diff --git a/DESCRIPTION b/DESCRIPTION index 91c23d4e1..d21b86701 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9196 +Version: 2.1.1.9197 Date: 2025-03-13 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index ada161a18..1bd760bb3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9196 +# AMR 2.1.1.9197 *(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).)* @@ -12,7 +12,6 @@ This package now supports not only tools for AMR data analysis in clinical setti ## New * **One Health implementation** * Function `as.sir()` now has extensive support for veterinary breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names. - * The CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when `guideline` is set to CLSI) * The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html). * The (new) `antimicrobials` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well. * `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q") diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index cbae728df..d45f489b4 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: 2.1.1.9196 +Version: 2.1.1.9197 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-2.1.1.9196.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9196.tar.gz deleted file mode 100644 index 0ea4ebb76..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9196.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9196-py3-none-any.whl b/PythonPackage/AMR/dist/amr-2.1.1.9197-py3-none-any.whl similarity index 86% rename from PythonPackage/AMR/dist/amr-2.1.1.9196-py3-none-any.whl rename to PythonPackage/AMR/dist/amr-2.1.1.9197-py3-none-any.whl index a2c282ec7..4644f9a6a 100644 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9196-py3-none-any.whl and b/PythonPackage/AMR/dist/amr-2.1.1.9197-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9197.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9197.tar.gz new file mode 100644 index 000000000..fa07e8a55 Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9197.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index 9eefd872c..aef0be4cd 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='2.1.1.9196', + version='2.1.1.9197', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 504d6cadd..4a257bb07 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -642,7 +642,7 @@ eucast_rules <- function(x, add_fn = font_red ) } - cols_ab <- c(cols_ab, setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s)) + cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s)) } } diff --git a/R/sir.R b/R/sir.R index 72043ff2c..a8fb93cc0 100755 --- a/R/sir.R +++ b/R/sir.R @@ -114,7 +114,7 @@ #' options(AMR_breakpoint_type = "animal") #' ``` #' -####### TODO When applying veterinary breakpoints (by setting `host` or by setting `breakpoint_type = "animal"`), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints. +###### TODO When applying veterinary breakpoints (by setting `host` or by setting `breakpoint_type = "animal"`), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints. #' #' ### After Interpretation #' diff --git a/data-raw/gpt_training_text_v2.1.1.9196.txt b/data-raw/gpt_training_text_v2.1.1.9197.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9196.txt rename to data-raw/gpt_training_text_v2.1.1.9197.txt index 994b1420b..004058736 100644 --- a/data-raw/gpt_training_text_v2.1.1.9196.txt +++ b/data-raw/gpt_training_text_v2.1.1.9197.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 2.1.1.9196. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9197. 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. ----------------------------------------------------------------------------------------------------