+ "aes_string" = "ggplot2",
+ "element_blank" = "ggplot2",
+ "element_line" = "ggplot2",
+ "element_text" = "ggplot2",
+ "facet_wrap" = "ggplot2",
+ "geom_text" = "ggplot2",
+ "ggplot" = "ggplot2",
+ "labs" = "ggplot2",
+ "layer" = "ggplot2",
+ "position_fill" = "ggplot2",
+ "scale_fill_manual" = "ggplot2",
+ "scale_y_continuous" = "ggplot2",
+ "theme" = "ggplot2",
+ "theme_minimal" = "ggplot2",
+ # ggplot_pca
+ "aes" = "ggplot2",
+ "arrow" = "ggplot2",
+ "element_blank" = "ggplot2",
+ "element_line" = "ggplot2",
+ "element_text" = "ggplot2",
+ "expand_limits" = "ggplot2",
+ "geom_path" = "ggplot2",
+ "geom_point" = "ggplot2",
+ "geom_segment" = "ggplot2",
+ "geom_text" = "ggplot2",
+ "ggplot" = "ggplot2",
+ "labs" = "ggplot2",
+ "theme" = "ggplot2",
+ "theme_minimal" = "ggplot2",
+ "unit" = "ggplot2",
+ "xlab" = "ggplot2",
+ "ylab" = "ggplot2",
+ # resistance_predict
+ "aes" = "ggplot2",
+ "geom_errorbar" = "ggplot2",
+ "geom_point" = "ggplot2",
+ "geom_ribbon" = "ggplot2",
+ "ggplot" = "ggplot2",
+ "labs" = "ggplot2"
+)
+
+import_functions <- c(import_functions, call_functions)
+for (i in seq_len(length(import_functions))) {
+ fn <- names(import_functions)[i]
+ pkg <- unname(import_functions[i])
+ # function should exist in foreign pkg namespace
+ if (pkg %in% rownames(installed.packages())) {
+ tst <- !is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE))
+ expect_true(tst,
+ info = ifelse(tst,
+ "All external function references exist.",
+ paste0("Function ", pkg, "::", fn, "() does not exist anymore")))
+ }
+}
diff --git a/tests/testthat/test-ab.R b/tests/testthat/test-ab.R
deleted file mode 100755
index eeaff7bf..00000000
--- a/tests/testthat/test-ab.R
+++ /dev/null
@@ -1,78 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("ab.R")
-
-test_that("as.ab works", {
- skip_on_cran()
-
- expect_equal(as.character(as.ab(c("J01FA01",
- "J 01 FA 01",
- "Erythromycin",
- "eryt",
- " eryt 123",
- "ERYT",
- "ERY",
- "erytromicine",
- "Erythrocin",
- "Romycin"))),
- rep("ERY", 10))
-
- expect_identical(class(as.ab("amox")), c("ab", "character"))
- expect_identical(class(antibiotics$ab), c("ab", "character"))
- expect_true(is.ab(as.ab("amox")))
- expect_output(print(as.ab("amox")))
- expect_output(print(data.frame(a = as.ab("amox"))))
-
- expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
- expect_warning(as.ab("UNKNOWN"))
- expect_warning(as.ab(""))
-
- expect_output(print(as.ab("amox")))
-
- expect_equal(as.character(as.ab("Phloxapen")),
- "FLC")
-
- expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
- c(NA, "TMP"))
-
- expect_equal(as.character(as.ab("Amoxy + clavulaanzuur")),
- "AMC")
-
- expect_equal(as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
- c("MEM", "AMC"))
-
- expect_message(as.ab("cipro mero"))
-
- # assigning and subsetting
- x <- antibiotics$ab
- expect_s3_class(x[1], "ab")
- expect_s3_class(x[[1]], "ab")
- expect_s3_class(c(x[1], x[9]), "ab")
- expect_s3_class(unique(x[1], x[9]), "ab")
- expect_warning(x[1] <- "invalid code")
- expect_warning(x[[1]] <- "invalid code")
- expect_warning(c(x[1], "test"))
-})
diff --git a/tests/testthat/test-ab_class_selectors.R b/tests/testthat/test-ab_class_selectors.R
deleted file mode 100644
index a02ff5da..00000000
--- a/tests/testthat/test-ab_class_selectors.R
+++ /dev/null
@@ -1,47 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("ab_class_selectors.R")
-
-test_that("Antibiotic class selectors work", {
- skip_on_cran()
-
- if (suppressWarnings(require("dplyr"))) {
- expect_lt(example_isolates %>% select(aminoglycosides()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(carbapenems()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(cephalosporins()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(cephalosporins_1st()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(cephalosporins_2nd()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(cephalosporins_3rd()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(cephalosporins_4th()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(cephalosporins_5th()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(glycopeptides()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(macrolides()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(oxazolidinones()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(penicillins()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% select(tetracyclines()) %>% ncol(), ncol(example_isolates))
- }
-})
diff --git a/tests/testthat/test-ab_property.R b/tests/testthat/test-ab_property.R
deleted file mode 100644
index 554da93f..00000000
--- a/tests/testthat/test-ab_property.R
+++ /dev/null
@@ -1,69 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("ab_property.R")
-
-test_that("ab_property works", {
- skip_on_cran()
-
- expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
- expect_identical(as.character(ab_atc("AMX")), "J01CA04")
- expect_identical(ab_cid("AMX"), as.integer(33613))
-
- expect_equal(class(ab_tradenames("AMX")), "character")
- expect_equal(class(ab_tradenames(c("AMX", "AMX"))), "list")
-
- expect_identical(ab_group("AMX", language = NULL), "Beta-lactams/penicillins")
- expect_identical(ab_atc_group1("AMX", language = NULL), "Beta-lactam antibacterials, penicillins")
- expect_identical(ab_atc_group2("AMX", language = NULL), "Penicillins with extended spectrum")
-
- expect_identical(ab_name("Fluclox", language = NULL), "Flucloxacillin")
- expect_identical(ab_name("fluklox", language = NULL), "Flucloxacillin")
- expect_identical(ab_name("floxapen", language = NULL), "Flucloxacillin")
- expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
- expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
-
- expect_identical(ab_ddd("AMX", "oral"), 1.5)
- expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g")
- expect_identical(ab_ddd("AMX", "iv"), 3)
- expect_identical(ab_ddd("AMX", "iv", units = TRUE), "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_equal(class(ab_info("AMX")), "list")
-
- expect_error(ab_property("amox", "invalid property"))
- expect_error(ab_name("amox", language = "INVALID"))
- expect_output(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_true(ab_url("AMX") %like% "whocc.no")
- expect_warning(ab_url("ASP"))
-})
diff --git a/tests/testthat/test-age.R b/tests/testthat/test-age.R
deleted file mode 100644
index 659cbafe..00000000
--- a/tests/testthat/test-age.R
+++ /dev/null
@@ -1,77 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("age.R")
-
-test_that("age works", {
- skip_on_cran()
- expect_equal(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
- reference = "2019-01-01"),
- c(39, 34, 29))
-
- expect_equal(age(x = c("2019-01-01", "2019-04-01", "2019-07-01"),
- reference = "2019-09-01",
- exact = TRUE),
- c(0.6656393, 0.4191781, 0.1698630),
- tolerance = 0.001)
-
- expect_error(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
- reference = c("2019-01-01", "2019-01-01")))
-
- expect_warning(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
- reference = "1975-01-01"))
-
- expect_warning(age(x = c("1800-01-01", "1805-01-01", "1810-01-01"),
- reference = "2019-01-01"))
-
- expect_equal(length(age(x = c("2019-01-01", NA), na.rm = TRUE)),
- 1)
-
-})
-
-test_that("age_groups works", {
- skip_on_cran()
- ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
-
- expect_equal(length(unique(age_groups(ages, 50))),
- 2)
- expect_equal(length(unique(age_groups(ages, c(50, 60)))),
- 3)
- expect_identical(class(age_groups(ages, "child")),
- c("ordered", "factor"))
-
- expect_identical(class(age_groups(ages, "elderly")),
- c("ordered", "factor"))
-
- expect_identical(class(age_groups(ages, "tens")),
- c("ordered", "factor"))
-
- expect_identical(class(age_groups(ages, "fives")),
- c("ordered", "factor"))
-
- expect_equal(length(age_groups(c(10, 20, 30, NA), na.rm = TRUE)),
- 3)
-
-})
diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R
deleted file mode 100644
index fd988c4e..00000000
--- a/tests/testthat/test-count.R
+++ /dev/null
@@ -1,106 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("count.R")
-
-test_that("counts work", {
- skip_on_cran()
-
- expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
- expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
- expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
-
- # AMX resistance in `example_isolates`
- expect_equal(count_R(example_isolates$AMX), 804)
- expect_equal(count_I(example_isolates$AMX), 3)
- expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
- expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
- suppressWarnings(count_IR(example_isolates$AMX)))
- expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
- count_SI(example_isolates$AMX))
-
-
- # warning for speed loss
- reset_all_thrown_messages()
- expect_warning(count_resistant(as.character(example_isolates$AMC)))
- reset_all_thrown_messages()
- expect_warning(count_resistant(example_isolates$AMC,
- as.character(example_isolates$GEN)))
-
- # check for errors
- expect_error(count_resistant("test", minimum = "test"))
- expect_error(count_resistant("test", as_percent = "test"))
- expect_error(count_susceptible("test", minimum = "test"))
- expect_error(count_susceptible("test", as_percent = "test"))
-
- expect_error(count_df(c("A", "B", "C")))
- expect_error(count_df(example_isolates[, "date"]))
-
- if (suppressWarnings(require("dplyr"))) {
- expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
- expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
- expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
- expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
- expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
- expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
- example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
- example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE))
-
- # count of cases
- expect_equal(example_isolates %>%
- group_by(hospital_id) %>%
- summarise(cipro = count_susceptible(CIP),
- genta = count_susceptible(GEN),
- combination = count_susceptible(CIP, GEN)) %>%
- pull(combination),
- c(253, 465, 192, 558))
-
- # count_df
- expect_equal(
- example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
- c(example_isolates$AMX %>% count_susceptible(),
- example_isolates$AMX %>% count_resistant())
- )
- expect_equal(
- example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
- c(suppressWarnings(example_isolates$AMX %>% count_S()),
- suppressWarnings(example_isolates$AMX %>% count_IR()))
- )
- expect_equal(
- example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
- c(suppressWarnings(example_isolates$AMX %>% count_S()),
- example_isolates$AMX %>% count_I(),
- example_isolates$AMX %>% count_R())
- )
-
- # grouping in rsi_calc_df() (= backbone of rsi_df())
- expect_true("hospital_id" %in% (example_isolates %>%
- group_by(hospital_id) %>%
- select(hospital_id, AMX, CIP, gender) %>%
- rsi_df() %>%
- colnames()))
- }
-
-})
diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R
deleted file mode 100644
index 9c4c0224..00000000
--- a/tests/testthat/test-data.R
+++ /dev/null
@@ -1,98 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 Berends MS, Luz CF et al. #
-# Developed at the University of Groningen, the Netherlands, in #
-# collaboration with non-profit organisations Certe Medical #
-# Diagnostics & Advice, and University Medical Center Groningen. #
-# #
-# This R package is free software; you can freely use and distribute #
-# it for both personal and commercial purposes under the terms of the #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by #
-# the Free Software Foundation. #
-# We created this package for both routine data analysis and academic #
-# research and it was publicly released in the hope that it will be #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
-# #
-# Visit our website for the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("data.R")
-
-test_that("data sets are valid", {
- skip_on_cran()
- expect_true(check_dataset_integrity()) # in misc.R
-
- # IDs should always be unique
- expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
- expect_identical(class(microorganisms$mo), c("mo", "character"))
- expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
- expect_identical(class(antibiotics$ab), c("ab", "character"))
-
- # check cross table reference
- expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
- expect_true(all(example_isolates$mo %in% microorganisms$mo))
- expect_true(all(microorganisms.translation$mo_new %in% microorganisms$mo))
- expect_true(all(rsi_translation$mo %in% microorganisms$mo))
- expect_true(all(rsi_translation$ab %in% antibiotics$ab))
- expect_true(all(intrinsic_resistant$microorganism %in% microorganisms$fullname)) # also important for mo_is_intrinsic_resistant()
- expect_true(all(intrinsic_resistant$antibiotic %in% antibiotics$name))
- expect_false(any(is.na(microorganisms.codes$code)))
- expect_false(any(is.na(microorganisms.codes$mo)))
- expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))
- expect_true(all(dosage$ab %in% antibiotics$ab))
- expect_true(all(dosage$name %in% antibiotics$name))
-
- # antibiotic names must always be coercible to their original AB code
- expect_identical(as.ab(antibiotics$name), antibiotics$ab)
-
- # there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
- datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
- for (i in seq_len(length(datasets))) {
- dataset <- get(datasets[i], envir = asNamespace("AMR"))
- expect_identical(dataset_UTF8_to_ASCII(dataset), dataset, label = datasets[i])
- }
-})
-
-test_that("creation of data sets is valid", {
- skip_on_cran()
-
- df <- AMR:::MO_lookup
- expect_lt(nrow(df[which(df$prevalence == 1), ]), nrow(df[which(df$prevalence == 2), ]))
- expect_lt(nrow(df[which(df$prevalence == 2), ]), nrow(df[which(df$prevalence == 3), ]))
- expect_true(all(c("mo", "fullname",
- "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
- "rank", "ref", "species_id", "source", "prevalence", "snomed",
- "kingdom_index", "fullname_lower", "g_species") %in% colnames(df)))
-
- expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
- "fullname_lower", "g_species") %in% colnames(AMR:::MO.old_lookup)))
-
- expect_s3_class(AMR:::MO_CONS, "mo")
-
-})
-
-test_that("CoL version info works", {
- skip_on_cran()
-
- expect_identical(class(catalogue_of_life_version()),
- c("catalogue_of_life_version", "list"))
-
- expect_output(print(catalogue_of_life_version()))
-})
-
-test_that("CoNS/CoPS are up to date", {
- uncategorised <- subset(microorganisms,
- genus == "Staphylococcus" &
- !species %in% c("", "aureus") &
- !mo %in% c(MO_CONS, MO_COPS))
- expect(NROW(uncategorised) == 0,
- failure_message = paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
- uncategorised$species, " (", uncategorised$mo, ")"))
-})
diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R
deleted file mode 100755
index 55c42202..00000000
--- a/tests/testthat/test-eucast_rules.R
+++ /dev/null
@@ -1,168 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("eucast_rules.R")
-
-test_that("EUCAST rules work", {
-
- skip_on_cran()
-
- # thoroughly check input table
- expect_equal(colnames(eucast_rules_file),
- c("if_mo_property", "like.is.one_of", "this_value",
- "and_these_antibiotics", "have_these_values",
- "then_change_these_antibiotics", "to_value",
- "reference.rule", "reference.rule_group",
- "reference.version",
- "note"))
- MOs_mentioned <- unique(eucast_rules_file$this_value)
- MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
- MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
- expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0)
-
- expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
- expect_error(eucast_rules(x = "text"))
- expect_error(eucast_rules(data.frame(a = "test")))
- expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
-
- expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE)))
-
- expect_identical(colnames(example_isolates),
- colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
- expect_output(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
-
- a <- data.frame(mo = c("Klebsiella pneumoniae",
- "Pseudomonas aeruginosa",
- "Enterobacter cloacae"),
- amox = "-", # Amoxicillin
- stringsAsFactors = FALSE)
- b <- data.frame(mo = c("Klebsiella pneumoniae",
- "Pseudomonas aeruginosa",
- "Enterobacter cloacae"),
- amox = "R", # Amoxicillin
- stringsAsFactors = FALSE)
- expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
- expect_output(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE))))
-
- a <- data.frame(mo = c("Staphylococcus aureus",
- "Streptococcus group A"),
- COL = "-", # Colistin
- stringsAsFactors = FALSE)
- b <- data.frame(mo = c("Staphylococcus aureus",
- "Streptococcus group A"),
- COL = "R", # Colistin
- stringsAsFactors = FALSE)
- expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
-
- # piperacillin must be R in Enterobacteriaceae when tica is R
- if (suppressWarnings(require("dplyr"))) {
- expect_equal(suppressWarnings(
- example_isolates %>%
- filter(mo_family(mo) == "Enterobacteriaceae") %>%
- mutate(TIC = as.rsi("R"),
- PIP = as.rsi("S")) %>%
- eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
- pull(PIP) %>%
- unique() %>%
- as.character()),
- "R")
- }
-
- # Azithromycin and Clarythromycin must be equal to Erythromycin
- a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
- ERY = example_isolates$ERY,
- AZM = as.rsi("R"),
- CLR = factor("R"),
- stringsAsFactors = FALSE),
- version_expertrules = 3.1,
- only_rsi_columns = FALSE)$CLR))
- b <- example_isolates$ERY
- expect_identical(a[!is.na(b)],
- b[!is.na(b)])
-
- # amox is inferred by benzylpenicillin in Kingella kingae
- expect_equal(
- suppressWarnings(
- as.list(eucast_rules(
- data.frame(mo = as.mo("Kingella kingae"),
- PEN = "S",
- AMX = "-",
- stringsAsFactors = FALSE)
- , info = FALSE))$AMX
- ),
- "S")
-
- # also test norf
- if (suppressWarnings(require("dplyr"))) {
- expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
- }
-
- # check verbose output
- expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
-
- # AmpC de-repressed cephalo mutants
- expect_identical(
- eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
- cefotax = as.rsi(c("S", "S"))),
- ampc_cephalosporin_resistance = TRUE,
- info = FALSE)$cefotax,
- as.rsi(c("S", "R")))
- expect_identical(
- eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
- cefotax = as.rsi(c("S", "S"))),
- ampc_cephalosporin_resistance = NA,
- info = FALSE)$cefotax,
- as.rsi(c("S", NA)))
- expect_identical(
- eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
- cefotax = as.rsi(c("S", "S"))),
- ampc_cephalosporin_resistance = NULL,
- info = FALSE)$cefotax,
