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https://github.com/msberends/AMR.git
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| ede1cdfd99 | |||
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1
.github/prehooks/commit-msg
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.github/prehooks/commit-msg
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@ -60,7 +60,6 @@ else
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fi
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fi
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git add data-raw/*
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git add data-raw/*
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||||||
git add PythonPackage/*
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||||||
git add -u
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git add -u
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||||||
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exit 0
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exit 0
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.github/prehooks/pre-commit
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.github/prehooks/pre-commit
vendored
@ -113,11 +113,7 @@ echo "${currentversion}" > .git/commit_version.tmp
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|||||||
|
|
||||||
# Generate GPT knowledge info for our Assistant (https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant)
|
# Generate GPT knowledge info for our Assistant (https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant)
|
||||||
bash data-raw/_generate_GPT_knowledge_input.sh "${currentversion}"
|
bash data-raw/_generate_GPT_knowledge_input.sh "${currentversion}"
|
||||||
cd data-raw
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|
||||||
bash _generate_python_wrapper.sh
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|
||||||
cd ..
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|
||||||
git add data-raw/*
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git add data-raw/*
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||||||
git add PythonPackage/*
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||||||
git add -u
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git add -u
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||||||
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||||||
exit 0
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exit 0
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||||||
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.github/workflows/check-current-testthat.yaml
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.github/workflows/check-current-testthat.yaml
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@ -94,3 +94,15 @@ jobs:
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|||||||
with:
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with:
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||||||
upload-snapshots: true
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upload-snapshots: true
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||||||
build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
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||||||
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||||||
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- name: Show files
|
||||||
|
if: matrix.config.os == 'ubuntu-latest'
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||||||
|
run: |
|
||||||
|
ls /home/runner/work/AMR/AMR/
|
||||||
|
ls /home/runner/work/AMR/AMR/check
|
||||||
|
ls /home/runner/work/AMR/AMR/check/**
|
||||||
|
ls /home/runner/work/AMR/AMR/check/**/tests*
|
||||||
|
ls /home/runner/work/AMR/AMR/check/**/tests*/testthat/
|
||||||
|
ls /home/runner/work/AMR/AMR/check/**/tests*/testthat/_snaps
|
||||||
|
shell: Rscript {0}
|
||||||
|
/home/runner/work/AMR/AMR/check/**/tests*/testthat/_snaps
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||||||
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.github/workflows/publish-to-pypi.yml
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.github/workflows/publish-to-pypi.yml
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@ -73,3 +73,26 @@ jobs:
|
|||||||
run: |
|
run: |
|
||||||
cd PythonPackage/AMR
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cd PythonPackage/AMR
|
||||||
python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*
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python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*
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- name: Git push to python-wrapper branch
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run: |
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||||||
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git config user.name "GitHub Actions"
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git config user.email "<>"
|
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||||||
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# Create and switch to python-wrapper branch (orphan if it doesn't exist)
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git fetch origin python-wrapper || true
|
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git checkout python-wrapper || git checkout --orphan python-wrapper
|
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||||||
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# Delete all existing files from the working tree (safely)
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||||||
|
git rm -rf . || true
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||||||
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rm -rf * || true
|
||||||
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||||||
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# Copy over only PythonPackage/AMR contents from main
|
||||||
|
git checkout main -- PythonPackage/AMR
|
||||||
|
mv PythonPackage/AMR/* .
|
||||||
|
rm -rf PythonPackage
|
||||||
|
|
||||||
|
# Commit and push if changes exist
|
||||||
|
git add .
