From 8249cfda466a1cbefd097ec2b9554b1d76a0d2ab Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Sun, 15 Dec 2024 20:32:55 +0100 Subject: [PATCH] (v2.1.1.9120) unit test fix --- DESCRIPTION | 4 ++-- NEWS.md | 3 ++- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- ...ny.whl => AMR-2.1.1.9120-py3-none-any.whl} | Bin 9960 -> 9959 bytes PythonPackage/AMR/dist/amr-2.1.1.9118.tar.gz | Bin 9724 -> 0 bytes PythonPackage/AMR/dist/amr-2.1.1.9120.tar.gz | Bin 0 -> 9730 bytes PythonPackage/AMR/setup.py | 2 +- ....txt => gpt_training_text_v2.1.1.9120.txt} | 15 +++++++++++---- inst/tinytest/test-mdro.R | 4 ++-- 9 files changed, 19 insertions(+), 11 deletions(-) rename PythonPackage/AMR/dist/{AMR-2.1.1.9118-py3-none-any.whl => AMR-2.1.1.9120-py3-none-any.whl} (84%) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9118.tar.gz create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9120.tar.gz rename data-raw/{gpt_training_text_v2.1.1.9118.txt => gpt_training_text_v2.1.1.9120.txt} (99%) 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 2c0f62a8b2a2b66cc61619efe26b601b452bc166..65c72e0da6dcd51a615c3e064314ae5dccd7ee60 100644 GIT binary patch delta 670 zcmaFi``ni|z?+#xgn@y9gTZi4|3+RLR%Rf**@yKOGnk>t8OzOKG^amullw#@ 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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),