unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9124
+Version: 1.8.2.9125
 Date: 2023-02-14
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9124
+# AMR 1.8.2.9125
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

inst/tinytest/test-age.R

@@ -49,15 +49,8 @@ expect_error(age(
   reference = c("2019-01-01", "2019-01-01")
 ))
 
-# expect_warning(age(
+# expect_warning(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"), reference = "1975-01-01"))
-  x = c("1980-01-01", "1985-01-01", "1990-01-01"),
+# expect_warning(age(x = c("1800-01-01", "1805-01-01", "1810-01-01"), reference = "2019-01-01"))
-  reference = "1975-01-01"
-))
-
-# expect_warning(age(
-  x = c("1800-01-01", "1805-01-01", "1810-01-01"),
-  reference = "2019-01-01"
-))
 
 expect_equal(
   length(age(x = c("2019-01-01", NA), na.rm = TRUE)),

inst/tinytest/test-count.R

@@ -47,10 +47,7 @@ expect_equal(
 # warning for speed loss
 # expect_warning(count_resistant(as.character(example_isolates$AMC)))
 
-# expect_warning(count_resistant(
+# expect_warning(count_resistant(example_isolates$AMC, as.character(example_isolates$GEN)))
-  example_isolates$AMC,
-  as.character(example_isolates$GEN)
-))
 
 # check for errors
 expect_error(count_resistant("test", minimum = "test"))

inst/tinytest/test-g.test.R

@@ -63,11 +63,7 @@ x <- as.data.frame(
 # expect_warning(g.test(x))
 expect_true(suppressWarnings(g.test(x)$p.value) < 1)
 
-# expect_warning(g.test(
+# expect_warning(g.test(x = c(772, 1611, 737), y = c(780, 1560, 780), rescale.p = TRUE))
-  x = c(772, 1611, 737),
-  y = c(780, 1560, 780),
-  rescale.p = TRUE
-))
 
 expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
 expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))

inst/tinytest/test-mdro.R

@@ -272,10 +272,10 @@ expect_error(custom_mdro_guideline("test"))
 expect_error(custom_mdro_guideline("test" ~ c(1:3)))
 expect_error(custom_mdro_guideline("test" ~ A))
 # expect_warning(mdro(example_isolates,
-  # since `test` gives an error, it will be ignored with a warning
+#   # since `test` gives an error, it will be ignored with a warning
-  guideline = custom_mdro_guideline(test ~ "A"),
+#   guideline = custom_mdro_guideline(test ~ "A"),
-  info = FALSE
+#   info = FALSE
-))
+# ))
 
 # print groups
 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {

inst/tinytest/test-proportion.R

@@ -115,15 +115,9 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
 
 # expect_warning(proportion_R(as.character(example_isolates$AMC)))
 # expect_warning(proportion_S(as.character(example_isolates$AMC)))
-# expect_warning(proportion_S(as.character(
+# expect_warning(proportion_S(as.character(example_isolates$AMC, example_isolates$GEN)))
-  example_isolates$AMC,
-  example_isolates$GEN
-)))
 
-# expect_warning(n_sir(as.character(
+# expect_warning(n_sir(as.character(example_isolates$AMC, example_isolates$GEN)))
-  example_isolates$AMC,
-  example_isolates$GEN
-)))
 expect_equal(
   suppressWarnings(n_sir(as.character(
     example_isolates$AMC,

inst/tinytest/test-rsi.R

@@ -236,10 +236,7 @@ expect_inherits(
   ))$amoxi),
   "sir"
 )
-# expect_warning(as.sir(data.frame(
+# expect_warning(as.sir(data.frame(mo = "E. coli", NIT = c("<= 2", 32))))
-  mo = "E. coli",
-  NIT = c("<= 2", 32)
-)))
 expect_message(as.sir(data.frame(
   mo = "E. coli",
   NIT = c("<= 2", 32),