WHONET/EARS-Net support

tests/testthat/test-atc.R

@@ -22,7 +22,7 @@
 context("atc.R")
 
 test_that("as.atc works", {
-  expect_equal(suppressWarnings(as.character(guess_atc(c("J01FA01",
+  expect_equal(suppressWarnings(as.character(as.atc(c("J01FA01",
                                                          "Erythromycin",
                                                          "eryt",
                                                          "ERYT",
@@ -45,4 +45,8 @@ test_that("as.atc works", {
   expect_equal(as.character(as.atc(c("nitro", "cipro"))),
                c("J01XE01", "J01MA02"))
 
+  # EARS-Net
+  expect_equal(as.character(as.atc("AMX")),
+               "J01CA04")
+
 })

tests/testthat/test-first_isolate.R

@@ -160,7 +160,7 @@ test_that("first isolates work", {
 
   # look for columns itself
   expect_message(first_isolate(septic_patients))
-  expect_error(first_isolate(septic_patients %>%
+  expect_message(first_isolate(septic_patients %>%
                                mutate(mo = as.character(mo)) %>%
                                left_join_microorganisms()))
 

tests/testthat/test-guess_ab_col.R

@@ -33,4 +33,13 @@ test_that("guess_ab_col works", {
                "tetr")
   expect_equal(guess_ab_col(septic_patients, "TETR"),
                "tetr")
+
+  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(guess_ab_col(df, as.atc("augmentin")),
+               "AMC_ED20")
 })