new EUCAST rules algorithm

2025-07-08 18:41:58 +02:00 · 2019-04-05 18:47:39 +02:00
parent 56d4b4719f
commit fbc9191b13
115 changed files with 1340 additions and 2174 deletions
--- a/tests/testthat.R
+++ b/tests/testthat.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 library(testthat)
--- a/tests/testthat/test-abname.R
+++ b/tests/testthat/test-abname.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("abname.R")
--- a/tests/testthat/test-age.R
+++ b/tests/testthat/test-age.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("age.R")
--- a/tests/testthat/test-atc.R
+++ b/tests/testthat/test-atc.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("atc.R")
--- a/tests/testthat/test-atc_property.R
+++ b/tests/testthat/test-atc_property.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("atc_property.R")
--- a/tests/testthat/test-availability.R
+++ b/tests/testthat/test-availability.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("availability.R")
--- a/tests/testthat/test-count.R
+++ b/tests/testthat/test-count.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("count.R")
--- a/tests/testthat/test-data.R
+++ b/tests/testthat/test-data.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("data.R")
@ -27,36 +27,13 @@ test_that("data sets are valid", {
  expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))

  # there should be no diacritics (i.e. non ASCII) characters in the datasets
-  library(dplyr)
-  # check only character variables:
-  test_microorganisms <- microorganisms %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
-  test_microorganisms.old <- microorganisms.old %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
-  test_antibiotics <- antibiotics %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
-  test_septic_patients <- septic_patients %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
-  # and compare them with their transformed version:
-  expect_identical(test_microorganisms,
-                   test_microorganisms %>%
-                     lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
-                     as.data.frame(stringsAsFactors = FALSE))
-
-  expect_identical(test_microorganisms.old,
-                   test_microorganisms.old %>%
-                     lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
-                     as.data.frame(stringsAsFactors = FALSE))
-
-  expect_identical(test_antibiotics,
-                   test_antibiotics %>%
-                     lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
-                     as.data.frame(stringsAsFactors = FALSE))
-
-  expect_identical(test_septic_patients,
-                   test_septic_patients %>%
-                     lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
-                     as.data.frame(stringsAsFactors = FALSE))
-
+  datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
+  for (i in 1:length(datasets)) {
+    dataset <- get(datasets[i], envir = asNamespace("AMR"))
+    expect_identical(dataset_UTF8_to_ASCII(dataset), dataset)
+  }
 })

-
 test_that("creation of data sets is valid", {
  df <- make()
  expect_lt(nrow(df[which(df$prevalence == 1), ]), nrow(df[which(df$prevalence == 2), ]))
--- a/tests/testthat/test-deprecated.R
+++ b/tests/testthat/test-deprecated.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("deprecated.R")
@ -30,8 +30,6 @@ test_that("deprecated functions work", {
  expect_identical(suppressWarnings(ratio(c(772, 1611, 737), ratio = "1:2:1")), c(780, 1560,  780))
  expect_identical(suppressWarnings(ratio(c(1752, 1895), ratio = c(1, 1))), c(1823.5, 1823.5))

-  expect_warning(guess_mo("esco"))
-  expect_warning(guess_atc("amox"))
  expect_warning(ab_property("amox"))
  expect_warning(ab_atc("amox"))
  expect_warning(ab_official("amox"))
--- a/tests/testthat/test-eucast_rules.R
+++ b/tests/testthat/test-eucast_rules.R
@ -16,13 +16,22 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("eucast_rules.R")

 test_that("EUCAST rules work", {

+  # thoroughly check input table
+  expect_true(file.exists(EUCAST_RULES_FILE_LOCATION))
+  eucast_input_file <- eucast_rules_file()
+  expect_equal(colnames(eucast_input_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"))
+
  expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))

  expect_identical(colnames(septic_patients),
@ -40,7 +49,6 @@ test_that("EUCAST rules work", {
                  stringsAsFactors = FALSE)
  expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
  expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
-  expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)

  a <- data.frame(mo = c("Staphylococcus aureus",
                         "Streptococcus group A"),
--- a/tests/testthat/test-filter_ab_class.R
+++ b/tests/testthat/test-filter_ab_class.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("filter_ab_class.R")
--- a/tests/testthat/test-first_isolate.R
+++ b/tests/testthat/test-first_isolate.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("first_isolate.R")
--- a/tests/testthat/test-freq.R
+++ b/tests/testthat/test-freq.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("freq.R")
--- a/tests/testthat/test-g.test.R
+++ b/tests/testthat/test-g.test.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("g.test.R")
--- a/tests/testthat/test-get_locale.R
+++ b/tests/testthat/test-get_locale.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("get_locale.R")
--- a/tests/testthat/test-ggplot_rsi.R
+++ b/tests/testthat/test-ggplot_rsi.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("ggplot_rsi.R")
--- a/tests/testthat/test-guess_ab_col.R
+++ b/tests/testthat/test-guess_ab_col.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("guess_ab_col.R")
--- a/tests/testthat/test-join_microorganisms.R
+++ b/tests/testthat/test-join_microorganisms.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("join_microorganisms.R")
--- a/tests/testthat/test-key_antibiotics.R
+++ b/tests/testthat/test-key_antibiotics.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("key_antibiotics.R")
--- a/tests/testthat/test-kurtosis.R
+++ b/tests/testthat/test-kurtosis.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("kurtosis.R")
--- a/tests/testthat/test-like.R
+++ b/tests/testthat/test-like.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("like.R")
--- a/tests/testthat/test-mdro.R
+++ b/tests/testthat/test-mdro.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("mdro.R")
--- a/tests/testthat/test-mic.R
+++ b/tests/testthat/test-mic.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("mic.R")
--- a/tests/testthat/test-misc.R
+++ b/tests/testthat/test-misc.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("misc.R")
--- a/tests/testthat/test-mo.R
+++ b/tests/testthat/test-mo.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("mo.R")
--- a/tests/testthat/test-mo_history.R
+++ b/tests/testthat/test-mo_history.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 # context("mo_history.R")
--- a/tests/testthat/test-mo_property.R
+++ b/tests/testthat/test-mo_property.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("mo_property.R")
--- a/tests/testthat/test-p.symbol.R
+++ b/tests/testthat/test-p.symbol.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("p.symbol.R")
--- a/tests/testthat/test-portion.R
+++ b/tests/testthat/test-portion.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("portion.R")
--- a/tests/testthat/test-read.4d.R
+++ b/tests/testthat/test-read.4d.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("read.4d.R")
--- a/tests/testthat/test-resistance_predict.R
+++ b/tests/testthat/test-resistance_predict.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("portion.R")
--- a/tests/testthat/test-rsi.R
+++ b/tests/testthat/test-rsi.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("rsi.R")
--- a/tests/testthat/test-skewness.R
+++ b/tests/testthat/test-skewness.R
@ -16,7 +16,7 @@
 # This R package was created for academic research and was publicly    #
 # released in the hope that it will be useful, but it comes WITHOUT    #
 # ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitab.io/AMR.     #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #

 context("skewness.R")