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(v2.1.1.9217) allow + in amr selectors

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dr. M.S. (Matthijs) Berends
2025-03-18 16:35:22 +01:00
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vignettes/AMR_for_Python.Rmd
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@ -24,22 +24,23 @@ knitr::opts_chunk$set(
# Introduction
The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) analysis. It provides extensive features for handling microbial and antimicrobial data. However, for those who work primarily in Python, we now have a more intuitive option available: the [`AMR` Python Package Index](https://pypi.org/project/AMR/).
The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) analysis. It provides extensive features for handling microbial and antimicrobial data. However, for those who work primarily in Python, we now have a more intuitive option available: the [`AMR` Python package](https://pypi.org/project/AMR/).
This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` package internally. Despite the need to have R installed, Python users can now easily work with AMR data directly through Python code.
This Python package is a wrapper around the `AMR` R package. It uses the `rpy2` package internally. Despite the need to have R installed, Python users can now easily work with AMR data directly through Python code.
# Prerequisites
This package was only tested with [`venv`](https://docs.python.org/3/library/venv.html). You can set up such a virtual environment by running:
This package was only tested with a [virtual environment (venv)](https://docs.python.org/3/library/venv.html). You can set up such an environment by running:
```python
# for linux and macOS:
# linux and macOS:
python -m venv /path/to/new/virtual/environment
# for Windows:
# Windows:
python -m venv C:\path\to\new\virtual\environment
```
Then you can [activate the environment](https://docs.python.org/3/library/venv.html#how-venvs-work), after the which the virtual environment is ready to work with.
Then you can [activate the environment](https://docs.python.org/3/library/venv.html#how-venvs-work), after which the venv is ready to work with.
# Install AMR