diff --git a/DESCRIPTION b/DESCRIPTION index ebd6c8f5e..3d3eab7eb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9188 +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")), diff --git a/NEWS.md b/NEWS.md index 5382df1de..069e4e0cb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9188 +# 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. -* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents two years ago. +* 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 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). diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index a6cae88a7..bdfd3c311 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: 2.1.1.9188 +Version: 2.1.1.9189 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-2.1.1.9188.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9188.tar.gz deleted file mode 100644 index d1d6caf3d..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9188.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9188-py3-none-any.whl b/PythonPackage/AMR/dist/amr-2.1.1.9189-py3-none-any.whl similarity index 52% rename from PythonPackage/AMR/dist/amr-2.1.1.9188-py3-none-any.whl rename to PythonPackage/AMR/dist/amr-2.1.1.9189-py3-none-any.whl index 741e00e8e..5f7c51a1c 100644 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9188-py3-none-any.whl and b/PythonPackage/AMR/dist/amr-2.1.1.9189-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9189.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9189.tar.gz new file mode 100644 index 000000000..c3394bc92 Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9189.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index a5d7f8e4a..45c40b7be 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='2.1.1.9188', + version='2.1.1.9189', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/data-raw/gpt_training_text_v2.1.1.9188.txt b/data-raw/gpt_training_text_v2.1.1.9189.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9188.txt rename to data-raw/gpt_training_text_v2.1.1.9189.txt index 70300339f..dcec36b26 100644 --- a/data-raw/gpt_training_text_v2.1.1.9188.txt +++ b/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 2.1.1.9188. 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] diff --git a/man/AMR.Rd b/man/AMR.Rd index 50cab1dee..7157defa5 100644 --- a/man/AMR.Rd +++ b/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] diff --git a/pkgdown/extra.js b/pkgdown/extra.js index f36e2e153..2f3e14e61 100644 --- a/pkgdown/extra.js +++ b/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"); - $(".citation h2:nth(1)").text("How to Cite"); + $(".template-citation-authors h1:nth(0)").text("Contributors and Citation"); + $(".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 = ' '; + // 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");