(v1.6.0.9000) custom EUCAST rules

tests/testthat/test-eucast_rules.R

@@ -80,11 +80,10 @@ test_that("EUCAST rules work", {
   library(dplyr, warn.conflicts = FALSE)
   expect_equal(suppressWarnings(
     example_isolates %>%
+      filter(mo_family(mo) == "Enterobacteriaceae") %>%
       mutate(TIC = as.rsi("R"),
              PIP = as.rsi("S")) %>%
       eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
-      left_join_microorganisms(by = "mo") %>%
-      filter(family == "Enterobacteriaceae") %>%
       pull(PIP) %>%
       unique() %>%
       as.character()),
@@ -145,3 +144,21 @@ test_that("EUCAST rules work", {
   expect_s3_class(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
   
 })
+
+test_that("Custom EUCAST rules work", {
+  
+  skip_on_cran()
+  x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
+                           AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
+  expect_output(print(x))
+  expect_output(print(c(x, x)))
+  expect_output(print(as.list(x, x)))
+  
+  # this custom rules makes 8 changes
+  expect_equal(nrow(eucast_rules(example_isolates,
+                                 rules = "custom",
+                                 custom_rules = x,
+                                 info = FALSE,
+                                 verbose = TRUE)),
+               8)
+})

tests/testthat/test-kurtosis.R

@@ -28,20 +28,20 @@ context("kurtosis.R")
 test_that("kurtosis works", {
   skip_on_cran()
   expect_equal(kurtosis(example_isolates$age),
-               3.549319,
+               5.227999,
                tolerance = 0.00001)
   
   expect_equal(unname(kurtosis(data.frame(example_isolates$age))),
-               3.549319,
+               5.227999,
                tolerance = 0.00001)
   expect_equal(unname(kurtosis(data.frame(example_isolates$age), excess = TRUE)),
-               0.549319,
+               2.227999,
                tolerance = 0.00001)
   
   expect_equal(kurtosis(matrix(example_isolates$age)),
-               3.549319,
+               5.227999,
                tolerance = 0.00001)
   expect_equal(kurtosis(matrix(example_isolates$age), excess = TRUE),
-               0.549319,
+               2.227999,
                tolerance = 0.00001)
 })

tests/testthat/test-mdro.R

@@ -228,8 +228,11 @@ test_that("mdro works", {
                                   "ERY == 'R' & age > 60" ~ "Elderly Type B",
                                   as_factor = TRUE)
   expect_output(print(custom))
+  expect_output(print(c(custom, custom)))
+  expect_output(print(as.list(custom, custom)))
+  
   expect_output(x <- mdro(example_isolates, guideline = custom, info = TRUE))
-  expect_equal(as.double(table(x)), c(1066, 43, 891))
+  expect_equal(as.double(table(x)), c(1070, 198, 732))
   
   expect_output(print(custom_mdro_guideline(AMX == "R" ~ "test", as_factor = FALSE)))
   expect_error(custom_mdro_guideline())

tests/testthat/test-skewness.R

@@ -28,12 +28,12 @@ context("skewness.R")
 test_that("skewness works", {
   skip_on_cran()
   expect_equal(skewness(example_isolates$age),
-               -0.8958019,
+               -1.212888,
                tolerance = 0.00001)
   expect_equal(unname(skewness(data.frame(example_isolates$age))),
-               -0.8958019,
+               -1.212888,
                tolerance = 0.00001)
   expect_equal(skewness(matrix(example_isolates$age)),
-               -0.8958019,
+               -1.212888,
                tolerance = 0.00001)
 })