(v0.7.1.9004) atc class removal

tests/testthat/test-ab.R

@@ -48,14 +48,6 @@ test_that("as.ab works", {
 
   expect_identical(class(pull(antibiotics, ab)), "ab")
 
-  # first 5 chars of official name
-  expect_equal(as.character(as.atc(c("nitro", "cipro"))),
-               c("J01XE01", "J01MA02"))
-
-  # EARS-Net
-  expect_equal(as.character(as.atc("AMX")),
-               "J01CA04")
-
   expect_equal(as.character(as.ab("Phloxapen")),
                "FLC")
 

tests/testthat/test-atc.R

@@ -1,39 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# Antimicrobial Resistance (AMR) Analysis                              #
-#                                                                      #
-# SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
-#                                                                      #
-# LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
-#                                                                      #
-# 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.                                        #
-#                                                                      #
-# 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.gitlab.io/AMR.    #
-# ==================================================================== #
-
-context("ab.R")
-
-test_that("as.atc works", {
-  expect_identical(class(as.atc("amox")), "atc")
-  expect_true(is.atc(as.atc("amox")))
-  expect_output(print(as.atc("amox")))
-  expect_output(print(data.frame(a = as.atc("amox"))))
-
-  expect_identical(class(pull(antibiotics, atc)), "atc")
-
-  expect_warning(as.atc("Z00ZZ00")) # not yet availatcle in data set
-  expect_warning(as.atc("UNKNOWN"))
-
-  expect_output(print(as.atc("amox")))
-
-
-
-})

tests/testthat/test-deprecated.R

@@ -23,18 +23,16 @@ context("deprecated.R")
 
 test_that("deprecated functions work", {
 
-  expect_error(suppressWarnings(ratio("A")))
-  expect_error(suppressWarnings(ratio(1, ratio = "abc")))
-  expect_error(suppressWarnings(ratio(c(1, 2), ratio = c(1, 2, 3))))
-  expect_warning(ratio(c(772, 1611, 737), ratio = "1:2:1"))
-  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))
+  # first 5 chars of official name
+  expect_equal(suppressWarnings(as.character(as.atc(c("nitro", "cipro")))),
+               c("J01XE01", "J01MA02"))
 
-  expect_warning(atc_property("amox"))
-  expect_warning(atc_official("amox"))
-  expect_warning(ab_official("amox"))
-  expect_warning(atc_name("amox"))
-  expect_warning(atc_trivial_nl("amox"))
-  expect_warning(atc_tradenames("amox"))
+  # EARS-Net
+  expect_equal(suppressWarnings(as.character(as.atc("AMX"))),
+               "J01CA04")
 
+  expect_equal(suppressWarnings(guess_ab_col(data.frame(AMP_ND10 = "R",
+                                                        AMC_ED20 = "S"),
+                                             as.atc("augmentin"))),
+               "AMC_ED20")
 })

tests/testthat/test-ggplot_rsi.R

@@ -36,32 +36,31 @@ test_that("ggplot_rsi works", {
       summarise_all(portion_IR) %>% as.double()
   )
 
+  print(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))
+  print(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))
+
   expect_equal(
-    (septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "Interpretation", facet = "Antibiotic"))$data %>%
+    (septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>%
       summarise_all(portion_IR) %>% as.double(),
     septic_patients %>% select(AMC, CIP) %>%
       summarise_all(portion_IR) %>% as.double()
   )
 
   expect_equal(
-    (septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "Antibiotic", facet = "Interpretation"))$data %>%
+    (septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>%
       summarise_all(portion_IR) %>% as.double(),
     septic_patients %>% select(AMC, CIP) %>%
       summarise_all(portion_IR) %>% as.double()
   )
 
   expect_equal(
-    (septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "Antibiotic",
-                                                           facet = "Interpretation",
-                                                           fun = count_df))$data %>%
+    (septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic",
+                                                         facet = "interpretation"))$data %>%
       summarise_all(count_IR) %>% as.double(),
     septic_patients %>% select(AMC, CIP) %>%
       summarise_all(count_IR) %>% as.double()
   )
 
-  expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
-  expect_error(geom_rsi(septic_patients, fun = "invalid"))
-
   # support for scale_type ab and mo
   expect_equal(class((data.frame(mo = as.mo(c("e. coli", "s aureus")),
                                  n = c(40, 100)) %>%

tests/testthat/test-guess_ab_col.R

@@ -40,6 +40,5 @@ test_that("guess_ab_col works", {
                "AMP_ND10")
   expect_equal(guess_ab_col(df, "J01CR02"),
                "AMC_ED20")
-  expect_equal(guess_ab_col(df, as.atc("augmentin")),
-               "AMC_ED20")
+
 })