- as.rsi(c("S", "S")))
-
- # EUCAST dosage -----------------------------------------------------------
- expect_equal(nrow(eucast_dosage(c("tobra", "genta", "cipro"))), 3)
- expect_s3_class(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
-
-})
-
-test_that("Custom EUCAST rules work", {
-
- skip_on_cran()
- x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
- AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I",
- AMX == "S" ~ AMC == "S")
- expect_output(print(x))
- expect_output(print(c(x, x)))
- expect_output(print(as.list(x, x)))
-
- # this custom rules makes 8 changes
- expect_equal(nrow(eucast_rules(example_isolates,
- rules = "custom",
- custom_rules = x,
- info = FALSE,
- verbose = TRUE)),
- 8)
-})
diff --git a/tests/testthat/test-filter_ab_class.R b/tests/testthat/test-filter_ab_class.R
deleted file mode 100644
index 94f55e43..00000000
--- a/tests/testthat/test-filter_ab_class.R
+++ /dev/null
@@ -1,54 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("filter_ab_class.R")
-
-test_that("ATC-group filtering works", {
- skip_on_cran()
-
- if (suppressWarnings(require("dplyr"))) {
- expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0)
- expect_gt(example_isolates %>% filter_aminoglycosides() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_carbapenems() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_cephalosporins() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_5th_cephalosporins() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_fluoroquinolones() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_glycopeptides() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_macrolides() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_oxazolidinones() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_penicillins() %>% ncol(), 0)
- expect_gt(example_isolates %>% filter_tetracyclines() %>% ncol(), 0)
-
- expect_gt(example_isolates %>% filter_carbapenems("R", "all") %>% nrow(), 0)
-
- expect_error(example_isolates %>% filter_carbapenems(result = "test"))
- expect_error(example_isolates %>% filter_carbapenems(scope = "test"))
- expect_message(example_isolates %>% select(1:3) %>% filter_carbapenems())
- }
-})
diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R
deleted file mode 100755
index 9b673eec..00000000
--- a/tests/testthat/test-first_isolate.R
+++ /dev/null
@@ -1,194 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("first_isolate.R")
-
-test_that("first isolates work", {
- skip_on_cran()
-
- # all four methods
- expect_equal(sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE),
- 1984)
- expect_equal(sum(first_isolate(x = example_isolates, method = "patient-based", info = TRUE), na.rm = TRUE),
- 1265)
- expect_equal(sum(first_isolate(x = example_isolates, method = "episode-based", info = TRUE), na.rm = TRUE),
- 1300)
- expect_equal(sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
- 1379)
-
- # Phenotype-based, using key antimicrobials
- expect_equal(sum(first_isolate(x = example_isolates,
- method = "phenotype-based",
- type = "keyantimicrobials",
- antifungal = NULL, info = TRUE), na.rm = TRUE),
- 1395)
- expect_equal(sum(first_isolate(x = example_isolates,
- method = "phenotype-based",
- type = "keyantimicrobials",
- antifungal = NULL, info = TRUE, ignore_I = FALSE), na.rm = TRUE),
- 1418)
-
-
- # 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),
- 941)
-
- # set 1500 random observations to be of specimen type 'Urine'
- random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
- x <- example_isolates
- x$specimen <- "Other"
- x[random_rows, "specimen"] <- "Urine"
- expect_lt(
- sum(
- first_isolate(x = x,
- 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 = x,
- 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"
- test_iso <- example_isolates
- test_iso$specimen <- "test"
- expect_message(first_isolate(test_iso,
- "date",
- "patient_id",
- col_mo = "mo",
- col_specimen = "specimen",
- filter_specimen = "something_unexisting",
- info = TRUE))
-
- # printing of exclusion message
- expect_message(first_isolate(example_isolates,
- col_date = "date",
- col_mo = "mo",
- col_patient_id = "patient_id",
- col_testcode = "gender",
- testcodes_exclude = "M",
- info = TRUE))
-
- # errors
- expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
- expect_error(first_isolate(example_isolates,
- col_date = "non-existing col",
- col_mo = "mo"))
-
- if (suppressWarnings(require("dplyr"))) {
- # if mo is not an mo class, result should be the same
- expect_identical(example_isolates %>%
- mutate(mo = as.character(mo)) %>%
- first_isolate(col_date = "date",
- col_mo = "mo",
- col_patient_id = "patient_id",
- info = FALSE),
- example_isolates %>%
- first_isolate(col_date = "date",
- col_mo = "mo",
- col_patient_id = "patient_id",
- info = FALSE))
-
- # support for WHONET
- expect_message(example_isolates %>%
- select(-patient_id) %>%
- mutate(`First name` = "test",
- `Last name` = "test",
- Sex = "Female") %>%
- first_isolate(info = TRUE))
-
- # groups
- x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
- y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
- expect_identical(x, y)
-
- }
-
- # missing dates should be no problem
- df <- example_isolates
- df[1:100, "date"] <- NA
- expect_equal(
- sum(
- first_isolate(x = df,
- col_date = "date",
- col_patient_id = "patient_id",
- col_mo = "mo",
- info = TRUE),
- na.rm = TRUE),
- 1382)
-
- # unknown MOs
- test_unknown <- example_isolates
- test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
- expect_equal(sum(first_isolate(test_unknown, include_unknown = FALSE)),
- 1108)
- expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)),
- 1591)
-
- test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
- expect_equal(sum(first_isolate(test_unknown)),
- 1108)
-
- # empty rsi results
- expect_equal(sum(first_isolate(example_isolates, include_untested_rsi = FALSE)),
- 1366)
-
- # shortcuts
- expect_identical(filter_first_isolate(example_isolates),
- subset(example_isolates, first_isolate(example_isolates)))
-
-
- # notice that all mo's are distinct, so all are TRUE
- expect_true(all(example_isolates %pm>%
- pm_distinct(mo, .keep_all = TRUE) %pm>%
- first_isolate(info = TRUE) == TRUE))
-
- # only one isolate, so return fast
- expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
-})
diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R
deleted file mode 100644
index 67be05b4..00000000
--- a/tests/testthat/test-ggplot_rsi.R
+++ /dev/null
@@ -1,90 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("ggplot_rsi.R")
-
-test_that("ggplot_rsi works", {
-
- skip_on_cran()
-
- skip_if_not_installed("ggplot2")
- skip_if_not_installed("dplyr")
-
- if (suppressWarnings(require("dplyr")) & suppressWarnings(require("ggplot2"))) {
-
- pdf(NULL) # prevent Rplots.pdf being created
-
- # data should be equal
- expect_equal(
- (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>% summarise_all(resistance) %>% as.double(),
- example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double()
- )
-
- print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))
- print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))
-
- expect_equal(
- (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>% summarise_all(resistance) %>% as.double(),
- example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double()
- )
-
- expect_equal(
- (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(resistance) %>% as.double(),
- example_isolates %>% select(AMC, CIP) %>% summarise_all(resistance) %>% as.double()
- )
-
- expect_equal(
- (example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>% summarise_all(count_resistant) %>% as.double(),
- example_isolates %>% select(AMC, CIP) %>% summarise_all(count_resistant) %>% as.double()
- )
-
- # support for scale_type ab and mo
- expect_equal(class((data.frame(mo = as.mo(c("e. coli", "s aureus")),
- n = c(40, 100)) %>%
- ggplot(aes(x = mo, y = n)) +
- geom_col())$data),
- "data.frame")
- expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")),
- n = c(40, 100)) %>%
- ggplot(aes(x = ab, y = n)) +
- geom_col())$data),
- "data.frame")
-
- expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")),
- n = c(40, 100)) %>%
- ggplot(aes(x = ab, y = n)) +
- geom_col())$data),
- "data.frame")
-
- # support for manual colours
- expect_equal(class((ggplot(data.frame(x = c("Value1", "Value2", "Value3"),
- y = c(1, 2, 3),
- z = c("Value4", "Value5", "Value6"))) +
- geom_col(aes(x = x, y = y, fill = z)) +
- scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R"))$data),
- "data.frame")
-
- }
-})
diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R
deleted file mode 100755
index 51698e29..00000000
--- a/tests/testthat/test-mdro.R
+++ /dev/null
@@ -1,251 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("mdro.R")
-
-test_that("mdro works", {
-
- skip_on_cran()
-
- expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
- expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
- expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
- expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
-
- expect_output(suppressMessages(suppressWarnings(mdro(example_isolates, info = TRUE))))
- expect_output(suppressMessages(suppressWarnings(mdro(example_isolates, "eucast3.1", info = TRUE))))
- expect_output(outcome <- suppressMessages(suppressWarnings(eucast_exceptional_phenotypes(example_isolates, info = TRUE))))
