quasiquotation, alpha for geom_rsi

tests/testthat/test-count.R

@@ -0,0 +1,41 @@
+context("count.R")
+
+test_that("counts work", {
+  # amox resistance in `septic_patients`
+  expect_equal(count_R(septic_patients$amox), 659)
+  expect_equal(count_I(septic_patients$amox), 3)
+  expect_equal(count_S(septic_patients$amox), 336)
+  expect_equal(count_R(septic_patients$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$amox))
+
+  expect_equal(septic_patients %>% count_S(amcl), 1056)
+  expect_equal(septic_patients %>% count_S(amcl, gent), 1385)
+
+  # count of cases
+  expect_equal(septic_patients %>%
+                 group_by(hospital_id) %>%
+                 summarise(cipro = count_S(cipr),
+                           genta = count_S(gent),
+                           combination = count_S(cipr, gent)) %>%
+                 pull(combination),
+               c(192, 440, 184, 474))
+
+  # warning for speed loss
+  expect_warning(count_R(as.character(septic_patients$amcl)))
+  expect_warning(count_I(as.character(septic_patients$amcl)))
+  expect_warning(count_S(as.character(septic_patients$amcl,
+                                      septic_patients$gent)))
+  expect_warning(count_S(septic_patients$amcl,
+                         as.character(septic_patients$gent)))
+
+  # check for errors
+  expect_error(count_IR("test", minimum = "test"))
+  expect_error(count_IR("test", as_percent = "test"))
+  expect_error(count_I("test", minimum = "test"))
+  expect_error(count_I("test", as_percent = "test"))
+  expect_error(count_S("test", minimum = "test"))
+  expect_error(count_S("test", as_percent = "test"))
+
+})