new antibiotics

tests/testthat/test-eucast_rules.R

@@ -52,11 +52,11 @@ test_that("EUCAST rules work", {
 
   a <- data.frame(mo = c("Staphylococcus aureus",
                          "Streptococcus group A"),
-                  coli = "-",       # Colistin
+                  COL = "-",       # Colistin
                   stringsAsFactors = FALSE)
   b <- data.frame(mo = c("Staphylococcus aureus",
                          "Streptococcus group A"),
-                  coli = "R",       # Colistin
+                  COL = "R",       # Colistin
                   stringsAsFactors = FALSE)
   expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
 
@@ -64,30 +64,30 @@ test_that("EUCAST rules work", {
   library(dplyr)
   expect_equal(suppressWarnings(
     septic_patients %>%
-      mutate(tica = as.rsi("R"),
-             pipe = as.rsi("S")) %>%
+      mutate(TIC = as.rsi("R"),
+             PIP = as.rsi("S")) %>%
       eucast_rules(col_mo = "mo") %>%
       left_join_microorganisms() %>%
       filter(family == "Enterobacteriaceae") %>%
-      pull(pipe) %>%
+      pull(PIP) %>%
       unique() %>%
       as.character()),
     "R")
 
-  # azit and clar must be equal to eryt
+  # Azithromicin and Clarythromycin must be equal to Erythromycin
   a <- suppressWarnings(
     septic_patients %>%
       transmute(mo,
-                eryt,
-                azit = as.rsi("R"),
-                clar = as.rsi("R")) %>%
+                ERY,
+                AZM = as.rsi("R"),
+                CLR = as.rsi("R")) %>%
       eucast_rules(col_mo = "mo") %>%
-      pull(clar))
+      pull(CLR))
   b <-   suppressWarnings(
     septic_patients %>%
-      select(mo, eryt) %>%
+      select(mo, ERY) %>%
       eucast_rules(col_mo = "mo") %>%
-      pull(eryt))
+      pull(ERY))
 
   expect_identical(a[!is.na(b)],
                    b[!is.na(b)])
@@ -97,15 +97,15 @@ test_that("EUCAST rules work", {
     suppressWarnings(
       as.list(eucast_rules(
         data.frame(mo = as.mo("Kingella kingae"),
-                   peni = "S",
-                   amox = "-",
+                   PEN = "S",
+                   AMX = "-",
                    stringsAsFactors = FALSE)
-        , info = FALSE))$amox
+        , info = FALSE))$AMX
     ),
     "S")
 
   # also test norf
-  expect_output(suppressWarnings(eucast_rules(septic_patients %>% mutate(norf = "S", nali = "S"))))
+  expect_output(suppressWarnings(eucast_rules(septic_patients %>% mutate(NOR = "S", NAL = "S"))))
 
   # check verbose output
   expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))