From a1acb2f3ac8acd59201025851a4b7395066d8a09 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Mon, 2 Jul 2018 09:34:20 +0200
Subject: [PATCH] extra unit tests

---
 tests/testthat/test-first_isolates.R | 33 +++++++++++++++++++++++++++-
 tests/testthat/test-freq.R           |  8 +++----
 tests/testthat/test-g.test.R         | 11 ++++++++++
 tests/testthat/test-p.symbol.R       |  6 +++++
 4 files changed, 53 insertions(+), 5 deletions(-)
 create mode 100644 tests/testthat/test-p.symbol.R

diff --git a/tests/testthat/test-first_isolates.R b/tests/testthat/test-first_isolates.R
index 4a3e62c9..1079e5c0 100755
--- a/tests/testthat/test-first_isolates.R
+++ b/tests/testthat/test-first_isolates.R
@@ -16,7 +16,8 @@ test_that("first isolates work", {
                     col_patient_id = "patient_id",
                     col_bactid = "bactid",
                     info = FALSE),
-      na.rm = TRUE), 1959)
+      na.rm = TRUE),
+    1959)
 
   # septic_patients contains 1961 out of 2000 first *weighted* isolates
   expect_equal(
@@ -31,6 +32,19 @@ test_that("first isolates work", {
                       info = TRUE),
         na.rm = TRUE)),
     1961)
+  # and 1998 when using points
+  expect_equal(
+    suppressWarnings(
+      sum(
+        first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
+                      col_date = "date",
+                      col_patient_id = "patient_id",
+                      col_bactid = "bactid",
+                      col_keyantibiotics = "keyab",
+                      type = "points",
+                      info = TRUE),
+        na.rm = TRUE)),
+    1998)
 
   # septic_patients contains 1732 out of 2000 first non-ICU isolates
   expect_equal(
@@ -61,4 +75,21 @@ test_that("first isolates work", {
                     info = TRUE),
       na.rm = TRUE),
     1501)
+  # same, but now exclude ICU
+  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",
+                    col_icu = "ward_icu",
+                    icu_exclude = TRUE,
+                    info = TRUE),
+      na.rm = TRUE),
+    1501)
 })
diff --git a/tests/testthat/test-freq.R b/tests/testthat/test-freq.R
index 18099652..27f38b5d 100755
--- a/tests/testthat/test-freq.R
+++ b/tests/testthat/test-freq.R
@@ -1,12 +1,12 @@
 context("freq.R")
 
 test_that("frequency table works", {
-  expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), as.data.frame = TRUE)), 5)
-  expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), as.data.frame = TRUE)), 5)
+  expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
+  expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
 
   # date column of septic_patients should contain 1662 unique dates
-  expect_equal(nrow(freq(septic_patients$date, as.data.frame = TRUE)), 1662)
-  expect_equal(nrow(freq(septic_patients$date, as.data.frame = TRUE)),
+  expect_equal(nrow(freq(septic_patients$date)), 1662)
+  expect_equal(nrow(freq(septic_patients$date)),
                length(unique(septic_patients$date)))
 
   # int
diff --git a/tests/testthat/test-g.test.R b/tests/testthat/test-g.test.R
index 14febb54..5b601452 100644
--- a/tests/testthat/test-g.test.R
+++ b/tests/testthat/test-g.test.R
@@ -2,6 +2,8 @@ context("g.test.R")
 
 test_that("G-test works", {
 
+  # GOODNESS-OF-FIT
+
   # example 1: clearfield rice vs. red rice
   x <- c(772, 1611, 737)
   x.expected <- vector2ratio(x, ratio = "1:2:1")
@@ -16,4 +18,13 @@ test_that("G-test works", {
                expected = 0.01787343,
                tolerance = 0.00000001)
 
+  # INDEPENDENCE
+
+  # this should always yield a p value of around 0
+  x <- matrix(data = round(runif(4) * 100000, 0),
+              ncol = 2,
+              byrow = TRUE)
+  expect_lt(g.test(x),
+            0.0001)
+
 })
diff --git a/tests/testthat/test-p.symbol.R b/tests/testthat/test-p.symbol.R
new file mode 100644
index 00000000..8b40f351
--- /dev/null
+++ b/tests/testthat/test-p.symbol.R
@@ -0,0 +1,6 @@
+context("p.symbol.R")
+
+test_that("P symbol works", {
+  expect_identical(p.symbol(c(0.001, 0.01, 0.05, 0.1, 1)),
+                   c("***", "**", "*", ".", " "))
+})