- # check class
- expect_equal(class(outcome), c("ordered", "factor"))
-
- expect_output(outcome <- mdro(example_isolates, "nl", info = TRUE))
- # check class
- expect_equal(class(outcome), c("ordered", "factor"))
-
- # example_isolates should have these finding using Dutch guidelines
- expect_equal(as.double(table(outcome)),
- c(1970, 24, 6)) # 1970 neg, 24 unconfirmed, 6 pos
-
- expect_equal(brmo(example_isolates, info = FALSE),
- mdro(example_isolates, guideline = "BRMO", info = FALSE))
-
- # test Dutch P. aeruginosa MDRO
- expect_equal(
- as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
- cfta = "S",
- cipr = "S",
- mero = "S",
- imip = "S",
- gent = "S",
- tobr = "S",
- pita = "S"),
- guideline = "BRMO",
- col_mo = "mo",
- info = FALSE)),
- "Negative")
- expect_equal(
- as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
- cefta = "R",
- cipr = "R",
- mero = "R",
- imip = "R",
- gent = "R",
- tobr = "R",
- pita = "R"),
- guideline = "BRMO",
- col_mo = "mo",
- info = FALSE)),
- "Positive")
-
- # German 3MRGN and 4MRGN
- expect_equal(as.character(mrgn(
- data.frame(mo = c("E. coli", "E. coli", "K. pneumoniae", "E. coli",
- "A. baumannii", "A. baumannii", "A. baumannii",
- "P. aeruginosa", "P. aeruginosa", "P. aeruginosa"),
- PIP = c("S", "R", "R", "S",
- "S", "R", "R",
- "S", "R", "R"),
- CTX = c("S", "R", "R", "S",
- "R", "R", "R",
- "R", "R", "R"),
- IPM = c("S", "R", "S", "R",
- "R", "R", "S",
- "S", "R", "R"),
- CIP = c("S", "R", "R", "S",
- "R", "R", "R",
- "R", "S", "R"),
- stringsAsFactors = FALSE))),
- c("Negative", "4MRGN", "3MRGN", "4MRGN", "4MRGN", "4MRGN", "3MRGN", "Negative", "3MRGN", "4MRGN"))
-
- # MDR TB
- expect_equal(
- # select only rifampicine, mo will be determined automatically (as M. tuberculosis),
- # number of mono-resistant strains should be equal to number of rifampicine-resistant strains
- as.double(table(mdr_tb(example_isolates[, "RIF", drop = FALSE])))[2],
- count_R(example_isolates$RIF))
-
- sample_rsi <- function() {
- sample(c("S", "I", "R"),
- size = 5000,
- prob = c(0.5, 0.1, 0.4),
- replace = TRUE)
- }
- x <- data.frame(rifampicin = sample_rsi(),
- inh = sample_rsi(),
- gatifloxacin = sample_rsi(),
- eth = sample_rsi(),
- pza = sample_rsi(),
- MFX = sample_rsi(),
- KAN = sample_rsi())
- expect_gt(length(unique(mdr_tb(x))), 2)
-
- # check the guideline by Magiorakos et al. (2012), the default guideline
- stau <- data.frame(mo = c("S. aureus", "S. aureus", "S. aureus", "S. aureus"),
- GEN = c("R", "R", "S", "R"),
- RIF = c("S", "R", "S", "R"),
- CPT = c("S", "R", "R", "R"),
- OXA = c("S", "R", "R", "R"),
- CIP = c("S", "S", "R", "R"),
- MFX = c("S", "S", "R", "R"),
- SXT = c("S", "S", "R", "R"),
- FUS = c("S", "S", "R", "R"),
- VAN = c("S", "S", "R", "R"),
- TEC = c("S", "S", "R", "R"),
- TLV = c("S", "S", "R", "R"),
- TGC = c("S", "S", "R", "R"),
- CLI = c("S", "S", "R", "R"),
- DAP = c("S", "S", "R", "R"),
- ERY = c("S", "S", "R", "R"),
- LNZ = c("S", "S", "R", "R"),
- CHL = c("S", "S", "R", "R"),
- FOS = c("S", "S", "R", "R"),
- QDA = c("S", "S", "R", "R"),
- TCY = c("S", "S", "R", "R"),
- DOX = c("S", "S", "R", "R"),
- MNO = c("S", "S", "R", "R"),
- stringsAsFactors = FALSE)
- expect_equal(as.integer(mdro(stau)), c(1:4))
- expect_s3_class(mdro(stau, verbose = TRUE), "data.frame")
-
- ente <- data.frame(mo = c("Enterococcus", "Enterococcus", "Enterococcus", "Enterococcus"),
- GEH = c("R", "R", "S", "R"),
- STH = c("S", "R", "S", "R"),
- IPM = c("S", "R", "R", "R"),
- MEM = c("S", "R", "R", "R"),
- DOR = c("S", "S", "R", "R"),
- CIP = c("S", "S", "R", "R"),
- LVX = c("S", "S", "R", "R"),
- MFX = c("S", "S", "R", "R"),
- VAN = c("S", "S", "R", "R"),
- TEC = c("S", "S", "R", "R"),
- TGC = c("S", "S", "R", "R"),
- DAP = c("S", "S", "R", "R"),
- LNZ = c("S", "S", "R", "R"),
- AMP = c("S", "S", "R", "R"),
- QDA = c("S", "S", "R", "R"),
- DOX = c("S", "S", "R", "R"),
- MNO = c("S", "S", "R", "R"),
- stringsAsFactors = FALSE)
- expect_equal(as.integer(mdro(ente)), c(1:4))
- expect_s3_class(mdro(ente, verbose = TRUE), "data.frame")
-
- entero <- data.frame(mo = c("E. coli", "E. coli", "E. coli", "E. coli"),
- GEN = c("R", "R", "S", "R"), TOB = c("S", "R", "S", "R"),
- AMK = c("S", "R", "R", "R"), NET = c("S", "R", "R", "R"),
- CPT = c("S", "R", "R", "R"), TCC = c("S", "R", "R", "R"),
- TZP = c("S", "S", "R", "R"), ETP = c("S", "S", "R", "R"),
- IPM = c("S", "S", "R", "R"), MEM = c("S", "S", "R", "R"),
- DOR = c("S", "S", "R", "R"), CZO = c("S", "S", "R", "R"),
- CXM = c("S", "S", "R", "R"), CTX = c("S", "S", "R", "R"),
- CAZ = c("S", "S", "R", "R"), FEP = c("S", "S", "R", "R"),
- FOX = c("S", "S", "R", "R"), CTT = c("S", "S", "R", "R"),
- CIP = c("S", "S", "R", "R"), SXT = c("S", "S", "R", "R"),
- TGC = c("S", "S", "R", "R"), ATM = c("S", "S", "R", "R"),
- AMP = c("S", "S", "R", "R"), AMC = c("S", "S", "R", "R"),
- SAM = c("S", "S", "R", "R"), CHL = c("S", "S", "R", "R"),
- FOS = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
- TCY = c("S", "S", "R", "R"), DOX = c("S", "S", "R", "R"),
- MNO = c("S", "S", "R", "R"),
- stringsAsFactors = FALSE)
- expect_equal(as.integer(mdro(entero)), c(1:4))
- expect_s3_class(mdro(entero, verbose = TRUE), "data.frame")
-
- pseud <- data.frame(mo = c("P. aeruginosa", "P. aeruginosa", "P. aeruginosa", "P. aeruginosa"),
- GEN = c("R", "R", "S", "R"), TOB = c("S", "S", "S", "R"),
- AMK = c("S", "S", "R", "R"), NET = c("S", "S", "R", "R"),
- IPM = c("S", "R", "R", "R"), MEM = c("S", "S", "R", "R"),
- DOR = c("S", "S", "R", "R"), CAZ = c("S", "S", "R", "R"),
- FEP = c("S", "R", "R", "R"), CIP = c("S", "S", "R", "R"),
- LVX = c("S", "S", "R", "R"), TCC = c("S", "S", "R", "R"),
- TZP = c("S", "S", "R", "R"), ATM = c("S", "S", "R", "R"),
- FOS = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
- PLB = c("S", "S", "R", "R"),
- stringsAsFactors = FALSE)
- expect_equal(as.integer(mdro(pseud)), c(1:4))
- expect_s3_class(mdro(pseud, verbose = TRUE), "data.frame")
-
- acin <- data.frame(mo = c("A. baumannii", "A. baumannii", "A. baumannii", "A. baumannii"),
- GEN = c("R", "R", "S", "R"), TOB = c("S", "R", "S", "R"),
- AMK = c("S", "R", "R", "R"), NET = c("S", "R", "R", "R"),
- IPM = c("S", "S", "R", "R"), MEM = c("S", "R", "R", "R"),
- DOR = c("S", "S", "R", "R"), CIP = c("S", "S", "R", "R"),
- LVX = c("S", "S", "R", "R"), TZP = c("S", "S", "R", "R"),
- TCC = c("S", "S", "R", "R"), CTX = c("S", "S", "R", "R"),
- CRO = c("S", "S", "R", "R"), CAZ = c("S", "S", "R", "R"),
- FEP = c("S", "R", "R", "R"), SXT = c("S", "S", "R", "R"),
- SAM = c("S", "S", "R", "R"), COL = c("S", "S", "R", "R"),
- PLB = c("S", "S", "R", "R"), TCY = c("S", "S", "R", "R"),
- DOX = c("S", "S", "R", "R"), MNO = c("S", "S", "R", "R"),
- stringsAsFactors = FALSE)
- expect_equal(as.integer(mdro(acin)), c(1:4))
- expect_s3_class(mdro(acin, verbose = TRUE), "data.frame")
-
- # custom rules
- custom <- custom_mdro_guideline("CIP == 'R' & age > 60" ~ "Elderly Type A",
- "ERY == 'R' & age > 60" ~ "Elderly Type B",
- as_factor = TRUE)
- expect_output(print(custom))
- expect_output(print(c(custom, custom)))
- expect_output(print(as.list(custom, custom)))
-
- expect_output(x <- mdro(example_isolates, guideline = custom, info = TRUE))
- expect_equal(as.double(table(x)), c(1070, 198, 732))
-
- expect_output(print(custom_mdro_guideline(AMX == "R" ~ "test", as_factor = FALSE)))
- expect_error(custom_mdro_guideline())
- expect_error(custom_mdro_guideline("test"))
- expect_error(custom_mdro_guideline("test" ~ c(1:3)))
- expect_error(custom_mdro_guideline("test" ~ A))
- expect_warning(mdro(example_isolates,
- # since `test` gives an error, it will be ignored with a warning
- guideline = custom_mdro_guideline(test ~ "A"),
- info = FALSE))
-
- # print groups
- if (suppressWarnings(require("dplyr"))) {
- expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
- expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
- }
-})
diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R
deleted file mode 100755
index 2144a4d4..00000000
--- a/tests/testthat/test-mic.R
+++ /dev/null
@@ -1,143 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("mic.R")
-
-test_that("mic works", {
- skip_on_cran()
- expect_true(as.mic(8) == as.mic("8"))
- expect_true(as.mic("1") > as.mic("<=0.0625"))
- expect_true(as.mic("1") < as.mic(">=32"))
- expect_true(is.mic(as.mic(8)))
-
- expect_equal(as.double(as.mic(">=32")), 32)
- expect_equal(as.numeric(as.mic(">=32")), 32)
- expect_equal(as.integer(as.mic(">=32")), 32)
- expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
-
- # all levels should be valid MICs
- x <- as.mic(c(2, 4))
- expect_s3_class(x[1], "mic")
- expect_s3_class(x[[1]], "mic")
- expect_s3_class(c(x[1], x[9]), "mic")
- expect_s3_class(unique(x[1], x[9]), "mic")
- expect_s3_class(droplevels(c(x[1], x[9])), "mic")
- x[2] <- 32
- expect_s3_class(x, "mic")
- expect_warning(as.mic("INVALID VALUE"))
-
- pdf(NULL) # prevent Rplots.pdf being created
- expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
- expect_silent(plot(as.mic(c(1, 2, 4, 8))))
- expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
- expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr"))
- if (suppressWarnings(require("ggplot2"))) {
- expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8))), "gg")
- expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
- expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
- }
- expect_output(print(as.mic(c(1, 2, 4, 8))))
-
- expect_s3_class(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
-
- if (suppressWarnings(require("dplyr"))) {
- expect_output(print(tibble(m = as.mic(2:4))))
- }
-})
-
-test_that("mathematical functions on mic work", {
- skip_on_cran()
- x <- random_mic(50)
- x_double <- as.double(gsub("[<=>]+", "", as.character(x)))
- suppressWarnings(expect_identical(mean(x), mean(x_double)))
- suppressWarnings(expect_identical(median(x), median(x_double)))
- suppressWarnings(expect_identical(quantile(x), quantile(x_double)))
- suppressWarnings(expect_identical(abs(x), abs(x_double)))
- suppressWarnings(expect_identical(sign(x), sign(x_double)))
- suppressWarnings(expect_identical(sqrt(x), sqrt(x_double)))
- suppressWarnings(expect_identical(floor(x), floor(x_double)))
- suppressWarnings(expect_identical(ceiling(x), ceiling(x_double)))
- suppressWarnings(expect_identical(trunc(x), trunc(x_double)))
- suppressWarnings(expect_identical(round(x), round(x_double)))
- suppressWarnings(expect_identical(signif(x), signif(x_double)))
- suppressWarnings(expect_identical(exp(x), exp(x_double)))
- suppressWarnings(expect_identical(log(x), log(x_double)))
- suppressWarnings(expect_identical(log10(x), log10(x_double)))
- suppressWarnings(expect_identical(log2(x), log2(x_double)))
- suppressWarnings(expect_identical(expm1(x), expm1(x_double)))
- suppressWarnings(expect_identical(log1p(x), log1p(x_double)))
- suppressWarnings(expect_identical(cos(x), cos(x_double)))
- suppressWarnings(expect_identical(sin(x), sin(x_double)))
- suppressWarnings(expect_identical(tan(x), tan(x_double)))
- suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
- suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
- suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))
- suppressWarnings(expect_identical(acos(x), acos(x_double)))
- suppressWarnings(expect_identical(asin(x), asin(x_double)))
- suppressWarnings(expect_identical(atan(x), atan(x_double)))
- suppressWarnings(expect_identical(cosh(x), cosh(x_double)))
- suppressWarnings(expect_identical(sinh(x), sinh(x_double)))
- suppressWarnings(expect_identical(tanh(x), tanh(x_double)))
- suppressWarnings(expect_identical(acosh(x), acosh(x_double)))
- suppressWarnings(expect_identical(asinh(x), asinh(x_double)))
- suppressWarnings(expect_identical(atanh(x), atanh(x_double)))
- suppressWarnings(expect_identical(lgamma(x), lgamma(x_double)))
- suppressWarnings(expect_identical(gamma(x), gamma(x_double)))
- suppressWarnings(expect_identical(digamma(x), digamma(x_double)))
- suppressWarnings(expect_identical(trigamma(x), trigamma(x_double)))
- suppressWarnings(expect_identical(cumsum(x), cumsum(x_double)))
- suppressWarnings(expect_identical(cumprod(x), cumprod(x_double)))
- suppressWarnings(expect_identical(cummax(x), cummax(x_double)))
- suppressWarnings(expect_identical(cummin(x), cummin(x_double)))
- suppressWarnings(expect_identical(!x, !(x_double)))
-
- suppressWarnings(expect_identical(all(x), all(x_double)))
- suppressWarnings(expect_identical(any(x), any(x_double)))
- suppressWarnings(expect_identical(sum(x), sum(x_double)))
- suppressWarnings(expect_identical(prod(x), prod(x_double)))
- suppressWarnings(expect_identical(min(x), min(x_double)))
- suppressWarnings(expect_identical(max(x), max(x_double)))
- suppressWarnings(expect_identical(range(x), range(x_double)))
-
- el1 <- random_mic(50)
- el1_double <- as.double(gsub("[<=>]+", "", as.character(el1)))
- el2 <- random_mic(50)
- el2_double <- as.double(gsub("[<=>]+", "", as.character(el2)))
- suppressWarnings(expect_identical(el1 + el2, el1_double + el2_double))
- suppressWarnings(expect_identical(el1 - el2, el1_double - el2_double))
- suppressWarnings(expect_identical(el1 * el2, el1_double * el2_double))
- suppressWarnings(expect_identical(el1 / el2, el1_double / el2_double))
- suppressWarnings(expect_identical(el1 ^ el2, el1_double ^ el2_double))
- suppressWarnings(expect_identical(el1 %% el2, el1_double %% el2_double))
- suppressWarnings(expect_identical(el1 %/% el2, el1_double %/% el2_double))
- suppressWarnings(expect_identical(el1 & el2, el1_double & el2_double))
- suppressWarnings(expect_identical(el1 | el2, el1_double | el2_double))
- suppressWarnings(expect_identical(el1 == el2, el1_double == el2_double))
- suppressWarnings(expect_identical(el1 != el2, el1_double != el2_double))
- suppressWarnings(expect_identical(el1 < el2, el1_double < el2_double))
- suppressWarnings(expect_identical(el1 <= el2, el1_double <= el2_double))
- suppressWarnings(expect_identical(el1 >= el2, el1_double >= el2_double))
- suppressWarnings(expect_identical(el1 > el2, el1_double > el2_double))
-})
diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R
deleted file mode 100644
index c1e8a144..00000000
--- a/tests/testthat/test-mo.R
+++ /dev/null
@@ -1,308 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("mo.R")
-
-test_that("as.mo works", {
-
- skip_on_cran()
-
- MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
- expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
-
- expect_identical(
- as.character(as.mo(c("E. coli", "H. influenzae"))),
- c("B_ESCHR_COLI", "B_HMPHL_INFL"))
-
- expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
- expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
- expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
- expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
- expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
- expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
- expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
- expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
- expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
- expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
- expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
- expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
- expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
- expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
- expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
- expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
- expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
- expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
- expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
- expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
-
- expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))
-
-
- expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
-
- # GLIMS
- expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
-
- expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
- expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
- expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AERG")
- expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
- expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
- expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
- expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
-
- expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
- expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
- expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
- expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
- expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
- expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
-
-
- expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
-
- # prevalent MO
- expect_identical(
- suppressWarnings(as.character(
- as.mo(c("stau",
- "STAU",
- "staaur",
- "S. aureus",
- "S aureus",
- "Sthafilokkockus aureeuzz",
- "Staphylococcus aureus",
- "MRSA",
- "VISA")))),
- rep("B_STPHY_AURS", 9))
- expect_identical(
- as.character(
- as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))),
- rep("B_ESCHR_COLI", 6))
- # unprevalent MO
- expect_identical(
- as.character(
- as.mo(c("parnod",
- "P. nodosa",
- "P nodosa",
- "Paraburkholderia nodosa"))),
- rep("B_PRBRK_NODS", 4))
-
- # empty values
- expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4))
- expect_identical(as.character(as.mo(" ")), NA_character_)
- # too few characters
- expect_warning(as.mo("ab"))
-
- expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRSM", "K. pneu rhino", "esco")))),
- c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
-
- # check for Becker classification
- expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
- expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
- expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
- expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
- expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
- expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
- # aureus must only be influenced if Becker = "all"
- expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
- expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
- expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
-
- # check for Lancefield classification
- expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
- expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
- expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
- expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
- expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
- expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
- expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
- expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
- # Enterococci must only be influenced if Lancefield = "all"
- expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
- expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
- expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
- expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
- expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
- expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
- expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
- expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
- expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
-
- if (suppressWarnings(require("dplyr"))) {
- # select with one column
- expect_identical(
- example_isolates[1:10, ] %>%
- left_join_microorganisms() %>%
- select(genus) %>%
- as.mo() %>%
- as.character(),
- c("B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
- "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"))
-
- # select with two columns
- expect_identical(
- example_isolates[1:10, ] %>%
- pull(mo),
- example_isolates[1:10, ] %>%
- left_join_microorganisms() %>%
- select(genus, species) %>%
- as.mo())
-
- # too many columns
- expect_error(example_isolates %>% select(1:3) %>% as.mo())
-
- # test pull
- expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))),
- 2000)
- expect_true(example_isolates %>% pull(mo) %>% is.mo())
- }
-
- # unknown results
- expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
-
-
- # print
- expect_output(print(as.mo(c("B_ESCHR_COLI", NA))))
-
-
-
- # test data.frame
- expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
- 1)
-
- # check empty values
- expect_equal(as.character(suppressWarnings(as.mo(""))),
- NA_character_)
-
- # check less prevalent MOs
- expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
- expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
- expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
- expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN")
- expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
- expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
- expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
- expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
-
- # check old names
- expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
- print(mo_renamed())
- expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
-
- # check uncertain names
- expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
- expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
- expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
- expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
- expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
- expect_equal(suppressMessages(as.character(as.mo(c("s aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB"))
-
- # predefined reference_df
- expect_equal(as.character(as.mo("TestingOwnID",
- reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))),
- "B_ESCHR_COLI")
- expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"),
- reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))),
- c("B_ESCHR_COLI", "B_ESCHR_COLI"))
- expect_warning(as.mo("TestingOwnID", reference_df = NULL))
- expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
-
- # combination of existing mo and other code
- expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
- c("B_ESCHR_COLI", "B_ESCHR_COLI"))
-
- # from different sources
- expect_equal(as.character(as.mo(
- c("PRTMIR", "bclcer", "B_ESCHR_COLI"))),
- c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI"))
-
- # hard to find
- expect_equal(as.character(suppressMessages(as.mo(
- c("Microbacterium paraoxidans",
- "Streptococcus suis (bovis gr)",
- "Raoultella (here some text) terrigena")))),
- c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG"))
- expect_output(print(mo_uncertainties()))
- x <- as.mo("S. aur")
- # many hits
- expect_output(print(mo_uncertainties()))
-
- # Salmonella (City) are all actually Salmonella enterica spp (City)
- expect_equal(suppressMessages(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
- c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
-
- # no virusses
- expect_equal(as.character(as.mo("Virus")), NA_character_)
-
- # summary
- expect_equal(length(summary(example_isolates$mo)), 6)
-
- # WHONET codes and NA/NaN
- expect_equal(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
- rep(NA_character_, 3))
- expect_equal(as.character(as.mo("con")), "UNKNOWN")
- expect_equal(as.character(as.mo("xxx")), NA_character_)
- expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI"))
- expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
- rep("UNKNOWN", 3))
-
- expect_null(mo_failures())
-
- expect_error(translate_allow_uncertain(5))
-
- # debug mode
- expect_output(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
-
- # ..coccus
- expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
- c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN"))
- # yeasts and fungi
- expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
- c("F_YEAST", "F_FUNGUS"))
-
- if (suppressWarnings(require("dplyr"))) {
- # print tibble
- expect_output(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
- }
-
- # assigning and subsetting
- x <- example_isolates$mo
- expect_s3_class(x[1], "mo")
- expect_s3_class(x[[1]], "mo")
- expect_s3_class(c(x[1], x[9]), "mo")
- expect_warning(x[1] <- "invalid code")
- expect_warning(x[[1]] <- "invalid code")
- expect_warning(c(x[1], "test"))
-
- # ignoring patterns
- expect_equal(as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_pattern = "this")),
- c("B_ESCHR_COLI", NA))
-
- # frequency tables
- if (suppressWarnings(require("cleaner"))) {
- expect_s3_class(cleaner::freq(example_isolates$mo), "freq")
- }
-
-})
diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R
deleted file mode 100644
index 29c61533..00000000
--- a/tests/testthat/test-mo_property.R
+++ /dev/null
@@ -1,142 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("mo_property.R")
-
-test_that("mo_property works", {
-
- skip_on_cran()
-
- expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
- expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
- expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
- expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
- expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
- expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
- expect_equal(mo_genus("Escherichia coli"), "Escherichia")
- expect_equal(mo_species("Escherichia coli"), "coli")
- expect_equal(mo_subspecies("Escherichia coli"), "")
- expect_equal(mo_fullname("Escherichia coli"), "Escherichia coli")
- expect_equal(mo_name("Escherichia coli"), "Escherichia coli")
- expect_equal(mo_type("Escherichia coli", language = "en"), "Bacteria")
- expect_equal(mo_gramstain("Escherichia coli", language = "en"), "Gram-negative")
- expect_equal(class(mo_taxonomy("Escherichia coli")), "list")
- expect_equal(names(mo_taxonomy("Escherichia coli")), c("kingdom", "phylum", "class", "order",
- "family", "genus", "species", "subspecies"))
- expect_equal(mo_synonyms("Escherichia coli"), NULL)
- expect_gt(length(mo_synonyms("Candida albicans")), 1)
- expect_equal(class(mo_synonyms(c("Candida albicans", "Escherichia coli"))), "list")
- expect_equal(names(mo_info("Escherichia coli")), c("kingdom", "phylum", "class", "order",
- "family", "genus", "species", "subspecies",
- "synonyms", "gramstain", "url", "ref",
- "snomed"))
- expect_equal(class(mo_info(c("Escherichia coli", "Staphylococcus aureus"))), "list")
-
- expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
- expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
- expect_equal(mo_year("Escherichia coli"), 1919)
-
- expect_equal(mo_shortname("Escherichia coli"), "E. coli")
- expect_equal(mo_shortname("Escherichia"), "Escherichia")
- expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
- expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
- expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")
- expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
- expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
-
- expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
- expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
-
- # test integrity
- MOs <- microorganisms
- expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
-
- # check languages
- expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
- expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
-
- expect_output(print(mo_gramstain("Escherichia coli", language = "en")))
- expect_output(print(mo_gramstain("Escherichia coli", language = "de")))
- expect_output(print(mo_gramstain("Escherichia coli", language = "nl")))
- expect_output(print(mo_gramstain("Escherichia coli", language = "es")))
- expect_output(print(mo_gramstain("Escherichia coli", language = "pt")))
- expect_output(print(mo_gramstain("Escherichia coli", language = "it")))
- expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
-
- expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
-
- dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
- expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
-
- # manual property function
- expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
- expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
- expect_identical(mo_property("Escherichia coli", property = "fullname"),
- mo_fullname("Escherichia coli"))
- expect_identical(mo_property("Escherichia coli", property = "genus"),
- mo_genus("Escherichia coli"))
- expect_identical(mo_property("Escherichia coli", property = "species"),
- mo_species("Escherichia coli"))
-
- expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
- expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
-
- expect_true(112283007 %in% mo_snomed("Escherichia coli"))
-
- # old codes must throw a warning in mo_* family
- expect_message(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
-
- # outcome of mo_fullname must always return the fullname from the data set
- x <- data.frame(mo = microorganisms$mo,
- # fullname from the original data:
- f1 = microorganisms$fullname,
- # newly created fullname based on MO code:
- f2 = mo_fullname(microorganisms$mo, language = "en"),
- stringsAsFactors = FALSE)
- expect_equal(nrow(subset(x, f1 != f2)), 0)
-
- # is gram pos/neg (also return FALSE for all non-bacteria)
- expect_equal(mo_is_gram_negative(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
- c(TRUE, FALSE, FALSE))
- expect_equal(mo_is_gram_positive(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
- c(FALSE, TRUE, FALSE))
- # is intrinsic resistant
- expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans"),
- "vanco"),
- c(TRUE, FALSE, FALSE))
-
- # with reference data
- expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
- "Escherichia coli")
-
- if (suppressWarnings(require("dplyr"))) {
- expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
- 730)
- expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),
- 1238)
- expect_equal(example_isolates %>% filter(mo_is_intrinsic_resistant(ab = "Vancomycin")) %>% nrow(),
- 710)
- }
-})
diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R
deleted file mode 100644
index 0475165e..00000000
--- a/tests/testthat/test-pca.R
+++ /dev/null
@@ -1,70 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("pca.R")
-
-test_that("PCA works", {
-
- skip_on_cran()
-
- resistance_data <- structure(list(order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
- genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
- AMC = c(0.00425, 0.13062, 0.10344),
- CXM = c(0.00425, 0.05376, 0.10344),
- CTX = c(0.00000, 0.02396, 0.05172),
- TOB = c(0.02325, 0.02597, 0.10344),
- TMP = c(0.08387, 0.39141, 0.18367)),
- class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
- row.names = c(NA, -3L),
- groups = structure(list(order = c("Bacillales", "Enterobacterales"),
- .rows = list(1L, 2:3)),
- row.names = c(NA, -2L),
- class = c("tbl_df", "tbl", "data.frame"),
- .drop = TRUE))
-
- pca_model <- pca(resistance_data)
-
- expect_s3_class(pca_model, "pca")
-
- pdf(NULL) # prevent Rplots.pdf being created
- if (suppressWarnings(require("ggplot2"))) {
- ggplot_pca(pca_model, ellipse = TRUE)
- ggplot_pca(pca_model, arrows_textangled = FALSE)
- }
-
- if (suppressWarnings(require("dplyr"))) {
- resistance_data <- example_isolates %>%
- group_by(order = mo_order(mo),
- genus = mo_genus(mo)) %>%
- summarise_if(is.rsi, resistance, minimum = 0)
- pca_result <- resistance_data %>%
- pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT")
- expect_s3_class(pca_result, "prcomp")
- if (suppressWarnings(require("ggplot2"))) {
- ggplot_pca(pca_result, ellipse = TRUE)
- ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
- }
- }
-})
diff --git a/tests/testthat/test-proportion.R b/tests/testthat/test-proportion.R
deleted file mode 100755
index 5949fa7c..00000000
--- a/tests/testthat/test-proportion.R
+++ /dev/null
@@ -1,140 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("proportion.R")
-
-test_that("proportions works", {
-
- skip_on_cran()
-
- expect_equal(proportion_R(example_isolates$AMX), resistance(example_isolates$AMX))
- expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX))
-
- # AMX resistance in `example_isolates`
- expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001)
- expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001)
- expect_equal(1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX),
- proportion_S(example_isolates$AMX))
- expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$AMX),
- proportion_IR(example_isolates$AMX))
- expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
- proportion_SI(example_isolates$AMX))
-
- expect_equal(example_isolates %>% proportion_SI(AMC),
- 0.7626397,
- tolerance = 0.0001)
- expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
- 0.9408,
- tolerance = 0.0001)
- expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
- 0.9382647,
- tolerance = 0.0001)
-
- if (suppressWarnings(require("dplyr"))) {
- # percentages
- expect_equal(example_isolates %>%
- group_by(hospital_id) %>%
- summarise(R = proportion_R(CIP, as_percent = TRUE),
- I = proportion_I(CIP, as_percent = TRUE),
- S = proportion_S(CIP, as_percent = TRUE),
- n = n_rsi(CIP),
- total = n()) %>%
- pull(n) %>%
- sum(),
- 1409)
-
- # count of cases
- expect_equal(example_isolates %>%
- group_by(hospital_id) %>%
- summarise(cipro_p = proportion_SI(CIP, as_percent = TRUE),
- cipro_n = n_rsi(CIP),
- genta_p = proportion_SI(GEN, as_percent = TRUE),
- genta_n = n_rsi(GEN),
- combination_p = proportion_SI(CIP, GEN, as_percent = TRUE),
- combination_n = n_rsi(CIP, GEN)) %>%
- pull(combination_n),
- c(305, 617, 241, 711))
-
- # proportion_df
- expect_equal(
- example_isolates %>% select(AMX) %>% proportion_df() %>% pull(value),
- c(example_isolates$AMX %>% proportion_SI(),
- example_isolates$AMX %>% proportion_R())
- )
- expect_equal(
- example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value),
- c(example_isolates$AMX %>% proportion_S(),
- example_isolates$AMX %>% proportion_IR())
- )
- expect_equal(
- example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
- c(example_isolates$AMX %>% proportion_S(),
- example_isolates$AMX %>% proportion_I(),
- example_isolates$AMX %>% proportion_R())
- )
- }
-
- reset_all_thrown_messages()
- expect_warning(proportion_R(as.character(example_isolates$AMC)))
- reset_all_thrown_messages()
- expect_warning(proportion_S(as.character(example_isolates$AMC)))
- reset_all_thrown_messages()
- expect_warning(proportion_S(as.character(example_isolates$AMC,
- example_isolates$GEN)))
- reset_all_thrown_messages()
- expect_warning(n_rsi(as.character(example_isolates$AMC,
- example_isolates$GEN)))
- expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
- example_isolates$GEN))),
- 1879)
-
- # check for errors
- expect_error(proportion_IR("test", minimum = "test"))
- expect_error(proportion_IR("test", as_percent = "test"))
- expect_error(proportion_I("test", minimum = "test"))
- expect_error(proportion_I("test", as_percent = "test"))
- expect_error(proportion_S("test", minimum = "test"))
- expect_error(proportion_S("test", as_percent = "test"))
- expect_error(proportion_S("test", also_single_tested = TRUE))
-
- # check too low amount of isolates
- expect_identical(suppressWarnings(proportion_R(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
- NA_real_)
- expect_identical(suppressWarnings(proportion_I(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
- NA_real_)
- expect_identical(suppressWarnings(proportion_S(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
- NA_real_)
-
- # warning for speed loss
- reset_all_thrown_messages()
- expect_warning(proportion_R(as.character(example_isolates$GEN)))
- reset_all_thrown_messages()
- expect_warning(proportion_I(as.character(example_isolates$GEN)))
- reset_all_thrown_messages()
- expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
-
- expect_error(proportion_df(c("A", "B", "C")))
- expect_error(proportion_df(example_isolates[, "date"]))
-})
diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R
deleted file mode 100644
index 9b7f751e..00000000
--- a/tests/testthat/test-resistance_predict.R
+++ /dev/null
@@ -1,102 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("resistance_predict.R")
-
-test_that("prediction of rsi works", {
- skip_on_cran()
-
- if (suppressWarnings(require("dplyr"))) {
- expect_output(AMX_R <- example_isolates %>%
- filter(mo == "B_ESCHR_COLI") %>%
- rsi_predict(col_ab = "AMX",
- col_date = "date",
- model = "binomial",
- minimum = 10,
- info = TRUE) %>%
- pull("value"))
- # AMX resistance will increase according to data set `example_isolates`
- expect_true(AMX_R[3] < AMX_R[20])
- }
-
- expect_output(x <- suppressMessages(resistance_predict(example_isolates,
- col_ab = "AMX",
- year_min = 2010,
- model = "binomial",
- info = TRUE)))
- pdf(NULL) # prevent Rplots.pdf being created
- expect_silent(plot(x))
- if (suppressWarnings(require("ggplot2"))) {
- expect_silent(ggplot_rsi_predict(x))
- expect_silent(ggplot(x))
- expect_error(ggplot_rsi_predict(example_isolates))
- }
-
- expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- model = "binomial",
- col_ab = "AMX",
- col_date = "date",
- info = TRUE))
- expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- model = "loglin",
- col_ab = "AMX",
- col_date = "date",
- info = TRUE))
- expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- model = "lin",
- col_ab = "AMX",
- col_date = "date",
- info = TRUE))
-
- expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- model = "INVALID MODEL",
