diff --git a/DESCRIPTION b/DESCRIPTION index 7bde9963..0a43bb80 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9118 -Date: 2024-12-14 +Version: 2.1.1.9120 +Date: 2024-12-15 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 2d322645..ae6ba381 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9118 +# AMR 2.1.1.9120 *(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).)* @@ -73,6 +73,7 @@ This package now supports not only tools for AMR data analysis in clinical setti * Updated the prevalence calculation to include genera from the World Health Organization's (WHO) Priority Pathogen List * Improved algorithm of `first_isolate()` when using the phenotype-based method, to prioritise records with the highest availability of SIR values * `scale_y_percent()` can now cope with ranges outside the 0-100% range +* Support for new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024) ## Other * 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`. diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index 00e50958..d41c9396 100644 --- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO +++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 2.1 Name: AMR -Version: 2.1.1.9118 +Version: 2.1.1.9120 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-2.1.1.9118-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9120-py3-none-any.whl similarity index 84% rename from PythonPackage/AMR/dist/AMR-2.1.1.9118-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9120-py3-none-any.whl index 2c0f62a8..65c72e0d 100644 Binary files a/PythonPackage/AMR/dist/AMR-2.1.1.9118-py3-none-any.whl and b/PythonPackage/AMR/dist/AMR-2.1.1.9120-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9118.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9118.tar.gz deleted file mode 100644 index f6a69c42..00000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9118.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9120.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9120.tar.gz new file mode 100644 index 00000000..fc8f95c6 Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9120.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index 2ec93781..1854d100 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='2.1.1.9118', + version='2.1.1.9120', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/data-raw/gpt_training_text_v2.1.1.9118.txt b/data-raw/gpt_training_text_v2.1.1.9120.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9118.txt rename to data-raw/gpt_training_text_v2.1.1.9120.txt index 09a5cab3..6ae8f2a0 100644 --- a/data-raw/gpt_training_text_v2.1.1.9118.txt +++ b/data-raw/gpt_training_text_v2.1.1.9120.txt @@ -1,5 +1,5 @@ This files contains all context you must know about the AMR package for R. -First and foremost, you are trained on version 2.1.1.9118. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9120. Remember this whenever someone asks which AMR package version you’re at. -------------------------------- THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'NAMESPACE': @@ -6140,7 +6140,7 @@ Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed} } } \description{ -Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines. +Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines. } \details{ These functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}. @@ -6174,10 +6174,17 @@ The international guideline for multi-drug resistant tuberculosis - World Health The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6} \item \code{guideline = "BRMO"} -The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (\href{https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh}{link}) +The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" (\href{https://www.sri-richtlijnen.nl/brmo}{link}) + +Also: +\itemize{ +\item \code{guideline = "BRMO 2017"} + +The former Dutch national guideline - Werkgroep Infectiepreventie (WIP), RIVM, last revision as of 2017: "Bijzonder Resistente Micro-Organismen (BRMO)" +} } -Please suggest your own (country-specific) guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}. +Please suggest to implement guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}. } \section{Using Custom Guidelines}{ diff --git a/inst/tinytest/test-mdro.R b/inst/tinytest/test-mdro.R index a8113874..8dda697a 100755 --- a/inst/tinytest/test-mdro.R +++ b/inst/tinytest/test-mdro.R @@ -45,8 +45,8 @@ expect_identical(class(outcome), c("ordered", "factor")) # example_isolates should have these finding using Dutch guidelines expect_equal( as.double(table(outcome)), - c(1954, 24, 6) -) # 1954 neg, 24 unconfirmed, 6 pos, rest is NA + c(1994, 0, 6) +) expect_equal( brmo(example_isolates, info = FALSE),