From 32024e597ae623bdf896aeb5383a3c7dcb450201 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Mon, 10 Mar 2025 12:16:45 +0100
Subject: [PATCH] (v2.1.1.9191) unit tests

---
 DESCRIPTION                                   |   4 +--
 NEWS.md                                       |   2 +-
 PythonPackage/AMR/AMR.egg-info/PKG-INFO       |   2 +-
 PythonPackage/AMR/dist/amr-2.1.1.9190.tar.gz  | Bin 10081 -> 0 bytes
 ...ny.whl => amr-2.1.1.9191-py3-none-any.whl} | Bin 10280 -> 10280 bytes
 PythonPackage/AMR/dist/amr-2.1.1.9191.tar.gz  | Bin 0 -> 10095 bytes
 PythonPackage/AMR/setup.py                    |   2 +-
 R/antibiogram.R                               |  20 +++++++++++--
 ....txt => gpt_training_text_v2.1.1.9191.txt} |   2 +-
 tests/testthat/test-antibiogram.R             |  27 +++++++++---------
 10 files changed, 37 insertions(+), 22 deletions(-)
 delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9190.tar.gz
 rename PythonPackage/AMR/dist/{amr-2.1.1.9190-py3-none-any.whl => amr-2.1.1.9191-py3-none-any.whl} (86%)
 create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9191.tar.gz
 rename data-raw/{gpt_training_text_v2.1.1.9190.txt => gpt_training_text_v2.1.1.9191.txt} (99%)

diff --git a/DESCRIPTION b/DESCRIPTION
index 325bd5761..447740bce 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9190
-Date: 2025-03-09
+Version: 2.1.1.9191
+Date: 2025-03-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by
diff --git a/NEWS.md b/NEWS.md
index b1c800194..8744f4fc5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9190
+# AMR 2.1.1.9191
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 
diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO
index 4ed58b8b5..c4630b60b 100644
--- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO
+++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9190
+Version: 2.1.1.9191
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends
diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9190.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9190.tar.gz
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diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py
index 32d4a3300..2f142ed28 100644
--- a/PythonPackage/AMR/setup.py
+++ b/PythonPackage/AMR/setup.py
@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9190',
+    version='2.1.1.9191',
     packages=find_packages(),
     install_requires=[
         'rpy2',
diff --git a/R/antibiogram.R b/R/antibiogram.R
index 4d4015829..f348dca07 100755
--- a/R/antibiogram.R
+++ b/R/antibiogram.R
@@ -870,7 +870,9 @@ antibiogram.default <- function(x,
   if (formatting_type == 20) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), "%,", n_susceptible, "/", n_tested, ")"))
   if (formatting_type == 21) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), " (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), ",N=", n_susceptible, "/", n_tested, ")"))
   if (formatting_type == 22) out <- out %pm>% pm_summarise(out_value = paste0(round(coverage * 100, digits = digits), "% (", round(lower_ci * 100, digits = digits), "-", round(upper_ci * 100, digits = digits), "%,N=", n_susceptible, "/", n_tested, ")"))
-  out$out_value[out$out_value %like% "^NA"] <- NA_character_
+  if (formatting_type >= 4) {
+    out$out_value[out$out_value %like% "^NA"] <- NA_character_
+  }
 
   # transform names of antimicrobials
   ab_naming_function <- function(x, t, l, s) {
@@ -1260,6 +1262,15 @@ autoplot.antibiogram <- function(object, ...) {
   if (!"mo" %in% colnames(df)) {
     df$mo <- ""
   }
+  groups <- colnames(df)[seq_len(which(colnames(df) %in% c("mo", "ab"))[1] - 1)]
+  group_name <- paste(groups, collapse = "/")
+  if (length(groups) > 1) {
+    df$syndromic_group <- apply(df[groups], 1, function(x) {
+      paste(stats::na.omit(x), collapse = "/")
+    })
+  } else if ("syndromic_group" %in% colnames(df)) {
+    group_name <- colnames(object)[1]
+  }
   out <- ggplot2::ggplot(df,
     mapping = ggplot2::aes(
       x = ab,
@@ -1272,7 +1283,6 @@ autoplot.antibiogram <- function(object, ...) {
     )
   ) +
     ggplot2::geom_col(position = ggplot2::position_dodge2(preserve = "single")) +
-    ggplot2::facet_wrap("mo") +
     ggplot2::geom_errorbar(
       mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
       position = ggplot2::position_dodge2(preserve = "single", width = 1)
@@ -1281,11 +1291,15 @@ autoplot.antibiogram <- function(object, ...) {
       y = ifelse(isTRUE(attributes(object)$combine_SI), "%SI", "%S"),
       x = NULL,
       fill = if ("syndromic_group" %in% colnames(df)) {
-        colnames(object)[1]
+        group_name
       } else {
         NULL
       }
     )
+  if (!all(df$mo == "", na.rm = TRUE)) {
+    out <- out +
+      ggplot2::facet_wrap("mo")
+  }
   out
 }
 
