add tests using testthat

tests/testthat/test-first_isolates.R

@@ -0,0 +1,23 @@
+context("first_isolates.R")
+
+test_that("keyantibiotics work", {
+  expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
+  expect_true(key_antibiotics_equal("SSS", "SSS"))
+  expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
+  expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
+})
+
+
+test_that("guess_bactid works", {
+  expect_equal(guess_bactid("E. coli"), "ESCCOL")
+  expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
+})
+
+test_that("first isolates work", {
+  # septic_patients contains 1960 out of 2000 first isolates
+  expect_equal(sum(first_isolate(septic_patients,
+                             "date",
+                             "patient_id",
+                             "bactid",
+                             info = FALSE)), 1960)
+})