- col_ab = "AMX",
- col_date = "date",
- info = TRUE))
- expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- model = "binomial",
- col_ab = "NOT EXISTING COLUMN",
- col_date = "date",
- info = TRUE))
- expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- model = "binomial",
- col_ab = "AMX",
- col_date = "NOT EXISTING COLUMN",
- info = TRUE))
- expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- col_ab = "AMX",
- col_date = "NOT EXISTING COLUMN",
- info = TRUE))
- expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- col_ab = "AMX",
- col_date = "date",
- info = TRUE))
- # almost all E. coli are MEM S in the Netherlands :)
- expect_error(resistance_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
- model = "binomial",
- col_ab = "MEM",
- col_date = "date",
- info = TRUE))
-})
diff --git a/tests/testthat/test-rsi.R b/tests/testthat/test-rsi.R
deleted file mode 100644
index d51eaf57..00000000
--- a/tests/testthat/test-rsi.R
+++ /dev/null
@@ -1,192 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("rsi.R")
-
-test_that("rsi works", {
-
- skip_on_cran()
-
- expect_true(as.rsi("S") < as.rsi("I"))
- expect_true(as.rsi("I") < as.rsi("R"))
- expect_true(is.rsi(as.rsi("S")))
-
- x <- example_isolates$AMX
- expect_s3_class(x[1], "rsi")
- expect_s3_class(x[[1]], "rsi")
- expect_s3_class(c(x[1], x[9]), "rsi")
- expect_s3_class(unique(x[1], x[9]), "rsi")
-
- pdf(NULL) # prevent Rplots.pdf being created
- expect_silent(barplot(as.rsi(c("S", "I", "R"))))
- expect_silent(plot(as.rsi(c("S", "I", "R"))))
- if (suppressWarnings(require("ggplot2"))) expect_s3_class(ggplot(as.rsi(c("S", "I", "R"))), "gg")
- expect_output(print(as.rsi(c("S", "I", "R"))))
-
- expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
-
- expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
-
- expect_equal(summary(as.rsi(c("S", "R"))),
- structure(c("Class" = "rsi",
- "%R" = "50.0% (n=1)",
- "%SI" = "50.0% (n=1)",
- "- %S" = "50.0% (n=1)",
- "- %I" = " 0.0% (n=0)"), class = c("summaryDefault", "table")))
-
- expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
- rep(FALSE, length(example_isolates)))
-
- expect_error(as.rsi.mic(as.mic(16)))
- expect_error(as.rsi.disk(as.disk(16)))
-
- expect_error(get_guideline("this one does not exist"))
-
- if (suppressWarnings(require("dplyr"))) {
- # 40 rsi columns
- expect_equal(example_isolates %>%
- mutate_at(vars(PEN:RIF), as.character) %>%
- lapply(is.rsi.eligible) %>%
- as.logical() %>%
- sum(),
- 40)
- expect_equal(sum(is.rsi(example_isolates)), 40)
-
- expect_output(print(tibble(ab = as.rsi("S"))))
- }
-
- if (suppressWarnings(require("skimr"))) {
- expect_s3_class(skim(example_isolates),
- "data.frame")
- if (suppressWarnings(require("dplyr"))) {
- expect_s3_class(example_isolates %>%
- mutate(m = as.mic(2),
- d = as.disk(20)) %>%
- skim(),
- "data.frame")
- }
- }
-
-})
-
-test_that("mic2rsi works", {
-
- skip_on_cran()
-
- # S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
- expect_equal(as.character(
- as.rsi(x = as.mic(c(0.125, 0.5, 1, 2, 4)),
- mo = "B_STRPT_PNMN",
- ab = "AMP",
- guideline = "EUCAST 2020")),
- c("S", "S", "I", "I", "R"))
- # S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
- expect_equal(as.character(
- as.rsi(x = as.mic(c(1, 2, 4, 8, 16)),
- mo = "B_STRPT_PNMN",
- ab = "AMX",
- guideline = "CLSI 2019")),
- c("S", "S", "I", "R", "R"))
-
- # cutoffs at MIC = 8
- expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
- as.rsi("S"))
- expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
- as.rsi("R"))
-
- if (suppressWarnings(require("dplyr"))) {
- expect_true(suppressWarnings(example_isolates %>%
- mutate(amox_mic = as.mic(2)) %>%
- select(mo, amox_mic) %>%
- as.rsi() %>%
- pull(amox_mic) %>%
- is.rsi()))
- }
-})
-
-test_that("disk2rsi works", {
-
- skip_on_cran()
-
- expect_equal(as.character(
- as.rsi(x = as.disk(22),
- mo = "B_STRPT_PNMN",
- ab = "ERY",
- guideline = "CLSI")),
- "S")
- expect_equal(as.character(
- as.rsi(x = as.disk(18),
- mo = "B_STRPT_PNMN",
- ab = "ERY",
- guideline = "CLSI")),
- "I")
- expect_equal(as.character(
- as.rsi(x = as.disk(10),
- mo = "B_STRPT_PNMN",
- ab = "ERY",
- guideline = "CLSI")),
- "R")
-
- if (suppressWarnings(require("dplyr"))) {
- expect_true(example_isolates %>%
- mutate(amox_disk = as.disk(15)) %>%
- select(mo, amox_disk) %>%
- as.rsi(guideline = "CLSI") %>%
- pull(amox_disk) %>%
- is.rsi())
- }
-
- # frequency tables
- if (suppressWarnings(require("cleaner"))) {
- expect_s3_class(cleaner::freq(example_isolates$AMX), "freq")
- }
-})
-
-test_that("data.frame2rsi works", {
-
- skip_on_cran()
-
- df <- data.frame(microorganism = "Escherichia coli",
- AMP = as.mic(8),
- CIP = as.mic(0.256),
- GEN = as.disk(18),
- TOB = as.disk(16),
- ERY = "R", # note about assigning class
- CLR = "V") # note about cleaning
- expect_s3_class(suppressWarnings(as.rsi(df)),
- "data.frame")
-
- expect_s3_class(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli",
- amoxi = c("R", "S", "I", "invalid")))$amoxi),
- "rsi")
- expect_warning(as.rsi(data.frame(mo = "E. coli",
- NIT = c("<= 2", 32))))
- expect_message(as.rsi(data.frame(mo = "E. coli",
- NIT = c("<= 2", 32),
- uti = TRUE)))
- expect_message(as.rsi(data.frame(mo = "E. coli",
- NIT = c("<= 2", 32),
- specimen = c("urine", "blood"))))
-})
diff --git a/tests/testthat/test-zzz.R b/tests/testthat/test-zzz.R
deleted file mode 100644
index 3891d353..00000000
--- a/tests/testthat/test-zzz.R
+++ /dev/null
@@ -1,117 +0,0 @@
-# ==================================================================== #
-# TITLE #
-# Antimicrobial Resistance (AMR) Data Analysis for R #
-# #
-# SOURCE #
-# https://github.com/msberends/AMR #
-# #
-# LICENCE #
-# (c) 2018-2021 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. #
-# #
-# 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 the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
-# ==================================================================== #
-
-context("zzz.R")
-
-test_that("imports work", {
- skip_on_cran()
-
- # Check if these function still exist in the package (all are in Suggests field)
- # Since GitHub Action runs every night, we will get emailed when a dependency fails based on this unit test
-
- # functions used by import_fn()
- import_functions <- c(
- "anti_join" = "dplyr",
- "cur_column" = "dplyr",
- "full_join" = "dplyr",
- "has_internet" = "curl",
- "html_attr" = "rvest",
- "html_children" = "rvest",
- "html_node" = "rvest",
- "html_nodes" = "rvest",
- "html_table" = "rvest",
- "html_text" = "rvest",
- "inner_join" = "dplyr",
- "insertText" = "rstudioapi",
- "left_join" = "dplyr",
- "new_pillar_shaft_simple" = "pillar",
- "read_html" = "xml2",
- "right_join" = "dplyr",
- "semi_join" = "dplyr",
- "showQuestion" = "rstudioapi")
-
- # functions that are called directly
- call_functions <- c(
- # cleaner
- "freq.default" = "cleaner",
- # skimr
- "inline_hist" = "skimr",
- "sfl" = "skimr",
- # set_mo_source
- "read_excel" = "readxl",
- # ggplot_rsi
- "aes_string" = "ggplot2",
- "element_blank" = "ggplot2",
- "element_line" = "ggplot2",
- "element_text" = "ggplot2",
- "facet_wrap" = "ggplot2",
- "geom_text" = "ggplot2",
- "ggplot" = "ggplot2",
- "labs" = "ggplot2",
- "layer" = "ggplot2",
- "position_fill" = "ggplot2",
- "scale_fill_manual" = "ggplot2",
- "scale_y_continuous" = "ggplot2",
- "theme" = "ggplot2",
- "theme_minimal" = "ggplot2",
- # ggplot_pca
- "aes" = "ggplot2",
- "arrow" = "ggplot2",
- "element_blank" = "ggplot2",
- "element_line" = "ggplot2",
- "element_text" = "ggplot2",
- "expand_limits" = "ggplot2",
- "geom_path" = "ggplot2",
- "geom_point" = "ggplot2",
- "geom_segment" = "ggplot2",
- "geom_text" = "ggplot2",
- "ggplot" = "ggplot2",
- "labs" = "ggplot2",
- "theme" = "ggplot2",
- "theme_minimal" = "ggplot2",
- "unit" = "ggplot2",
- "xlab" = "ggplot2",
- "ylab" = "ggplot2",
- # resistance_predict
- "aes" = "ggplot2",
- "geom_errorbar" = "ggplot2",
- "geom_point" = "ggplot2",
- "geom_ribbon" = "ggplot2",
- "ggplot" = "ggplot2",
- "labs" = "ggplot2"
- )
-
- import_functions <- c(import_functions, call_functions)
-
- for (i in seq_len(length(import_functions))) {
- fn <- names(import_functions)[i]
- pkg <- unname(import_functions[i])
- # function should exist in foreign pkg namespace
- if (pkg %in% rownames(installed.packages())) {
- expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
- failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore"))
- }
- }
-})
diff --git a/tests/testthat.R b/tests/tinytest.R
old mode 100755
new mode 100644
similarity index 76%
rename from tests/testthat.R
rename to tests/tinytest.R
index 42c8134b..e4cd572b
--- a/tests/testthat.R
+++ b/tests/tinytest.R
@@ -23,14 +23,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
-# the testthat package is in Suggests, but very old R versions will not be
-# able to install it. Yet, we want basic R CMD CHECK's in those R versions
-# as well, so only run unit tests in later R versions:
-if (require("testthat", warn.conflicts = FALSE)) {
+# test only on GitHub Actions and at home - not on CRAN as tests are lengthy
+if (identical(Sys.getenv("R_TINYTEST"), "true")) {
+ library(tinytest)
library(AMR)
- # print non-base packages
- print(as.data.frame(utils::installed.packages())[which(is.na(as.data.frame(utils::installed.packages())$Priority)),
- "Version",
- drop = FALSE])
- test_check("AMR")
+ test_package("AMR")
}