From eafe9bd113b18e38e710c8812201d57ba970ad6f Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Thu, 13 Mar 2025 15:51:58 +0100 Subject: [PATCH] (v2.1.1.9197) Final fixes for vetmed --- DESCRIPTION | 2 +- NEWS.md | 3 +-- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- PythonPackage/AMR/dist/amr-2.1.1.9196.tar.gz | Bin 10086 -> 0 bytes ...ny.whl => amr-2.1.1.9197-py3-none-any.whl} | Bin 10280 -> 10279 bytes PythonPackage/AMR/dist/amr-2.1.1.9197.tar.gz | Bin 0 -> 10113 bytes PythonPackage/AMR/setup.py | 2 +- R/eucast_rules.R | 2 +- R/sir.R | 2 +- ....txt => gpt_training_text_v2.1.1.9197.txt} | 2 +- 10 files changed, 7 insertions(+), 8 deletions(-) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9196.tar.gz rename PythonPackage/AMR/dist/{amr-2.1.1.9196-py3-none-any.whl => amr-2.1.1.9197-py3-none-any.whl} (86%) create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9197.tar.gz rename data-raw/{gpt_training_text_v2.1.1.9196.txt => gpt_training_text_v2.1.1.9197.txt} (99%) 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 0ea4ebb76ef5113f412e6820c35ec516897dd644..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10086 zcmch5WlS7Uw=M4OR@~jSFt`*iR@_|%m*VbDTigp2*A|CCi#rszqJujO%-nuAFE8)c z`*&~7S=lS=tn8d*|Jcc*Nkl_qyqLE~fLXeFa`AKX{X1fOV#3_smY#6u!GT`u?alVk 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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. ----------------------------------------------------------------------------------------------------