fortify code with more tests

NEWS

@@ -12,8 +12,9 @@
 - For parameters of functions `first_isolate`, `EUCAST_rules` the column names are now case-insensitive
 - Functions `as.rsi` and `as.mic` now add the package name and version as attribute
 - Expanded README.md
-- Added unit testing with Travis CI (https://travis-ci.org/msberends/AMR)
+- Added unit testing with the `testthat` package
-- Added code coverage checking with Codecov (https://codecov.io/gh/msberends/AMR/tree/master/R)
+- Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
+- Added Line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
 
 ## 0.1.1
 - `EUCAST_rules` applies for amoxicillin even if ampicillin is missing

tests/testthat/test-first_isolates.R

@@ -14,18 +14,18 @@ test_that("guess_bactid works", {
 
 test_that("first isolates work", {
   # septic_patients contains 1960 out of 2000 first isolates
-  septic_ptns <- septic_patients
+  #septic_ptns <- septic_patients
-  expect_equal(sum(first_isolate(tbl = septic_ptns,
+  expect_equal(sum(first_isolate(tbl = septic_patients,
                                  col_date = "date",
                                  col_patient_id = "patient_id",
                                  col_bactid = "bactid",
                                  info = FALSE)), 1960)
 
-  # septic_patients contains 1962 out of 2000 first weighted isolates
+  # septic_patients contains 1962 out of 2000 first *weighted* isolates
-  septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
+  #septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
   expect_equal(
     suppressWarnings(sum(
-      first_isolate(tbl = septic_ptns,
+      first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
                     col_date = "date",
                     col_patient_id = "patient_id",
                     col_bactid = "bactid",
@@ -33,4 +33,20 @@ test_that("first isolates work", {
                     type = "keyantibiotics",
                     info = TRUE))),
     1962)
+
+  # set 1500 random observations to be of specimen type 'Urine'
+  random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
+  expect_lt(sum(
+    first_isolate(tbl = mutate(septic_patients,
+                               specimen = if_else(row_number() %in% random_rows,
+                                                  "Urine",
+                                                  "Unknown")),
+                  col_date = "date",
+                  col_patient_id = "patient_id",
+                  col_bactid = "bactid",
+                  col_specimen = "specimen",
+                  filter_specimen = "Urine",
+                  info = TRUE)),
+    1501)
+
 })

tests/testthat/test-joins.R

@@ -4,6 +4,8 @@ test_that("joins work", {
   unjoined <- septic_patients
   inner <- septic_patients %>% inner_join_microorganisms()
   left <- septic_patients %>% left_join_microorganisms()
+  semi <- septic_patients %>% semi_join_microorganisms()
+  anti <- septic_patients %>% anti_join_microorganisms()
   suppressWarnings(right <- septic_patients %>% right_join_microorganisms())
   suppressWarnings(full <- septic_patients %>% full_join_microorganisms())
 
@@ -13,6 +15,13 @@ test_that("joins work", {
   expect_true(ncol(unjoined) < ncol(left))
   expect_true(nrow(unjoined) == nrow(left))
 
+  expect_true(ncol(semi) == ncol(semi))
+  expect_true(nrow(semi) == nrow(semi))
+
+  expect_true(nrow(anti) == 0)
+
   expect_true(nrow(unjoined) < nrow(right))
   expect_true(nrow(unjoined) < nrow(full))
+
+  expect_equal(nrow(left_join_microorganisms("ESCCOL")), 1)
 })

tests/testthat/test-rsi_analysis.R

@@ -2,36 +2,71 @@ context("rsi_analysis.R")
 
 test_that("rsi works", {
   # amox resistance in `septic_patients` should be around 53.86%
-  amox_R <- septic_patients %>% summarise(amox = rsi(amox)) %>% pull(amox)
+  expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
-  expect_equal(amox_R, 0.5386, tolerance = 0.0001)
+  expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
   expect_equal(rsi_df(septic_patients,
                       ab = "amox",
-                      info = FALSE), 0.5386, tolerance = 0.0001)
+                      info = FALSE),
-  # and pita+genta susceptibility around 98.09%
+               0.5386,
+               tolerance = 0.0001)
+  # pita+genta susceptibility around 98.09%
+  expect_equal(rsi(septic_patients$pita,
+                   septic_patients$gent,
+                   interpretation = "S",
+                   info = TRUE),
+               0.9809,
+               tolerance = 0.0001)
   expect_equal(rsi_df(septic_patients,
                       ab = c("pita", "gent"),
                       interpretation = "S",
-                      info = FALSE), 0.9809, tolerance = 0.0001)
+                      info = FALSE),
+               0.9809,
+               tolerance = 0.0001)
+  # mero+pita+genta susceptibility around 98.58%
+  expect_equal(rsi_df(septic_patients,
+                      ab = c("mero", "pita", "gent"),
+                      interpretation = "IS",
+                      info = FALSE),
+               0.9858,
+               tolerance = 0.0001)
 })
 
 test_that("prediction of rsi works", {
-  amox_R <- rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+  amox_R <- septic_patients %>%
+    filter(bactid == "ESCCOL") %>%
+    rsi_predict(col_ab = "amox",
+                col_date = "date",
+                info = FALSE) %>%
+    pull("probR")
+  # amox resistance will decrease using dataset `septic_patients`
+  expect_true(amox_R[2] > amox_R[20])
+
+  expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
+                            model = "binomial",
                             col_ab = "amox",
                             col_date = "date",
-                        info = FALSE)
+                            info = TRUE))
-  amox_R <- amox_R %>% pull("probR")
+  expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
-  # amox resistance will decrease according to `septic_patients`
+                            model = "loglin",
-  expect_true(amox_R[2] > amox_R[20])
+                            col_ab = "amox",
-  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                            col_date = "date",
+                            info = TRUE))
+  expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
+                            model = "lin",
+                            col_ab = "amox",
+                            col_date = "date",
+                            info = TRUE))
+
+  expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
                            model = "INVALID MODEL",
                            col_ab = "amox",
                            col_date = "date",
                            info = FALSE))
-  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+  expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
                            col_ab = "NOT EXISTING COLUMN",
                            col_date = "date",
                            info = FALSE))
-  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+  expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
                            col_ab = "amox",
                            col_date = "NOT EXISTING COLUMN",
                            info = FALSE))