(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

tests/testthat/test-_all_examples.R

@@ -0,0 +1,37 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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 more info: https://msberends.github.io/AMR.    #
+# ==================================================================== #
+
+# context("All examples")
+# 
+# # run all examples (will take forever)
+# exported_functions <- ls("package:AMR")
+# 
+# for (i in seq_len(length(exported_functions))) {
+#   test_that(paste(exported_functions[i], "works"), {
+#     skip_on_cran()
+#     expect_output(suppressWarnings(example(exported_functions[i], 
+#                                            package = "AMR", 
+#                                            give.lines = TRUE,
+#                                            run.dontrun = TRUE,
+#                                            run.donttest = TRUE)),
+#                   label = paste0("Examples of function ", exported_functions[i]))
+#   })
+# }

tests/testthat/test-ab.R

@@ -37,7 +37,7 @@ test_that("as.ab works", {
                rep("ERY", 10))
 
   expect_identical(class(as.ab("amox")), c("ab", "character"))
-  expect_identical(class(pull(antibiotics, ab)), 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"))))

tests/testthat/test-ab_property.R

@@ -41,7 +41,7 @@ test_that("ab_property works", {
   expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
   expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
 
-  expect_identical(ab_ddd("AMX", "oral"), 1)
+  expect_identical(ab_ddd("AMX", "oral"), 1.5)
   expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g")
   expect_identical(ab_ddd("AMX", "iv"), 1)
   expect_identical(ab_ddd("AMX", "iv", units = TRUE), "g")

tests/testthat/test-mic.R

@@ -42,9 +42,10 @@ test_that("mic works", {
   barplot(as.mic(c(1, 2, 4, 8)))
   plot(as.mic(c(1, 2, 4, 8)))
   print(as.mic(c(1, 2, 4, 8)))
-
-  expect_equal(summary(as.mic(c(2, 8))), c("Class" = "mic",
-                                           "<NA>" = "0",
-                                           "Min." = "2",
-                                           "Max." = "8"))
+  
+  expect_equal(summary(as.mic(c(2, 8))), 
+               structure(c("Class" = "mic",
+                           "<NA>" = "0",
+                           "Min." = "2",
+                           "Max." = "8"), class = c("summaryDefault", "table")))
 })

tests/testthat/test-rsi.R

@@ -81,7 +81,7 @@ test_that("mic2rsi works", {
            mo = "B_STRPT_PNMN",
            ab = "AMX",
            guideline = "EUCAST")),
-    "R")
+    "I")
 
   expect_true(example_isolates %>%
                 mutate(amox_mic = as.mic(2)) %>%