diff --git a/data-raw/gpt_training_text_v2.1.1.9190.txt b/data-raw/gpt_training_text_v2.1.1.9191.txt
similarity index 99%
rename from data-raw/gpt_training_text_v2.1.1.9190.txt
rename to data-raw/gpt_training_text_v2.1.1.9191.txt
index 5175c93ed..710ec980e 100644
--- a/data-raw/gpt_training_text_v2.1.1.9190.txt
+++ b/data-raw/gpt_training_text_v2.1.1.9191.txt
@@ -1,6 +1,6 @@
 This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
 
-First and foremost, you are trained on version 2.1.1.9190. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9191. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the  file, the  file, and all the  files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------
diff --git a/tests/testthat/test-antibiogram.R b/tests/testthat/test-antibiogram.R
index 16a828992..ab0af208f 100644
--- a/tests/testthat/test-antibiogram.R
+++ b/tests/testthat/test-antibiogram.R
@@ -31,18 +31,18 @@ test_that("antibiogram works", {
   # Traditional antibiogram ----------------------------------------------
 
   ab1 <- antibiogram(example_isolates,
-    antibiotics = c(aminoglycosides(), carbapenems())
+    antimicrobials = c(aminoglycosides(), carbapenems())
   )
 
   ab2 <- antibiogram(example_isolates,
-    antibiotics = aminoglycosides(),
+    antimicrobials = aminoglycosides(),
     ab_transform = "atc",
     mo_transform = "gramstain",
     add_total_n = TRUE
   )
 
   ab3 <- antibiogram(example_isolates,
-    antibiotics = carbapenems(),
+    antimicrobials = carbapenems(),
     ab_transform = "ab",
     mo_transform = "name",
     formatting_type = 1
@@ -58,14 +58,14 @@ test_that("antibiogram works", {
 
   # Combined antibiogram -------------------------------------------------
 
-  # combined antibiotics yield higher empiric coverage
+  # combined antibiogram yield higher empiric coverage
   ab4 <- antibiogram(example_isolates,
-    antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
+    antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
     mo_transform = "gramstain"
   )
 
   ab5 <- antibiogram(example_isolates,
-    antibiotics = c("TZP", "TZP+TOB"),
+    antimicrobials = c("TZP", "TZP+TOB"),
     mo_transform = "gramstain",
     ab_transform = "name",
     sep = " & ",
@@ -81,7 +81,7 @@ test_that("antibiogram works", {
 
   # the data set could contain a filter for e.g. respiratory specimens
   ab6 <- antibiogram(example_isolates,
-    antibiotics = c(aminoglycosides(), carbapenems()),
+    antimicrobials = c(aminoglycosides(), carbapenems()),
     syndromic_group = "ward",
     ab_transform = NULL
   )
@@ -90,7 +90,7 @@ test_that("antibiogram works", {
   # (i.e., this table will be in Dutch on Dutch systems)
   ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
   ab7 <- antibiogram(ex1,
-    antibiotics = aminoglycosides(),
+    antimicrobials = aminoglycosides(),
     ab_transform = "name",
     syndromic_group = ifelse(ex1$ward == "ICU",
       "IC", "Geen IC"
@@ -108,7 +108,7 @@ test_that("antibiogram works", {
 
   # the data set could contain a filter for e.g. respiratory specimens
   ab8 <- suppressWarnings(antibiogram(example_isolates,
-    antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
+    antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
     wisca = TRUE
   ))
 
@@ -118,11 +118,12 @@ test_that("antibiogram works", {
   expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
 
   # grouped tibbles
-
   if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
-    ab9 <- example_isolates %>%
-      group_by(ward, gender) %>%
-      wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
+    expect_warning(
+      ab9 <- example_isolates %>%
+        group_by(ward, gender) %>%
+        wisca(antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"))
+    )
     expect_equal(colnames(ab9), c("ward", "gender", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
   }