new EUCAST rules: clinical breakpoints

tests/testthat/test-count.R

@@ -2,18 +2,18 @@ context("count.R")
 
 test_that("counts work", {
   # amox resistance in `septic_patients`
-  expect_equal(count_R(septic_patients$amox), 662)
+  expect_equal(count_R(septic_patients$amox), 683)
   expect_equal(count_I(septic_patients$amox), 3)
-  expect_equal(count_S(septic_patients$amox), 335)
+  expect_equal(count_S(septic_patients$amox), 486)
   expect_equal(count_R(septic_patients$amox) + count_I(septic_patients$amox),
                count_IR(septic_patients$amox))
   expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
                count_SI(septic_patients$amox))
 
   library(dplyr)
-  expect_equal(septic_patients %>% count_S(amcl), 1057)
-  expect_equal(septic_patients %>% count_S(amcl, gent), 1396)
-  expect_equal(septic_patients %>% count_all(amcl, gent), 1517)
+  expect_equal(septic_patients %>% count_S(amcl), 1291)
+  expect_equal(septic_patients %>% count_S(amcl, gent), 1609)
+  expect_equal(septic_patients %>% count_all(amcl, gent), 1747)
   expect_identical(septic_patients %>% count_all(amcl, gent),
                    septic_patients %>% count_S(amcl, gent) +
                      septic_patients %>% count_IR(amcl, gent))

tests/testthat/test-eucast.R

@@ -8,30 +8,26 @@ test_that("EUCAST rules work", {
   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
+  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
+  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, info = FALSE)), b)
   expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
 
-  a <- data.frame(mo =
-                    c("STAAUR",  # Staphylococcus aureus
-                      "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
-                  coli = "-",           # Colistin
+  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
+  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, info = FALSE)), b)
 
@@ -48,17 +44,35 @@ test_that("EUCAST rules work", {
       unique() %>%
       as.character()),
     "R")
+
   # azit and clar must be equal to eryt
-  expect_equal(suppressWarnings(
+  a <- suppressWarnings(
     septic_patients %>%
-      mutate(azit = as.rsi("R"),
-             clar = as.rsi("R")) %>%
+      transmute(mo,
+                eryt,
+                azit = as.rsi("R"),
+                clar = as.rsi("R")) %>%
       EUCAST_rules(col_mo = "mo") %>%
-      pull(clar)),
-    suppressWarnings(
-      septic_patients %>%
-        EUCAST_rules(col_mo = "mo") %>%
-        left_join_microorganisms() %>%
-        pull(eryt)))
+      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_message(suppressWarnings(EUCAST_rules(septic_patients, verbose = TRUE)))
 
 })

tests/testthat/test-portion.R

@@ -2,8 +2,8 @@ context("portion.R")
 
 test_that("portions works", {
   # amox resistance in `septic_patients`
-  expect_equal(portion_R(septic_patients$amox), 0.662, tolerance = 0.0001)
-  expect_equal(portion_I(septic_patients$amox), 0.003, tolerance = 0.0001)
+  expect_equal(portion_R(septic_patients$amox), 0.5827645, tolerance = 0.0001)
+  expect_equal(portion_I(septic_patients$amox), 0.0025597, tolerance = 0.0001)
   expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
                portion_S(septic_patients$amox))
   expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
@@ -12,17 +12,17 @@ test_that("portions works", {
                portion_SI(septic_patients$amox))
 
   expect_equal(septic_patients %>% portion_S(amcl),
-               0.6706853,
+               0.7062363,
                tolerance = 0.001)
   expect_equal(septic_patients %>% portion_S(amcl, gent),
-               0.9202373,
+               0.9210074,
                tolerance = 0.001)
 
   # amcl+genta susceptibility around 92.1%
   expect_equal(suppressWarnings(rsi(septic_patients$amcl,
                                     septic_patients$gent,
                                     interpretation = "S")),
-               0.9202373,
+               0.9210074,
                tolerance = 0.000001)
 
   # percentages
@@ -57,7 +57,7 @@ test_that("portions works", {
                                     septic_patients$gent)))
   expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
                                                    septic_patients$gent))),
-               1576)
+               1828)
 
   # check for errors
   expect_error(portion_IR("test", minimum = "test"))
@@ -83,16 +83,16 @@ test_that("portions works", {
 })
 
 test_that("old rsi works", {
-  # amox resistance in `septic_patients` should be around 66.33%
-  expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.665, tolerance = 0.0001)
-  expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.665, tolerance = 0.0001)
+  # amox resistance in `septic_patients` should be around 58.53%
+  expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5853, tolerance = 0.0001)
+  expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5853, tolerance = 0.0001)
 
   # pita+genta susceptibility around 98.09%
   expect_equal(suppressWarnings(rsi(septic_patients$pita,
                                     septic_patients$gent,
                                     interpretation = "S",
                                     info = TRUE)),
-               0.9540412,
+               0.9498886,
                tolerance = 0.0001)
 
   # count of cases