|
||||||
|
git commit -m "Python wrapper update" || echo "No changes to commit"
|
||||||
|
git push origin python-wrapper --force
|
||||||
|
|||||||
@ -1,5 +1,5 @@
|
|||||||
Package: AMR
|
Package: AMR
|
||||||
Version: 2.1.1.9203
|
Version: 2.1.1.9207
|
||||||
Date: 2025-03-15
|
Date: 2025-03-15
|
||||||
Title: Antimicrobial Resistance Data Analysis
|
Title: Antimicrobial Resistance Data Analysis
|
||||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||||
|
|||||||
2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
|
|||||||
# AMR 2.1.1.9203
|
# AMR 2.1.1.9207
|
||||||
|
|
||||||
*(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).)*
|
*(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).)*
|
||||||
|
|
||||||
|
|||||||
@ -1,223 +0,0 @@
|
|||||||
Metadata-Version: 2.2
|
|
||||||
Name: AMR
|
|
||||||
Version: 2.1.1.9203
|
|
||||||
Summary: A Python wrapper for the AMR R package
|
|
||||||
Home-page: https://github.com/msberends/AMR
|
|
||||||
Author: Matthijs Berends
|
|
||||||
Author-email: m.s.berends@umcg.nl
|
|
||||||
License: GPL 2
|
|
||||||
Project-URL: Bug Tracker, https://github.com/msberends/AMR/issues
|
|
||||||
Classifier: Programming Language :: Python :: 3
|
|
||||||
Classifier: Operating System :: OS Independent
|
|
||||||
Requires-Python: >=3.6
|
|
||||||
Description-Content-Type: text/markdown
|
|
||||||
Requires-Dist: rpy2
|
|
||||||
Requires-Dist: numpy
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||||||
Requires-Dist: pandas
|
|
||||||
Dynamic: author
|
|
||||||
Dynamic: author-email
|
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||||||
Dynamic: classifier
|
|
||||||
Dynamic: description
|
|
||||||
Dynamic: description-content-type
|
|
||||||
Dynamic: home-page
|
|
||||||
Dynamic: license
|
|
||||||
Dynamic: project-url
|
|
||||||
Dynamic: requires-dist
|
|
||||||
Dynamic: requires-python
|
|
||||||
Dynamic: summary
|
|
||||||
|
|
||||||
---
|
|
||||||
title: "AMR for Python"
|
|
||||||
output:
|
|
||||||
rmarkdown::html_vignette:
|
|
||||||
toc: true
|
|
||||||
toc_depth: 3
|
|
||||||
vignette: >
|
|
||||||
%\VignetteIndexEntry{AMR for Python}
|
|
||||||
%\VignetteEncoding{UTF-8}
|
|
||||||
%\VignetteEngine{knitr::rmarkdown}
|
|
||||||
editor_options:
|
|
||||||
chunk_output_type: console
|
|
||||||
---
|
|
||||||
|
|
||||||
```{r setup, include = FALSE, results = 'markup'}
|
|
||||||
knitr::opts_chunk$set(
|
|
||||||
warning = FALSE,
|
|
||||||
collapse = TRUE,
|
|
||||||
comment = "#>",
|
|
||||||
fig.width = 7.5,
|
|
||||||
fig.height = 5
|
|
||||||
)
|
|
||||||
```
|
|
||||||
|
|
||||||
# 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/).
|
|
||||||
|
|
||||||
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.
|
|
||||||
|
|
||||||
# Install
|
|
||||||
|
|
||||||
1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
|
|
||||||
|
|
||||||
```bash
|
|
||||||
pip install AMR
|
|
||||||
```
|
|
||||||
|
|
||||||
2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
|
|
||||||
|
|
||||||
For Linux:
|
|
||||||
|
|
||||||
```bash
|
|
||||||
# Ubuntu / Debian
|
|
||||||
sudo apt install r-base
|
|
||||||
# Fedora:
|
|
||||||
sudo dnf install R
|
|
||||||
# CentOS/RHEL
|
|
||||||
sudo yum install R
|
|
||||||
```
|
|
||||||
|
|
||||||
For macOS (using [Homebrew](https://brew.sh)):
|
|
||||||
|
|
||||||
```bash
|
|
||||||
brew install r
|
|
||||||
```
|
|
||||||
|
|
||||||
For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R.
|
|
||||||
|
|
||||||
# Examples of Usage
|
|
||||||
|
|
||||||
## Cleaning Taxonomy
|
|
||||||
|
|
||||||
Here’s an example that demonstrates how to clean microorganism and drug names using the `AMR` Python package:
|
|
||||||
|
|
||||||
```python
|
|
||||||
import pandas as pd
|
|
||||||
import AMR
|
|
||||||
|
|
||||||
# Sample data
|
|
||||||
data = {
|
|
||||||
"MOs": ['E. coli', 'ESCCOL', 'esco', 'Esche coli'],
|
|
||||||
"Drug": ['Cipro', 'CIP', 'J01MA02', 'Ciproxin']
|
|
||||||
}
|
|
||||||
df = pd.DataFrame(data)
|
|
||||||
|
|
||||||
# Use AMR functions to clean microorganism and drug names
|
|
||||||
df['MO_clean'] = AMR.mo_name(df['MOs'])
|
|
||||||
df['Drug_clean'] = AMR.ab_name(df['Drug'])
|
|
||||||
|
|
||||||
# Display the results
|
|
||||||
print(df)
|
|
||||||
```
|
|
||||||
|
|
||||||
| MOs | Drug | MO_clean | Drug_clean |
|
|
||||||
|-------------|-----------|--------------------|---------------|
|
|
||||||
| E. coli | Cipro | Escherichia coli | Ciprofloxacin |
|
|
||||||
| ESCCOL | CIP | Escherichia coli | Ciprofloxacin |
|
|
||||||
| esco | J01MA02 | Escherichia coli | Ciprofloxacin |
|
|
||||||
| Esche coli | Ciproxin | Escherichia coli | Ciprofloxacin |
|
|
||||||
|
|
||||||
### Explanation
|
|
||||||
|
|
||||||
* **mo_name:** This function standardises microorganism names. Here, different variations of *Escherichia coli* (such as "E. coli", "ESCCOL", "esco", and "Esche coli") are all converted into the correct, standardised form, "Escherichia coli".
