(v2.1.1.9186) replace antibiotics with antimicrobials!

tests/testthat/test-ggplot_sir.R

@@ -27,111 +27,113 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE) &&
-  AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
-  pdf(NULL) # prevent Rplots.pdf being created
+test_that("ggplot_sir works", {
+  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE) &&
+    AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
+    pdf(NULL) # prevent Rplots.pdf being created
 
-  # data should be equal
-  expect_equal(
-    (example_isolates %>%
-      select(AMC, CIP) %>%
-      ggplot_sir())$data %>%
-      summarise_all(resistance) %>%
-      as.double(),
-    example_isolates %>%
-      select(AMC, CIP) %>%
-      summarise_all(resistance) %>%
-      as.double()
-  )
+    # data should be equal
+    expect_equal(
+      (example_isolates %>%
+        select(AMC, CIP) %>%
+        ggplot_sir())$data %>%
+        summarise_all(resistance) %>%
+        as.double(),
+      example_isolates %>%
+        select(AMC, CIP) %>%
+        summarise_all(resistance) %>%
+        as.double()
+    )
 
-  expect_inherits(
-    example_isolates %>%
-      select(AMC, CIP) %>%
-      ggplot_sir(x = "interpretation", facet = "antibiotic"),
-    "gg"
-  )
-  expect_inherits(
-    example_isolates %>%
-      select(AMC, CIP) %>%
-      ggplot_sir(x = "antibiotic", facet = "interpretation"),
-    "gg"
-  )
+    expect_inherits(
+      example_isolates %>%
+        select(AMC, CIP) %>%
+        ggplot_sir(x = "interpretation", facet = "antibiotic"),
+      "gg"
+    )
+    expect_inherits(
+      example_isolates %>%
+        select(AMC, CIP) %>%
+        ggplot_sir(x = "antibiotic", facet = "interpretation"),
+      "gg"
+    )
 
-  expect_equal(
-    (example_isolates %>%
-      select(AMC, CIP) %>%
-      ggplot_sir(x = "interpretation", facet = "antibiotic"))$data %>%
-      summarise_all(resistance) %>%
-      as.double(),
-    example_isolates %>%
-      select(AMC, CIP) %>%
-      summarise_all(resistance) %>%
-      as.double()
-  )
+    expect_equal(
+      (example_isolates %>%
+        select(AMC, CIP) %>%
+        ggplot_sir(x = "interpretation", facet = "antibiotic"))$data %>%
+        summarise_all(resistance) %>%
+        as.double(),
+      example_isolates %>%
+        select(AMC, CIP) %>%
+        summarise_all(resistance) %>%
+        as.double()
+    )
 
-  expect_equal(
-    (example_isolates %>%
-      select(AMC, CIP) %>%
-      ggplot_sir(x = "antibiotic", facet = "interpretation"))$data %>%
-      summarise_all(resistance) %>%
-      as.double(),
-    example_isolates %>%
-      select(AMC, CIP) %>%
-      summarise_all(resistance) %>%
-      as.double()
-  )
+    expect_equal(
+      (example_isolates %>%
+        select(AMC, CIP) %>%
+        ggplot_sir(x = "antibiotic", facet = "interpretation"))$data %>%
+        summarise_all(resistance) %>%
+        as.double(),
+      example_isolates %>%
+        select(AMC, CIP) %>%
+        summarise_all(resistance) %>%
+        as.double()
+    )
 
-  expect_equal(
-    (example_isolates %>%
-      select(AMC, CIP) %>%
-      ggplot_sir(x = "antibiotic", facet = "interpretation"))$data %>%
-      summarise_all(count_resistant) %>%
-      as.double(),
-    example_isolates %>%
-      select(AMC, CIP) %>%
-      summarise_all(count_resistant) %>%
-      as.double()
-  )
+    expect_equal(
+      (example_isolates %>%
+        select(AMC, CIP) %>%
+        ggplot_sir(x = "antibiotic", facet = "interpretation"))$data %>%
+        summarise_all(count_resistant) %>%
+        as.double(),
+      example_isolates %>%
+        select(AMC, CIP) %>%
+        summarise_all(count_resistant) %>%
+        as.double()
+    )
 
-  # support for scale_type ab and mo
-  expect_inherits(
-    (data.frame(
-      mo = as.mo(c("e. coli", "s aureus")),
-      n = c(40, 100)
-    ) %>%
-      ggplot(aes(x = mo, y = n)) +
-      geom_col())$data,
-    "data.frame"
-  )
-  expect_inherits(
-    (data.frame(
-      ab = as.ab(c("amx", "amc")),
-      n = c(40, 100)
-    ) %>%
-      ggplot(aes(x = ab, y = n)) +
-      geom_col())$data,
-    "data.frame"
-  )
+    # support for scale_type ab and mo
+    expect_inherits(
+      (data.frame(
+        mo = as.mo(c("e. coli", "s aureus")),
+        n = c(40, 100)
+      ) %>%
+        ggplot(aes(x = mo, y = n)) +
+        geom_col())$data,
+      "data.frame"
+    )
+    expect_inherits(
+      (data.frame(
+        ab = as.ab(c("amx", "amc")),
+        n = c(40, 100)
+      ) %>%
+        ggplot(aes(x = ab, y = n)) +
+        geom_col())$data,
+      "data.frame"
+    )
 
-  expect_inherits(
-    (data.frame(
-      ab = as.ab(c("amx", "amc")),
-      n = c(40, 100)
-    ) %>%
-      ggplot(aes(x = ab, y = n)) +
-      geom_col())$data,
-    "data.frame"
-  )
+    expect_inherits(
+      (data.frame(
+        ab = as.ab(c("amx", "amc")),
+        n = c(40, 100)
+      ) %>%
+        ggplot(aes(x = ab, y = n)) +
+        geom_col())$data,
+      "data.frame"
+    )
 
-  # support for manual colours
-  expect_inherits(
-    suppressWarnings((ggplot(data.frame(
-      x = c("Value1", "Value2", "Value3"),
-      y = c(1, 2, 3),
-      z = c("Value4", "Value5", "Value6")
-    )) +
-      geom_col(aes(x = x, y = y, fill = z)) +
-      scale_sir_colours(aesthetics = "fill", Value4 = "S", Value5 = "I", Value6 = "R"))$data),
-    "data.frame"
-  )
-}
+    # support for manual colours
+    expect_inherits(
+      suppressWarnings((ggplot(data.frame(
+        x = c("Value1", "Value2", "Value3"),
+        y = c(1, 2, 3),
+        z = c("Value4", "Value5", "Value6")
+      )) +
+        geom_col(aes(x = x, y = y, fill = z)) +
+        scale_sir_colours(aesthetics = "fill", Value4 = "S", Value5 = "I", Value6 = "R"))$data),
+      "data.frame"
+    )
+  }
+})