diff --git a/DESCRIPTION b/DESCRIPTION index 1c16a0e99..abc0d3183 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9200 +Version: 2.1.1.9201 Date: 2025-03-14 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index ec2cae4e4..ecf2538d8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9200 +# AMR 2.1.1.9201 *(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).)* diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index 73e2fa51e..06759f58a 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: 2.1.1.9200 +Version: 2.1.1.9201 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-2.1.1.9200.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9200.tar.gz deleted file mode 100644 index c9f9c4a58..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9200.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9200-py3-none-any.whl b/PythonPackage/AMR/dist/amr-2.1.1.9201-py3-none-any.whl similarity index 86% rename from PythonPackage/AMR/dist/amr-2.1.1.9200-py3-none-any.whl rename to PythonPackage/AMR/dist/amr-2.1.1.9201-py3-none-any.whl index 63fc07bff..c41de98fc 100644 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9200-py3-none-any.whl and b/PythonPackage/AMR/dist/amr-2.1.1.9201-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9201.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9201.tar.gz new file mode 100644 index 000000000..bb4ebdcad Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9201.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index 95a66acb0..49a58a71a 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='2.1.1.9200', + version='2.1.1.9201', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/R/sir.R b/R/sir.R index 2c21d253f..85a2ce907 100755 --- a/R/sir.R +++ b/R/sir.R @@ -626,7 +626,7 @@ as.sir.disk <- function(x, ab = ab, guideline = guideline, uti = uti, - capped_mic_handling = FALSE, # there are no MICs here + capped_mic_handling = "standard", # will be ignored for non-MIC anyway add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, substitute_missing_r_breakpoint = substitute_missing_r_breakpoint, diff --git a/data-raw/gpt_training_text_v2.1.1.9200.txt b/data-raw/gpt_training_text_v2.1.1.9201.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9200.txt rename to data-raw/gpt_training_text_v2.1.1.9201.txt index bacbf05da..204f10be1 100644 --- a/data-raw/gpt_training_text_v2.1.1.9200.txt +++ b/data-raw/gpt_training_text_v2.1.1.9201.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 2.1.1.9200. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9201. 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. ----------------------------------------------------------------------------------------------------