MDRO update

2025-07-12 01:42:08 +02:00 · 2018-11-16 20:50:50 +01:00
parent fab64e6728
commit 4fcc2b409a
10 changed files with 207 additions and 186 deletions
--- a/tests/testthat/test-eucast_rules.R
+++ b/tests/testthat/test-eucast_rules.R
@ -0,0 +1,78 @@
+context("eucast_rules.R")
+
+test_that("EUCAST rules work", {
+
+  expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
+
+  expect_identical(colnames(septic_patients),
+                   colnames(suppressWarnings(eucast_rules(septic_patients))))
+
+  a <- data.frame(mo = c("KLEPNE",  # Klebsiella pneumoniae
+                         "PSEAER",  # Pseudomonas aeruginosa
+                         "ENTAER"), # Enterobacter aerogenes
+                  amox = "-",           # Amoxicillin
+                  stringsAsFactors = FALSE)
+  b <- data.frame(mo = c("KLEPNE",  # Klebsiella pneumoniae
+                         "PSEAER",  # Pseudomonas aeruginosa
+                         "ENTAER"), # Enterobacter aerogenes
+                  amox = "R",       # Amoxicillin
+                  stringsAsFactors = FALSE)
+  expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
+  expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
+  expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
+
+  a <- data.frame(mo = c("STAAUR",  # Staphylococcus aureus
+                         "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "-",       # Colistin
+                  stringsAsFactors = FALSE)
+  b <- data.frame(mo = c("STAAUR",  # Staphylococcus aureus
+                         "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "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(
+    septic_patients %>%
+      mutate(tica = as.rsi("R"),
+             pipe = as.rsi("S")) %>%
+      eucast_rules(col_mo = "mo") %>%
+      left_join_microorganisms() %>%
+      filter(family == "Enterobacteriaceae") %>%
+      pull(pipe) %>%
+      unique() %>%
+      as.character()),
+    "R")
+
+  # azit and clar must be equal to eryt
+  a <- suppressWarnings(
+    septic_patients %>%
+      transmute(mo,
+                eryt,
+                azit = as.rsi("R"),
+                clar = as.rsi("R")) %>%
+      eucast_rules(col_mo = "mo") %>%
+      pull(clar))
+  b <-   suppressWarnings(
+    septic_patients %>%
+      select(mo, eryt) %>%
+      eucast_rules(col_mo = "mo") %>%
+      pull(eryt))
+
+  expect_identical(a[!is.na(b)],
+                   b[!is.na(b)])
+
+  # amox is inferred by benzylpenicillin in Kingella kingae
+  expect_equal(
+    as.list(eucast_rules(
+      data.frame(mo = as.mo("Kingella kingae"),
+                 peni = "S",
+                 amox = "-",
+                 stringsAsFactors = FALSE)
+      , info = FALSE))$amox,
+    "S")
+
+  expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))
+
+})