(v2.1.1.9189) Add the awesome Aislinn Cook

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9187
+Version: 2.1.1.9189
 Date: 2025-03-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@@ -9,6 +9,7 @@ Authors@R: c(
   person(given = c("Matthijs", "S."),               family = "Berends",     role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.s.berends@umcg.nl"),
   person(given = c("Dennis"),                       family = "Souverein",   role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
   person(given = c("Erwin", "E.", "A."),            family = "Hassing",     role = c("aut", "ctb")),
+  person(given = c("Aislinn"),                      family = "Cook",        role = "ctb", comment = c(ORCID = "0000-0002-9189-7815")),
   person(given = c("Andrew", "P."),                 family = "Norgan",      role = "ctb", comment = c(ORCID = "0000-0002-2955-2066")),
   person(given = c("Anita"),                        family = "Williams",    role = "ctb", comment = c(ORCID = "0000-0002-5295-8451")),
   person(given = c("Annick"),                       family = "Lenglet",     role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9187
+# AMR 2.1.1.9189
 
 *(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).)*
 
@@ -6,8 +6,8 @@
 This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island's Atlantic Veterinary College](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
 
 ## Breaking
-* Dataset `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Calling `antibiotics` will still work, but now returns a warning.
+* Dataset `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Using `antibiotics` will still work, but now returns a warning.
-* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents two years ago.
+* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over two years ago.
 
 ## New
 * **One Health implementation**
@@ -95,7 +95,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * Added console colours support of `sir` class for Positron
 
 ## Other
-* Added Dr. Larisse Bolton as contributor for her fantastic implementation of WISCA in a mathematically solid way
+* Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
 * Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
 * Greatly improved `vctrs` integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as `dplyr`'s `bind_rows()`, `rowwise()` and `c_across()` are now supported for e.g. columns of class `mic`. Despite this, this `AMR` package is still zero-dependent on any other package, including `dplyr` and `vctrs`.
 * Greatly updated and expanded documentation
@@ -103,7 +103,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
 
 ## Older Versions
 
-This changelog only contains changes from AMR v3.0 (February 2025) and later.
+This changelog only contains changes from AMR v3.0 (March 2025) and later.
 
 * For prior v2 versions, please see [our v2 archive](https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md).
 * For prior v1 versions, please see [our v1 archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9187
+Version: 2.1.1.9189
 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='2.1.1.9189',
     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.",
+    df$mo <- ""
-      call = FALSE
-    )
   }
   if ("syndromic_group" %in% colnames(df)) {
     # barplot in base R does not support facets - paste columns together
@@ -1226,9 +1250,7 @@ barplot.antibiogram <- function(height, ...) {
 autoplot.antibiogram <- function(object, ...) {
   df <- attributes(object)$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.",
+    df$mo <- ""
-      call = FALSE
-    )
   }
   out <- ggplot2::ggplot(df,
     mapping = ggplot2::aes(
@@ -1243,6 +1265,10 @@ autoplot.antibiogram <- function(object, ...) {
   ) +
     ggplot2::geom_col(position = ggplot2::position_dodge2(preserve = "single")) +
     ggplot2::facet_wrap("mo") +
+    ggplot2::geom_errorbar(
+      mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
+      position = ggplot2::position_dodge2(preserve = "single", width = 1)
+    ) +
     ggplot2::labs(
       y = ifelse(isTRUE(attributes(object)$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_v2.1.1.9189.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 2.1.1.9189. 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.
 ----------------------------------------------------------------------------------------------------
@@ -879,6 +879,7 @@ Authors:
 
 Other contributors:
 \itemize{
+  \item Aislinn Cook (\href{https://orcid.org/0000-0002-9189-7815}{ORCID}) [contributor]
   \item Andrew P. Norgan (\href{https://orcid.org/0000-0002-2955-2066}{ORCID}) [contributor]
   \item Anita Williams (\href{https://orcid.org/0000-0002-5295-8451}{ORCID}) [contributor]
   \item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]

man/AMR.Rd

@@ -61,6 +61,7 @@ Authors:
 
 Other contributors:
 \itemize{
+  \item Aislinn Cook (\href{https://orcid.org/0000-0002-9189-7815}{ORCID}) [contributor]
   \item Andrew P. Norgan (\href{https://orcid.org/0000-0002-2955-2066}{ORCID}) [contributor]
   \item Anita Williams (\href{https://orcid.org/0000-0002-5295-8451}{ORCID}) [contributor]
   \item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]

pkgdown/extra.js

@@ -35,8 +35,9 @@ $(document).ready(function() {
 
   // replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
   $(".developers h2").text("Maintainers");
-  $(".citation h2:nth(0)").text("All contributors");
+  $(".template-citation-authors h1:nth(0)").text("Contributors and Citation");
-  $(".citation h2:nth(1)").text("How to Cite");
+  $(".template-citation-authors h2:nth(0)").text("All contributors");
+  $(".template-citation-authors h2:nth(1)").text("How to Cite");
 
   // remove \donttest and \dontrun texts in Examples
   if ($("#ref-examples ~ div pre").length > 0) {
@@ -69,6 +70,8 @@ $(document).ready(function() {
     if (typeof(x) != "undefined") {
       const prefix = '<img src="lang_';
       const suffix = '.svg" style="height: 13px !important; border: 1px solid #cccccc; aspect-ratio: 1 / 0.6; object-fit: cover; vertical-align: initial !important;"> ';
+      // bit weird, but we refer to languages here! So "uk" is Ukrain, not UK - take "en" for that.
+      x = x.replace("Aislinn", prefix + "en" + suffix + "Aislinn");
       x = x.replace("Alex", prefix + "de" + suffix + "Alex");
       x = x.replace("Andrew", prefix + "us" + suffix + "Andrew");
       x = x.replace("Anita", prefix + "au" + suffix + "Anita");

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