CI tests

tests/testthat/test-ab.R

@@ -36,6 +36,9 @@ test_that("as.ab works", {
 
   expect_identical(class(as.ab("amox")), "ab")
   expect_identical(class(pull(antibiotics, ab)), "ab")
+  expect_true(is.ab(as.ab("amox")))
+  expect_output(print(as.ab("amox")))
+  expect_output(print(data.frame(a = as.ab("amox"))))
 
   expect_warning(as.ab("Z00ZZ00")) # not yet available in data set
   expect_warning(as.ab("UNKNOWN"))

tests/testthat/test-atc.R

@@ -0,0 +1,39 @@
+# ==================================================================== #
+# 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-count.R

@@ -51,8 +51,7 @@ test_that("counts work", {
   # count_df
   expect_equal(
     septic_patients %>% select(AMX) %>% count_df() %>% pull(Value),
-    c(septic_patients$AMX %>% count_S(),
-      septic_patients$AMX %>% count_I(),
+    c(septic_patients$AMX %>% count_SI(),
       septic_patients$AMX %>% count_R())
   )
   expect_equal(
@@ -60,6 +59,12 @@ test_that("counts work", {
     c(septic_patients$AMX %>% count_S(),
       septic_patients$AMX %>% count_IR())
   )
+  expect_equal(
+    septic_patients %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(Value),
+    c(septic_patients$AMX %>% count_S(),
+      septic_patients$AMX %>% count_I(),
+      septic_patients$AMX %>% count_R())
+  )
 
   # warning for speed loss
   expect_warning(count_R(as.character(septic_patients$AMC)))

tests/testthat/test-portion.R

@@ -101,8 +101,7 @@ test_that("portions works", {
   # portion_df
   expect_equal(
     septic_patients %>% select(AMX) %>% portion_df() %>% pull(Value),
-    c(septic_patients$AMX %>% portion_S(),
-      septic_patients$AMX %>% portion_I(),
+    c(septic_patients$AMX %>% portion_SI(),
       septic_patients$AMX %>% portion_R())
   )
   expect_equal(
@@ -110,6 +109,12 @@ test_that("portions works", {
     c(septic_patients$AMX %>% portion_S(),
       septic_patients$AMX %>% portion_IR())
   )
+  expect_equal(
+    septic_patients %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(Value),
+    c(septic_patients$AMX %>% portion_S(),
+      septic_patients$AMX %>% portion_I(),
+      septic_patients$AMX %>% portion_R())
+  )
 
 
 })

tests/testthat/test-rsi.R

@@ -54,3 +54,53 @@ test_that("rsi works", {
                40)
 
 })
+
+test_that("mic2rsi works", {
+  expect_equal(as.character(
+    as.rsi(x = as.mic(0.125),
+                      mo = "B_STRPT_PNE",
+                      ab = "AMX",
+                      guideline = "EUCAST")),
+    "S")
+  expect_equal(as.character(
+    as.rsi(x = as.mic(4),
+           mo = "B_STRPT_PNE",
+           ab = "AMX",
+           guideline = "EUCAST")),
+    "R")
+
+  expect_true(septic_patients %>%
+                mutate(amox_mic = as.mic(2)) %>%
+                select(mo, amox_mic) %>%
+                as.rsi() %>%
+                pull(amox_mic) %>%
+                is.rsi())
+})
+
+test_that("disk2rsi works", {
+  expect_equal(as.character(
+    as.rsi(x = as.disk(22),
+           mo = "B_STRPT_PNE",
+           ab = "ERY",
+           guideline = "CLSI")),
+    "S")
+  expect_equal(as.character(
+    as.rsi(x = as.disk(18),
+           mo = "B_STRPT_PNE",
+           ab = "ERY",
+           guideline = "CLSI")),
+    "I")
+  expect_equal(as.character(
+    as.rsi(x = as.disk(10),
+           mo = "B_STRPT_PNE",
+           ab = "ERY",
+           guideline = "CLSI")),
+    "R")
+
+  expect_true(septic_patients %>%
+                mutate(amox_disk = as.disk(15)) %>%
+                select(mo, amox_disk) %>%
+                as.rsi(guideline = "CLSI") %>%
+                pull(amox_disk) %>%
+                is.rsi())
+})