(v1.1.0.9004) lose dependencies

tests/testthat/test-eucast_rules.R

@@ -24,24 +24,24 @@ context("eucast_rules.R")
 test_that("EUCAST rules work", {
   
   skip_on_cran()
-
+  
   # thoroughly check input table
   expect_equal(colnames(eucast_rules_file),
                c("if_mo_property", "like.is.one_of", "this_value",
                  "and_these_antibiotics", "have_these_values",
                  "then_change_these_antibiotics", "to_value",
                  "reference.rule", "reference.rule_group"))
-
+  
   expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
   expect_error(eucast_rules(x = "text"))
   expect_error(eucast_rules(data.frame(a = "test")))
   expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
   
   expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE)))
-
+  
   expect_identical(colnames(example_isolates),
                    colnames(suppressWarnings(eucast_rules(example_isolates))))
-
+  
   a <- data.frame(mo = c("Klebsiella pneumoniae",
                          "Pseudomonas aeruginosa",
                          "Enterobacter aerogenes"),
@@ -54,7 +54,7 @@ test_that("EUCAST rules work", {
                   stringsAsFactors = FALSE)
   expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
   expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
-
+  
   a <- data.frame(mo = c("Staphylococcus aureus",
                          "Streptococcus group A"),
                   COL = "-",       # Colistin
@@ -64,7 +64,7 @@ test_that("EUCAST rules work", {
                   COL = "R",       # Colistin
                   stringsAsFactors = FALSE)
   expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
-
+  
   # piperacillin must be R in Enterobacteriaceae when tica is R
   library(dplyr)
   expect_equal(suppressWarnings(
@@ -78,25 +78,17 @@ test_that("EUCAST rules work", {
       unique() %>%
       as.character()),
     "R")
-
+  
   # Azithromicin and Clarythromycin must be equal to Erythromycin
-  a <- suppressWarnings(
-    example_isolates %>%
-      transmute(mo,
-                ERY,
-                AZM = as.rsi("R"),
-                CLR = as.rsi("R")) %>%
-      eucast_rules(col_mo = "mo") %>%
-      pull(CLR))
-  b <-   suppressWarnings(
-    example_isolates %>%
-      select(mo, ERY) %>%
-      eucast_rules(col_mo = "mo") %>%
-      pull(ERY))
-
+  a <- eucast_rules(data.frame(mo = example_isolates$mo,
+                               ERY = example_isolates$ERY,
+                               AZM = as.rsi("R"),
+                               CLR = as.rsi("R"),
+                               stringsAsFactors = FALSE))$CLR
+  b <- example_isolates$ERY
   expect_identical(a[!is.na(b)],
                    b[!is.na(b)])
-
+  
   # amox is inferred by benzylpenicillin in Kingella kingae
   expect_equal(
     suppressWarnings(
@@ -108,11 +100,11 @@ test_that("EUCAST rules work", {
         , info = FALSE))$AMX
     ),
     "S")
-
+  
   # also test norf
   expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
-
+  
   # check verbose output
   expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, info = TRUE)))
-
+  
 })