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(v2.1.1.9156) fix for knitr in WISCA

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dr. M.S. (Matthijs) Berends 2025-02-23 19:18:42 +01:00
parent aa8f6af185
commit b10989f431
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9 changed files with 6 additions and 6 deletions
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DESCRIPTION
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Package: AMR
Version: 2.1.1.9155
Version: 2.1.1.9156
Date: 2025-02-23
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 2.1.1.9155
# AMR 2.1.1.9156
*(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).)*

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PythonPackage/AMR/AMR.egg-info/PKG-INFO
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Metadata-Version: 2.2
Name: AMR
Version: 2.1.1.9155
Version: 2.1.1.9156
Summary: A Python wrapper for the AMR R package
Home-page: https://github.com/msberends/AMR
Author: Matthijs Berends

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PythonPackage/AMR/dist/AMR-2.1.1.9155-py3-none-any.whl → PythonPackage/AMR/dist/AMR-2.1.1.9156-py3-none-any.whl vendored
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PythonPackage/AMR/dist/amr-2.1.1.9155.tar.gz vendored
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PythonPackage/AMR/dist/amr-2.1.1.9156.tar.gz vendored Normal file
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PythonPackage/AMR/setup.py
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@ -2,7 +2,7 @@ from setuptools import setup, find_packages
setup(
name='AMR',
version='2.1.1.9155',
version='2.1.1.9156',
packages=find_packages(),
install_requires=[
'rpy2',

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R/antibiogram.R
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@ -1245,7 +1245,7 @@ knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.ka
meet_criteria(italicise, allow_class = "logical", has_length = 1)
meet_criteria(na, allow_class = "character", has_length = 1, allow_NA = TRUE)
if (isTRUE(italicise) && "mo" %in% colnames(attributes(x)$long_numeric)) {
if (!isTRUE(attributes(x)$wisca) && isTRUE(italicise) && "mo" %in% colnames(attributes(x)$long_numeric)) {
# make all microorganism names italic, according to nomenclature
names_col <- ifelse(isTRUE(attributes(x)$has_syndromic_group), 2, 1)
x[[names_col]] <- italicise_taxonomy(x[[names_col]], type = "markdown")

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data-raw/gpt_training_text_v2.1.1.9155.txt → data-raw/gpt_training_text_v2.1.1.9156.txt
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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 2.1.1.9155. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9156. 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.
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