|
|
||||||
|
|
||||||
* **ab_name**: Similarly, this function standardises antimicrobial names. The different representations of ciprofloxacin (e.g., "Cipro", "CIP", "J01MA02", and "Ciproxin") are all converted to the standard name, "Ciprofloxacin".
|
|
||||||
|
|
||||||
## Calculating AMR
|
|
||||||
|
|
||||||
```python
|
|
||||||
import AMR
|
|
||||||
import pandas as pd
|
|
||||||
|
|
||||||
df = AMR.example_isolates
|
|
||||||
result = AMR.resistance(df["AMX"])
|
|
||||||
print(result)
|
|
||||||
```
|
|
||||||
|
|
||||||
```
|
|
||||||
[0.59555556]
|
|
||||||
```
|
|
||||||
|
|
||||||
## Generating Antibiograms
|
|
||||||
|
|
||||||
One of the core functions of the `AMR` package is generating an antibiogram, a table that summarises the antimicrobial susceptibility of bacterial isolates. Here’s how you can generate an antibiogram from Python:
|
|
||||||
|
|
||||||
```python
|
|
||||||
result2a = AMR.antibiogram(df[["mo", "AMX", "CIP", "TZP"]])
|
|
||||||
print(result2a)
|
|
||||||
```
|
|
||||||
|
|
||||||
| Pathogen | Amoxicillin | Ciprofloxacin | Piperacillin/tazobactam |
|
|
||||||
|-----------------|-----------------|-----------------|--------------------------|
|
|
||||||
| CoNS | 7% (10/142) | 73% (183/252) | 30% (10/33) |
|
|
||||||
| E. coli | 50% (196/392) | 88% (399/456) | 94% (393/416) |
|
|
||||||
| K. pneumoniae | 0% (0/58) | 96% (53/55) | 89% (47/53) |
|
|
||||||
| P. aeruginosa | 0% (0/30) | 100% (30/30) | None |
|
|
||||||
| P. mirabilis | None | 94% (34/36) | None |
|
|
||||||
| S. aureus | 6% (8/131) | 90% (171/191) | None |
|
|
||||||
| S. epidermidis | 1% (1/91) | 64% (87/136) | None |
|
|
||||||
| S. hominis | None | 80% (56/70) | None |
|
|
||||||
| S. pneumoniae | 100% (112/112) | None | 100% (112/112) |
|
|
||||||
|
|
||||||
|
|
||||||
```python
|
|
||||||
result2b = AMR.antibiogram(df[["mo", "AMX", "CIP", "TZP"]], mo_transform = "gramstain")
|
|
||||||
print(result2b)
|
|
||||||
```
|
|
||||||
|
|
||||||
| Pathogen | Amoxicillin | Ciprofloxacin | Piperacillin/tazobactam |
|
|
||||||
|----------------|-----------------|------------------|--------------------------|
|
|
||||||
| Gram-negative | 36% (226/631) | 91% (621/684) | 88% (565/641) |
|
|
||||||
| Gram-positive | 43% (305/703) | 77% (560/724) | 86% (296/345) |
|
|
||||||
|
|
||||||
|
|
||||||
In this example, we generate an antibiogram by selecting various antibiotics.
