more unit tests

NEWS.md

@@ -1,4 +1,6 @@
 # 0.2.0.90xx (development version)
+**Published on CRAN: (unpublished)**
+
 #### New
 * **BREAKING**: `rsi_df` was removed in favour of new functions `R`, `IR`, `SI` and `S` to selectively calculate resistance or susceptibility. These functions use **hybrid evaluation**, which means that calculations are not done in R directly but rather in C++ using the `Rcpp` package, making them 20 to 30 times faster. The function `rsi` still works, but is deprecated.
 * **BREAKING**: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call *key antibiotics*) to include more first isolates (afterwards called first *weighted* isolates) are now as follows:
@@ -53,6 +55,8 @@
 * Unit testing for R 3.0 and the latest available release: https://travis-ci.org/msberends/AMR
 
 # 0.2.0 (latest stable version)
+**Published on CRAN: 2018-05-03**
+
 #### New
 * Full support for Windows, Linux and macOS
 * Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
@@ -88,6 +92,8 @@
 * Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
 
 # 0.1.1
+**Published on CRAN: 2018-03-14**
+
 * `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
 * Edited column names to comply with GLIMS, the laboratory information system
 * Added more valid MIC values
@@ -95,4 +101,6 @@
 * Added barplots for `rsi` and `mic` classes
 
 # 0.1.0
+**Published on CRAN: 2018-02-22**
+
 * First submission to CRAN.

R/eucast.R

@@ -275,7 +275,7 @@ EUCAST_rules <- function(tbl,
 
   # join to microorganisms data set
   if (!tbl %>% pull(col_bactid) %>% is.bactid()) {
-    # warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
+    warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
   }
   tbl <- tbl %>% left_join_microorganisms(by = col_bactid, suffix = c("_tempmicroorganisms", ""))
 

R/first_isolate.R

@@ -171,7 +171,7 @@ first_isolate <- function(tbl,
 
   if (!is.na(col_bactid)) {
     if (!tbl %>% pull(col_bactid) %>% is.bactid()) {
-      # warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
+      warning("Improve integrity of the `", col_bactid, "` column by transforming it with 'as.bactid'.")
     }
     # join to microorganisms data set
     tbl <- tbl %>% left_join_microorganisms(by = col_bactid)

tests/testthat/test-eucast.R

@@ -16,7 +16,8 @@ test_that("EUCAST rules work", {
                       "ENTAER"), # Enterobacter aerogenes
                   amox = "R",           # Amoxicillin
                   stringsAsFactors = FALSE)
-  expect_identical(EUCAST_rules(a, info = FALSE), b)
+  expect_warning(EUCAST_rules(a, info = FALSE))
+  expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
   expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
 
   a <- data.frame(bactid =
@@ -29,7 +30,7 @@ test_that("EUCAST rules work", {
                       "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
                   coli = "R",           # Colistin
                   stringsAsFactors = FALSE)
-  expect_equal(EUCAST_rules(a, info = FALSE), b)
+  expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
 })
 
 test_that("MO properties work", {

tests/testthat/test-freq.R

@@ -66,5 +66,20 @@ test_that("frequency table works", {
                      pull(age) %>%
                      sort())
 
+  # check format
+  expect_identical(septic_patients %>%
+                     freq(age) %>%
+                     format() %>%
+                     apply(2, class) %>%
+                     unname(),
+                   rep("character", 5))
+
+  # check tibble
+  expect_identical(septic_patients %>%
+                     freq(age) %>%
+                     as_tibble() %>%
+                     class() %>%
+                     .[1],
+                   "tbl_df")
 })
 

tests/testthat/test-resistance.R

@@ -43,6 +43,25 @@ test_that("resistance works", {
   expect_warning(susceptibility(as.character(septic_patients$amcl,
                                              septic_patients$gent)))
 
+
+  # check for errors
+  expect_error(IR(septic_patients %>% select(amox, amcl)))
+  expect_error(IR("test", minimum = "test"))
+  expect_error(IR("test", as_percent = "test"))
+  expect_error(S("test", minimum = "test"))
+  expect_error(S("test", as_percent = "test"))
+  expect_error(S(septic_patients %>% select(amox, amcl)))
+  expect_error(S("R", septic_patients %>% select(amox, amcl)))
+
+  # check too low amount of isolates
+  expect_identical(IR(septic_patients$amox, minimum = nrow(septic_patients) + 1),
+                   NA)
+  expect_identical(S(septic_patients$amox, minimum = nrow(septic_patients) + 1),
+                   NA)
+
+  # warning for speed loss
+  expect_warning(S(septic_patients$amcl, as.character(septic_patients$gent)))
+
 })
 
 test_that("old rsi works", {
@@ -129,4 +148,9 @@ test_that("prediction of rsi works", {
                            col_ab = "amox",
                            col_date = "NOT EXISTING COLUMN",
                            info = TRUE))
+  # almost all E. coli are mero S in the Netherlands :)
+  expect_error(resistance_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
+                                  col_ab = "mero",
+                                  col_date = "date",
+                                  info = TRUE))
 })