From 8d37c75860f01c51093bf70ac2ad9a1944c7adcc Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Tue, 14 Feb 2023 15:59:40 +0100
Subject: [PATCH] unit tests

---
 DESCRIPTION                     |  2 +-
 NEWS.md                         |  2 +-
 inst/tinytest/test-age.R        | 11 ++---------
 inst/tinytest/test-count.R      |  5 +----
 inst/tinytest/test-g.test.R     |  6 +-----
 inst/tinytest/test-mdro.R       |  8 ++++----
 inst/tinytest/test-proportion.R | 10 ++--------
 inst/tinytest/test-rsi.R        |  5 +----
 8 files changed, 13 insertions(+), 36 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 57b6f0c9..09caf244 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9124
+Version: 1.8.2.9125
 Date: 2023-02-14
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 52b1cfd8..bb8e0cf6 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9124
+# AMR 1.8.2.9125
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 
diff --git a/inst/tinytest/test-age.R b/inst/tinytest/test-age.R
index 0952ceb1..5e8bf005 100644
--- a/inst/tinytest/test-age.R
+++ b/inst/tinytest/test-age.R
@@ -49,15 +49,8 @@ expect_error(age(
   reference = c("2019-01-01", "2019-01-01")
 ))
 
-# expect_warning(age(
-  x = c("1980-01-01", "1985-01-01", "1990-01-01"),
-  reference = "1975-01-01"
-))
-
-# expect_warning(age(
-  x = c("1800-01-01", "1805-01-01", "1810-01-01"),
-  reference = "2019-01-01"
-))
+# expect_warning(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"), reference = "1975-01-01"))
+# expect_warning(age(x = c("1800-01-01", "1805-01-01", "1810-01-01"), reference = "2019-01-01"))
 
 expect_equal(
   length(age(x = c("2019-01-01", NA), na.rm = TRUE)),
diff --git a/inst/tinytest/test-count.R b/inst/tinytest/test-count.R
index 73c2fcf4..9af023e0 100644
--- a/inst/tinytest/test-count.R
+++ b/inst/tinytest/test-count.R
@@ -47,10 +47,7 @@ expect_equal(
 # warning for speed loss
 # expect_warning(count_resistant(as.character(example_isolates$AMC)))
 
-# expect_warning(count_resistant(
-  example_isolates$AMC,
-  as.character(example_isolates$GEN)
-))
+# expect_warning(count_resistant(example_isolates$AMC, as.character(example_isolates$GEN)))
 
 # check for errors
 expect_error(count_resistant("test", minimum = "test"))
diff --git a/inst/tinytest/test-g.test.R b/inst/tinytest/test-g.test.R
index 0c934b74..f3fb0af8 100644
--- a/inst/tinytest/test-g.test.R
+++ b/inst/tinytest/test-g.test.R
@@ -63,11 +63,7 @@ x <- as.data.frame(
 # expect_warning(g.test(x))
 expect_true(suppressWarnings(g.test(x)$p.value) < 1)
 
-# expect_warning(g.test(
-  x = c(772, 1611, 737),
-  y = c(780, 1560, 780),
-  rescale.p = TRUE
-))
+# expect_warning(g.test(x = c(772, 1611, 737), y = c(780, 1560, 780), rescale.p = TRUE))
 
 expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
 expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))
diff --git a/inst/tinytest/test-mdro.R b/inst/tinytest/test-mdro.R
index 6a7dde2d..6b829107 100755
--- a/inst/tinytest/test-mdro.R
+++ b/inst/tinytest/test-mdro.R
@@ -272,10 +272,10 @@ expect_error(custom_mdro_guideline("test"))
 expect_error(custom_mdro_guideline("test" ~ c(1:3)))
 expect_error(custom_mdro_guideline("test" ~ A))
 # expect_warning(mdro(example_isolates,
-  # since `test` gives an error, it will be ignored with a warning
-  guideline = custom_mdro_guideline(test ~ "A"),
-  info = FALSE
-))
+#   # since `test` gives an error, it will be ignored with a warning
+#   guideline = custom_mdro_guideline(test ~ "A"),
+#   info = FALSE
+# ))
 
 # print groups
 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
diff --git a/inst/tinytest/test-proportion.R b/inst/tinytest/test-proportion.R
index 5a042444..b80d3e3f 100755
--- a/inst/tinytest/test-proportion.R
+++ b/inst/tinytest/test-proportion.R
@@ -115,15 +115,9 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
 
 # expect_warning(proportion_R(as.character(example_isolates$AMC)))
 # expect_warning(proportion_S(as.character(example_isolates$AMC)))
-# expect_warning(proportion_S(as.character(
-  example_isolates$AMC,
-  example_isolates$GEN
-)))
+# expect_warning(proportion_S(as.character(example_isolates$AMC, example_isolates$GEN)))
 
-# expect_warning(n_sir(as.character(
-  example_isolates$AMC,
-  example_isolates$GEN
-)))
+# expect_warning(n_sir(as.character(example_isolates$AMC, example_isolates$GEN)))
 expect_equal(
   suppressWarnings(n_sir(as.character(
     example_isolates$AMC,
diff --git a/inst/tinytest/test-rsi.R b/inst/tinytest/test-rsi.R
index ef9fdd6e..e4ba121d 100644
--- a/inst/tinytest/test-rsi.R
+++ b/inst/tinytest/test-rsi.R
@@ -236,10 +236,7 @@ expect_inherits(
   ))$amoxi),
   "sir"
 )
-# expect_warning(as.sir(data.frame(
-  mo = "E. coli",
-  NIT = c("<= 2", 32)
-)))
+# expect_warning(as.sir(data.frame(mo = "E. coli", NIT = c("<= 2", 32))))
 expect_message(as.sir(data.frame(
   mo = "E. coli",
   NIT = c("<= 2", 32),