From a20293a0a31ad41a4668cd8de1f254d7abad3713 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Sun, 18 Sep 2022 16:35:45 +0200
Subject: [PATCH] fixes

---
 DESCRIPTION               |  2 +-
 NEWS.md                   |  6 +++---
 inst/tinytest/test-data.R | 16 +---------------
 3 files changed, 5 insertions(+), 19 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7cc70be3..6cff6dde 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9055
+Version: 1.8.1.9056
 Date: 2022-09-18
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 8ae49a75..23bf9e7c 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.1.9055
+# AMR 1.8.1.9056
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
@@ -49,7 +49,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
 * An enormous lot of code cleaning, fixing some small bugs on the way
 
 
-# `AMR` 1.8.1
+# AMR 1.8.1
 
 ### Changed
 * Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
@@ -69,7 +69,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
 * Fix for size of some image elements, as requested by CRAN
 
 
-# `AMR` 1.8.0
+# AMR 1.8.0
 
 ### Breaking changes
 * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
diff --git a/inst/tinytest/test-data.R b/inst/tinytest/test-data.R
index 300d5d1c..2ccc4cd5 100644
--- a/inst/tinytest/test-data.R
+++ b/inst/tinytest/test-data.R
@@ -23,8 +23,6 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-expect_true(AMR:::check_dataset_integrity()) # in misc.R
-
 # IDs should always be unique
 expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
 expect_identical(class(microorganisms$mo), c("mo", "character"))
@@ -68,24 +66,12 @@ expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(
 expect_true(all(c(
   "mo", "fullname",
   "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
-  "rank", "ref", "species_id", "source", "prevalence", "snomed",
+  "rank", "ref", "lpsn", "gbif", "status", "source", "prevalence", "snomed",
   "kingdom_index", "fullname_lower", "g_species"
 ) %in% colnames(df)))
 
-expect_true(all(c(
-  "fullname", "fullname_new", "ref", "prevalence",
-  "fullname_lower", "g_species"
-) %in% colnames(AMR:::MO.old_lookup)))
-
 expect_inherits(AMR:::MO_CONS, "mo")
 
-expect_identical(
-  class(catalogue_of_life_version()),
-  c("catalogue_of_life_version", "list")
-)
-
-expect_stdout(print(catalogue_of_life_version()))
-
 uncategorised <- subset(
   microorganisms,
   genus == "Staphylococcus" &