|
|
||||||
|
|
||||||
## Taxonomic Data Sets Now in Python!
|
|
||||||
|
|
||||||
As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antimicrobials`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
|
|
||||||
|
|
||||||
```python
|
|
||||||
AMR.microorganisms
|
|
||||||
```
|
|
||||||
|
|
||||||
| mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
|
|
||||||
|--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
|
|
||||||
| B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| ... | ... | ... | ... | ... | ... | ... | ... |
|
|
||||||
| B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
|
|
||||||
| B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
|
|
||||||
| B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
|
|
||||||
| F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
|
|
||||||
|
|
||||||
```python
|
|
||||||
AMR.antimicrobials
|
|
||||||
```
|
|
||||||
|
|
||||||
| ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
|
|
||||||
|-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
|
|
||||||
| AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
|
|
||||||
| ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
|
|
||||||
| ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
|
|
||||||
| ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
|
|
||||||
| AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
|
|
||||||
| ... | ... | ... | ... | ... | ... | ... | ... |
|
|
||||||
| VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
|
|
||||||
| VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
|
|
||||||
| XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
|
|
||||||
| ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
|
|
||||||
| ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
|
|
||||||
|
|
||||||
|
|
||||||
# Conclusion
|
|
||||||
|
|
||||||
With the `AMR` Python package, Python users can now effortlessly call R functions from the `AMR` R package. This eliminates the need for complex `rpy2` configurations and provides a clean, easy-to-use interface for antimicrobial resistance analysis. The examples provided above demonstrate how this can be applied to typical workflows, such as standardising microorganism and antimicrobial names or calculating resistance.
|
|
||||||
|
|
||||||
By just running `import AMR`, users can seamlessly integrate the robust features of the R `AMR` package into Python workflows.
|
|
||||||
|
|
||||||
Whether you're cleaning data or analysing resistance patterns, the `AMR` Python package makes it easy to work with AMR data in Python.
|
|
||||||
@ -1,10 +0,0 @@
|
|||||||
README.md
|
|
||||||
setup.py
|
|
||||||
AMR/__init__.py
|
|
||||||
AMR/datasets.py
|
|
||||||
AMR/functions.py
|
|
||||||
AMR.egg-info/PKG-INFO
|
|
||||||
AMR.egg-info/SOURCES.txt
|
|
||||||
AMR.egg-info/dependency_links.txt
|
|
||||||
AMR.egg-info/requires.txt
|
|
||||||
AMR.egg-info/top_level.txt
|
|
||||||
@ -1 +0,0 @@
|
|||||||
|
|
||||||
@ -1,3 +0,0 @@
|
|||||||
rpy2
|
|
||||||
numpy
|
|
||||||
pandas
|
|
||||||
@ -1 +0,0 @@
|
|||||||
AMR
|
|
||||||
@ -1,212 +0,0 @@
|
|||||||
from .datasets import example_isolates
|
|
||||||
from .datasets import microorganisms
|
|
||||||
from .datasets import antimicrobials
|
|
||||||
from .datasets import clinical_breakpoints
|
|
||||||
from .functions import ab_class
|
|
||||||
from .functions import ab_selector
|
|
||||||
from .functions import ab_from_text
|
|
||||||
from .functions import ab_name
|
|
||||||
from .functions import ab_cid
|
|
||||||
from .functions import ab_synonyms
|
|
||||||
from .functions import ab_tradenames
|
|
||||||
from .functions import ab_group
|
|
||||||
from .functions import ab_atc
|
|
||||||
from .functions import ab_atc_group1
|
|
||||||
from .functions import ab_atc_group2
|
|
||||||
from .functions import ab_loinc
|
|
||||||
from .functions import ab_ddd
|
|
||||||
from .functions import ab_ddd_units
|
|
||||||
from .functions import ab_info
|
|
||||||
from .functions import ab_url
|
|
||||||
from .functions import ab_property
|
|
||||||
from .functions import add_custom_antimicrobials
|
|
||||||
from .functions import clear_custom_antimicrobials
|
|
||||||
from .functions import add_custom_microorganisms
|
|
||||||
from .functions import clear_custom_microorganisms
|
|
||||||
from .functions import age
|
|
||||||
from .functions import age_groups
|
|
||||||
from .functions import antibiogram
|
|
||||||
