prepare for CRAN

inst/tinytest/test-ab_property.R

@@ -63,7 +63,7 @@ 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")
+  c("101477-8", "101478-6", "18864-9", "18865-6", "20374-5", "21066-6", "23618-2", "27-3", "28-1", "29-9", "30-7", "31-5", "32-3", "33-1", "3355-5", "33562-0", "33919-2", "34-9", "43883-8", "43884-6", "6979-9", "6980-7", "87604-5")
 )
 
 expect_true(ab_url("AMX") %like% "whocc.no")

inst/tinytest/test-antibiogram.R

@@ -78,19 +78,19 @@ ab6 <- antibiogram(example_isolates,
                    syndromic_group = "ward")
 
 # with a custom language, though this will be determined automatically
-# (i.e., this table will be in Spanish on Spanish systems)
+# (i.e., this table will be in Dutch on Dutch systems)
 ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
 ab7 <- antibiogram(ex1,
                    antibiotics = aminoglycosides(),
                    ab_transform = "name",
                    syndromic_group = ifelse(ex1$ward == "ICU",
-                                            "UCI", "No UCI"),
-                   language = "es")
+                                            "IC", "Geen IC"),
+                   language = "nl")
 
 expect_inherits(ab6, "antibiogram")
 expect_inherits(ab7, "antibiogram")
 expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
-expect_equal(colnames(ab7), c("Grupo sindrómico", "Patógeno (N min-max)", "Amikacina", "Gentamicina", "Tobramicina"))
+expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen (N min-max)", "Amikacine", "Gentamicine", "Tobramycine"))
 
 # Weighted-incidence syndromic combination antibiogram (WISCA) ---------
 

inst/tinytest/test-first_isolate.R

@@ -42,7 +42,7 @@ expect_equal(
 )
 expect_equal(
   sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
-  1379
+  1373
 )
 
 # Phenotype-based, using key antimicrobials
@@ -53,7 +53,7 @@ expect_equal(
     type = "keyantimicrobials",
     antifungal = NULL, info = TRUE
   ), na.rm = TRUE),
-  1395
+  1376
 )
 expect_equal(
   sum(first_isolate(
@@ -62,7 +62,7 @@ expect_equal(
     type = "keyantimicrobials",
     antifungal = NULL, info = TRUE, ignore_I = FALSE
   ), na.rm = TRUE),
-  1418
+  1396
 )
 
 
@@ -93,7 +93,7 @@ expect_true(
     col_specimen = "specimen",
     filter_specimen = "Urine",
     info = TRUE
-  ), na.rm = TRUE) < 1501
+  ), na.rm = TRUE) < 1400
 )
 # same, but now exclude ICU
 expect_true(
@@ -107,7 +107,7 @@ expect_true(
     col_icu = x$ward == "ICU",
     icu_exclude = TRUE,
     info = TRUE
-  ), na.rm = TRUE) < 1501
+  ), na.rm = TRUE) < 1000
 )
 
 # "No isolates found"
@@ -193,7 +193,7 @@ expect_equal(
     ),
     na.rm = TRUE
   ),
-  1382
+  1376
 )
 
 # unknown MOs
@@ -201,23 +201,23 @@ 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
+  1106
 )
 expect_equal(
   sum(first_isolate(test_unknown, include_unknown = TRUE)),
-  1591
+  1589
 )
 
 test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
 expect_equal(
   sum(first_isolate(test_unknown)),
-  1108
+  1106
 )
 
 # empty sir results
 expect_equal(
   sum(first_isolate(example_isolates, include_untested_sir = FALSE)),
-  1366
+  1360
 )
 
 # shortcuts