(v2.1.1.9188) fix antibiogram plot

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9187
+Version: 2.1.1.9188
 Date: 2025-03-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9187
+# AMR 2.1.1.9188
 
 *(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).)*
 

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9187
+Version: 2.1.1.9188
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9187',
+    version='2.1.1.9188',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/antibiogram.R

@@ -769,6 +769,32 @@ antibiogram.default <- function(x,
     # prepare for definitive output
     out <- out_wisca
     wisca_parameters <- wisca_parameters[, colnames(wisca_parameters)[!colnames(wisca_parameters) %in% c(levels(NA_sir_), "lower_ci", "upper_ci", "group")], drop = FALSE]
+    if (isTRUE(has_syndromic_group)) {
+      long_numeric <- out_wisca %pm>%
+        pm_ungroup() %pm>%
+        pm_select(
+          syndromic_group = syndromic_group,
+          ab = ab,
+          coverage = coverage,
+          lower_ci = lower_ci,
+          upper_ci = upper_ci,
+          n_total = n_total,
+          n_tested = n_tested,
+          n_susceptible = n_susceptible
+        )
+    } else {
+      long_numeric <- out_wisca %pm>%
+        pm_ungroup() %pm>%
+        pm_select(
+          ab = ab,
+          coverage = coverage,
+          lower_ci = lower_ci,
+          upper_ci = upper_ci,
+          n_total = n_total,
+          n_tested = n_tested,
+          n_susceptible = n_susceptible
+        )
+    }
   }
 
   out$digits <- digits # since pm_sumarise() cannot work with an object outside the current frame
@@ -1170,9 +1196,7 @@ tbl_format_footer.antibiogram <- function(x, ...) {
 plot.antibiogram <- function(x, ...) {
   df <- attributes(x)$long_numeric
   if (!"mo" %in% colnames(df)) {
-    stop_("Plotting antibiograms using `plot()` is only possible if they were not created using dplyr groups. See `?antibiogram` for how to retrieve numeric values in a long format for advanced plotting.",
-      call = FALSE
-    )
+    df$mo <- ""
   }
   if ("syndromic_group" %in% colnames(df)) {
     # barplot in base R does not support facets - paste columns together
@@ -1226,9 +1250,7 @@ barplot.antibiogram <- function(height, ...) {
 autoplot.antibiogram <- function(object, ...) {
   df <- attributes(object)$long_numeric
   if (!"mo" %in% colnames(df)) {
-    stop_("Plotting antibiograms using `autoplot()` is only possible if they were not created using dplyr groups. See `?antibiogram` for how to retrieve numeric values in a long format for advanced plotting.",
-      call = FALSE
-    )
+    df$mo <- ""
   }
   out <- ggplot2::ggplot(df,
     mapping = ggplot2::aes(
@@ -1243,6 +1265,10 @@ autoplot.antibiogram <- function(object, ...) {
   ) +
     ggplot2::geom_col(position = ggplot2::position_dodge2(preserve = "single")) +
     ggplot2::facet_wrap("mo") +
+    ggplot2::geom_errorbar(
+      mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
+      position = ggplot2::position_dodge2(preserve = "single", width = 1)
+    ) +
     ggplot2::labs(
       y = ifelse(isTRUE(attributes(object)$combine_SI), "%SI", "%S"),
       x = NULL,
@@ -1252,14 +1278,6 @@ autoplot.antibiogram <- function(object, ...) {
         NULL
       }
     )
-  if (isTRUE(attributes(object)$wisca)) {
-    out <- out +
-      ggplot2::geom_errorbar(
-        mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
-        position = ggplot2::position_dodge2(preserve = "single"),
-        width = 0.5
-      )
-  }
   out
 }
 

data-raw/gpt_training_text_v2.1.1.9188.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 2.1.1.9187. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9188. 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.
 ----------------------------------------------------------------------------------------------------

tests/testthat/test-antibiogram.R

@@ -113,6 +113,8 @@ test_that("antibiogram works", {
   ))
 
   expect_inherits(ab8, "antibiogram")
+  expect_inherits(retrieve_wisca_parameters(ab8), "data.frame")
+  expect_inherits(attributes(ab8)$long_numeric, "data.frame")
   expect_equal(colnames(ab8), c("Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
 
   # grouped tibbles