from .functions import wisca
|
|
||||||
from .functions import retrieve_wisca_parameters
|
|
||||||
from .functions import aminoglycosides
|
|
||||||
from .functions import aminopenicillins
|
|
||||||
from .functions import antifungals
|
|
||||||
from .functions import antimycobacterials
|
|
||||||
from .functions import betalactams
|
|
||||||
from .functions import betalactams_with_inhibitor
|
|
||||||
from .functions import carbapenems
|
|
||||||
from .functions import cephalosporins
|
|
||||||
from .functions import cephalosporins_1st
|
|
||||||
from .functions import cephalosporins_2nd
|
|
||||||
from .functions import cephalosporins_3rd
|
|
||||||
from .functions import cephalosporins_4th
|
|
||||||
from .functions import cephalosporins_5th
|
|
||||||
from .functions import fluoroquinolones
|
|
||||||
from .functions import glycopeptides
|
|
||||||
from .functions import isoxazolylpenicillins
|
|
||||||
from .functions import lincosamides
|
|
||||||
from .functions import lipoglycopeptides
|
|
||||||
from .functions import macrolides
|
|
||||||
from .functions import monobactams
|
|
||||||
from .functions import nitrofurans
|
|
||||||
from .functions import oxazolidinones
|
|
||||||
from .functions import penicillins
|
|
||||||
from .functions import phenicols
|
|
||||||
from .functions import polymyxins
|
|
||||||
from .functions import quinolones
|
|
||||||
from .functions import rifamycins
|
|
||||||
from .functions import streptogramins
|
|
||||||
from .functions import tetracyclines
|
|
||||||
from .functions import trimethoprims
|
|
||||||
from .functions import ureidopenicillins
|
|
||||||
from .functions import amr_class
|
|
||||||
from .functions import amr_selector
|
|
||||||
from .functions import administrable_per_os
|
|
||||||
from .functions import administrable_iv
|
|
||||||
from .functions import not_intrinsic_resistant
|
|
||||||
from .functions import as_ab
|
|
||||||
from .functions import is_ab
|
|
||||||
from .functions import ab_reset_session
|
|
||||||
from .functions import as_av
|
|
||||||
from .functions import is_av
|
|
||||||
from .functions import as_disk
|
|
||||||
from .functions import is_disk
|
|
||||||
from .functions import as_mic
|
|
||||||
from .functions import is_mic
|
|
||||||
from .functions import rescale_mic
|
|
||||||
from .functions import mic_p50
|
|
||||||
from .functions import mic_p90
|
|
||||||
from .functions import as_mo
|
|
||||||
from .functions import is_mo
|
|
||||||
from .functions import mo_uncertainties
|
|
||||||
from .functions import mo_renamed
|
|
||||||
from .functions import mo_failures
|
|
||||||
from .functions import mo_reset_session
|
|
||||||
from .functions import mo_cleaning_regex
|
|
||||||
from .functions import as_sir
|
|
||||||
from .functions import is_sir
|
|
||||||
from .functions import is_sir_eligible
|
|
||||||
from .functions import sir_interpretation_history
|
|
||||||
from .functions import atc_online_property
|
|
||||||
from .functions import atc_online_groups
|
|
||||||
from .functions import atc_online_ddd
|
|
||||||
from .functions import atc_online_ddd_units
|
|
||||||
from .functions import av_from_text
|
|
||||||
from .functions import av_name
|
|
||||||
from .functions import av_cid
|
|
||||||
from .functions import av_synonyms
|
|
||||||
from .functions import av_tradenames
|
|
||||||
from .functions import av_group
|
|
||||||
from .functions import av_atc
|
|
||||||
from .functions import av_loinc
|
|
||||||
from .functions import av_ddd
|
|
||||||
from .functions import av_ddd_units
|
|
||||||
from .functions import av_info
|
|
||||||
from .functions import av_url
|
|
||||||
from .functions import av_property
|
|
||||||
from .functions import availability
|
|
||||||
from .functions import bug_drug_combinations
|
|
||||||
from .functions import count_resistant
|
|
||||||
from .functions import count_susceptible
|
|
||||||
from .functions import count_S
|
|
||||||
from .functions import count_SI
|
|
||||||
from .functions import count_I
|
|
||||||
from .functions import count_IR
|
|
||||||
from .functions import count_R
|
|
||||||
from .functions import count_all
|
|
||||||
from .functions import n_sir
|
|
||||||
from .functions import count_df
|
|
||||||
from .functions import custom_eucast_rules
|
|
||||||
from .functions import eucast_rules
|
|
||||||
from .functions import eucast_dosage
|
|
||||||
from .functions import export_ncbi_biosample
|
|
