ggplot_rsi example update, more unit tests

tests/testthat/test-atc.R

@@ -33,10 +33,13 @@ test_that("guess_atc works", {
                rep("J01FA01", 8))
 
   expect_identical(class(as.atc("amox")), "atc")
-
+  expect_identical(class(pull(antibiotics, atc)), "atc")
   expect_identical(ab_trivial_nl("Cefmenoxim"), "Cefmenoxim")
 
   expect_warning(as.atc("Z00ZZ00")) # not yet available in data set
+  expect_warning(as.atc("UNKNOWN"))
+
+  expect_output(print(as.atc("amox")))
 
   # first 5 chars of official name
   expect_equal(as.character(as.atc(c("nitro", "cipro"))),

tests/testthat/test-bactid.R

@@ -10,10 +10,13 @@ test_that("as.bactid works", {
   expect_equal(as.character(as.bactid("Escherichia  species")), "ESC")
   expect_equal(as.character(as.bactid(" ESCCOL ")), "ESCCOL")
   expect_equal(as.character(as.bactid("klpn")), "KLEPNE")
+  expect_equal(as.character(as.bactid("Klebsiella")), "KLE")
+  expect_equal(as.character(as.bactid("coagulase negative")), "STACNS")
 
   expect_equal(as.character(as.bactid("P. aer")), "PSEAER") # not Pasteurella aerogenes
 
   expect_equal(as.character(as.bactid("Negative rods")), "GNR")
+  expect_equal(as.character(as.bactid("Gram negative rods")), "GNR")
 
   # GLIMS
   expect_equal(as.character(as.bactid("shiboy")), "SHIBOY")
@@ -65,6 +68,8 @@ test_that("as.bactid works", {
   expect_identical(as.character(guess_bactid("S. salivarius",  Lancefield = FALSE)),  "STCSAL")
   expect_identical(as.character(guess_bactid("S. salivarius",  Lancefield = TRUE)),   "STCGRK") # group K
 
+  library(dplyr)
+
   # select with one column
   expect_identical(
     septic_patients[1:10,] %>%
@@ -88,6 +93,9 @@ test_that("as.bactid works", {
   # unknown results
   expect_warning(as.bactid(c("INVALID", "Yeah, unknown")))
 
+  # too many columns
+  expect_error(septic_patients %>% select(1:3) %>% as.bactid())
+
   # print
   expect_output(print(as.bactid(c("ESCCOL", NA))))
 

tests/testthat/test-eucast.R

@@ -1,6 +1,10 @@
 context("eucast.R")
 
 test_that("EUCAST rules work", {
+
+  expect_error(EUCAST_rules(septic_patients, col_bactid = "Non-existing"))
+
+
   expect_identical(colnames(septic_patients),
                    colnames(suppressWarnings(EUCAST_rules(septic_patients))))
 
@@ -31,4 +35,31 @@ test_that("EUCAST rules work", {
                   coli = "R",           # Colistin
                   stringsAsFactors = FALSE)
   expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
+
+  # pita must be R in Enterobacteriaceae when tica is R
+  library(dplyr)
+  expect_equal(suppressWarnings(
+    septic_patients %>%
+      mutate(tica = as.rsi("R"),
+             pita = as.rsi("S")) %>%
+      EUCAST_rules(col_bactid = "bactid") %>%
+      left_join_microorganisms() %>%
+      filter(family == "Enterobacteriaceae") %>%
+      pull(pita) %>%
+      unique() %>%
+      as.character()),
+    "R")
+  # azit and clar must be equal to eryt
+  expect_equal(suppressWarnings(
+    septic_patients %>%
+      mutate(azit = as.rsi("R"),
+             clar = as.rsi("R")) %>%
+      EUCAST_rules(col_bactid = "bactid") %>%
+      pull(clar)),
+    suppressWarnings(
+      septic_patients %>%
+        EUCAST_rules(col_bactid = "bactid") %>%
+        left_join_microorganisms() %>%
+        pull(eryt)))
+
 })

tests/testthat/test-first_isolate.R

@@ -25,6 +25,20 @@ test_that("first isolates work", {
                       info = TRUE),
         na.rm = TRUE)),
     1426)
+  # and 1449 when not ignoring I
+  expect_equal(
+    suppressWarnings(
+      sum(
+        first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
+                      col_date = "date",
+                      col_patient_id = "patient_id",
+                      col_bactid = "bactid",
+                      col_keyantibiotics = "keyab",
+                      ignore_I = FALSE,
+                      type = "keyantibiotics",
+                      info = TRUE),
+        na.rm = TRUE)),
+    1449)
   # and 1430 when using points
   expect_equal(
     suppressWarnings(
@@ -86,10 +100,34 @@ test_that("first isolates work", {
       na.rm = TRUE),
     1501)
 
+  # "No isolates found"
   expect_message(septic_patients %>%
                    mutate(specimen = "test") %>%
                    mutate(first = first_isolate(., "date", "patient_id",
-                                                col_bactid = "bactid", col_specimen = "specimen",
-                                                filter_specimen = "something_unexisting")))
+                                                col_bactid = "bactid",
+                                                col_specimen = "specimen",
+                                                filter_specimen = "something_unexisting",
+                                                output_logical = FALSE)))
+
+  # printing of exclusion message
+  expect_output(septic_patients %>%
+                            first_isolate(col_date = "date",
+                                          col_bactid = "bactid",
+                                          col_patient_id = "patient_id",
+                                          col_testcode = "sex",
+                                          testcodes_exclude = "M"))
+
+  # errors
   expect_error(first_isolate("date", "patient_id", col_bactid = "bactid"))
+  expect_error(first_isolate(septic_patients))
+  expect_error(first_isolate(septic_patients,
+                             col_date = "non-existing col",
+                             col_bactid = "bactid"))
+
+  expect_warning(septic_patients %>%
+                   mutate(bactid = as.character(bactid)) %>%
+                   first_isolate(col_date = "date",
+                                 col_bactid = "bactid",
+                                 col_patient_id = "patient_id"))
+
 })