From 967ee86757e31eaae0900d90ceb41356dac10e5c Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Tue, 17 Jul 2018 11:18:36 +0200
Subject: [PATCH] add unit tests

---
 tests/testthat/test-g.test.R     |  5 +++
 tests/testthat/test-resistance.R | 52 +++++++++++++++++++++++++++++---
 2 files changed, 53 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-g.test.R b/tests/testthat/test-g.test.R
index 15d7a4ba..bf46f2a3 100644
--- a/tests/testthat/test-g.test.R
+++ b/tests/testthat/test-g.test.R
@@ -18,6 +18,7 @@ test_that("G-test works", {
                expected = 0.01787343,
                tolerance = 0.00000001)
 
+
   # INDEPENDENCE
 
   x <- matrix(data = round(runif(4) * 100000, 0),
@@ -26,4 +27,8 @@ test_that("G-test works", {
   expect_lt(g.test(x)$p.value,
             1)
 
+  expect_warning(g.test(x = c(772, 1611, 737),
+                        y = c(780, 1560, 780),
+                        rescale.p = TRUE))
+
 })
diff --git a/tests/testthat/test-resistance.R b/tests/testthat/test-resistance.R
index b43204e0..e93a7208 100755
--- a/tests/testthat/test-resistance.R
+++ b/tests/testthat/test-resistance.R
@@ -35,12 +35,56 @@ test_that("resistance works", {
 
 })
 
+test_that("old rsi works", {
+  # amox resistance in `septic_patients` should be around 53.86%
+  expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
+  expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
+  expect_equal(rsi_df(septic_patients,
+                      ab = "amox",
+                      info = TRUE),
+               0.5756,
+               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 = TRUE),
+               0.9809,
+               tolerance = 0.0001)
+  # more than 2 not allowed
+  expect_error(rsi_df(septic_patients,
+                      ab = c("mero", "pita", "gent"),
+                      interpretation = "IS",
+                      info = TRUE))
+
+  # count of cases
+  expect_equal(septic_patients %>%
+                 group_by(hospital_id) %>%
+                 summarise(cipro_S = rsi(cipr, interpretation = "S",
+                                         as_percent = TRUE, warning = FALSE),
+                           cipro_n = n_rsi(cipr),
+                           genta_S = rsi(gent, interpretation = "S",
+                                         as_percent = TRUE, warning = FALSE),
+                           genta_n = n_rsi(gent),
+                           combination_S = rsi(cipr, gent, interpretation = "S",
+                                               as_percent = TRUE, warning = FALSE),
+                           combination_n = n_rsi(cipr, gent)) %>%
+                 pull(combination_n),
+               c(138, 474, 170, 464, 183))
+})
+
 test_that("prediction of rsi works", {
   amox_R <- septic_patients %>%
     filter(bactid == "ESCCOL") %>%
     rsi_predict(col_ab = "amox",
                 col_date = "date",
-                info = FALSE) %>%
+                info = TRUE) %>%
     pull("probR")
   # amox resistance will decrease using dataset `septic_patients`
   expect_true(amox_R[2] > amox_R[20])
@@ -65,13 +109,13 @@ test_that("prediction of rsi works", {
                            model = "INVALID MODEL",
                            col_ab = "amox",
                            col_date = "date",
-                           info = FALSE))
+                           info = TRUE))
   expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
                            col_ab = "NOT EXISTING COLUMN",
                            col_date = "date",
-                           info = FALSE))
+                           info = TRUE))
   expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
                            col_ab = "amox",
                            col_date = "NOT EXISTING COLUMN",
-                           info = FALSE))
+                           info = TRUE))
 })