||||||
from .functions import first_isolate
|
|
||||||
from .functions import filter_first_isolate
|
|
||||||
from .functions import g_test
|
|
||||||
from .functions import is_new_episode
|
|
||||||
from .functions import ggplot_pca
|
|
||||||
from .functions import ggplot_sir
|
|
||||||
from .functions import geom_sir
|
|
||||||
from .functions import guess_ab_col
|
|
||||||
from .functions import italicise_taxonomy
|
|
||||||
from .functions import italicize_taxonomy
|
|
||||||
from .functions import inner_join_microorganisms
|
|
||||||
from .functions import left_join_microorganisms
|
|
||||||
from .functions import right_join_microorganisms
|
|
||||||
from .functions import full_join_microorganisms
|
|
||||||
from .functions import semi_join_microorganisms
|
|
||||||
from .functions import anti_join_microorganisms
|
|
||||||
from .functions import key_antimicrobials
|
|
||||||
from .functions import all_antimicrobials
|
|
||||||
from .functions import kurtosis
|
|
||||||
from .functions import like
|
|
||||||
from .functions import mdro
|
|
||||||
from .functions import custom_mdro_guideline
|
|
||||||
from .functions import brmo
|
|
||||||
from .functions import mrgn
|
|
||||||
from .functions import mdr_tb
|
|
||||||
from .functions import mdr_cmi2012
|
|
||||||
from .functions import eucast_exceptional_phenotypes
|
|
||||||
from .functions import mean_amr_distance
|
|
||||||
from .functions import amr_distance_from_row
|
|
||||||
from .functions import mo_matching_score
|
|
||||||
from .functions import mo_name
|
|
||||||
from .functions import mo_fullname
|
|
||||||
from .functions import mo_shortname
|
|
||||||
from .functions import mo_subspecies
|
|
||||||
from .functions import mo_species
|
|
||||||
from .functions import mo_genus
|
|
||||||
from .functions import mo_family
|
|
||||||
from .functions import mo_order
|
|
||||||
from .functions import mo_class
|
|
||||||
from .functions import mo_phylum
|
|
||||||
from .functions import mo_kingdom
|
|
||||||
from .functions import mo_domain
|
|
||||||
from .functions import mo_type
|
|
||||||
from .functions import mo_status
|
|
||||||
from .functions import mo_pathogenicity
|
|
||||||
from .functions import mo_gramstain
|
|
||||||
from .functions import mo_is_gram_negative
|
|
||||||
from .functions import mo_is_gram_positive
|
|
||||||
from .functions import mo_is_yeast
|
|
||||||
from .functions import mo_is_intrinsic_resistant
|
|
||||||
from .functions import mo_oxygen_tolerance
|
|
||||||
from .functions import mo_is_anaerobic
|
|
||||||
from .functions import mo_snomed
|
|
||||||
from .functions import mo_ref
|
|
||||||
from .functions import mo_authors
|
|
||||||
from .functions import mo_year
|
|
||||||
from .functions import mo_lpsn
|
|
||||||
from .functions import mo_mycobank
|
|
||||||
from .functions import mo_gbif
|
|
||||||
from .functions import mo_rank
|
|
||||||
from .functions import mo_taxonomy
|
|
||||||
from .functions import mo_synonyms
|
|
||||||
from .functions import mo_current
|
|
||||||
from .functions import mo_group_members
|
|
||||||
from .functions import mo_info
|
|
||||||
from .functions import mo_url
|
|
||||||
from .functions import mo_property
|
|
||||||
from .functions import pca
|
|
||||||
from .functions import theme_sir
|
|
||||||
from .functions import labels_sir_count
|
|
||||||
from .functions import resistance
|
|
||||||
from .functions import susceptibility
|
|
||||||
from .functions import sir_confidence_interval
|
|
||||||
from .functions import proportion_R
|
|
||||||
from .functions import proportion_IR
|
|
||||||
from .functions import proportion_I
|
|
||||||
from .functions import proportion_SI
|
|
||||||
from .functions import proportion_S
|
|
||||||
from .functions import proportion_df
|
|
||||||
from .functions import sir_df
|
|
||||||
from .functions import random_mic
|
|
||||||
from .functions import random_disk
|
|
||||||
from .functions import random_sir
|
|
||||||
from .functions import resistance_predict
|
|
||||||
from .functions import sir_predict
|
|
||||||
from .functions import ggplot_sir_predict
|
|
||||||
from .functions import skewness
|
|
||||||
from .functions import top_n_microorganisms
|
|
||||||
from .functions import reset_AMR_locale
|
|
||||||
from .functions import translate_AMR
|
|
||||||
@ -1,79 +0,0 @@
|
|||||||
import os
|
|
||||||
import sys
|
|
||||||
from rpy2 import robjects
|
|
||||||
from rpy2.robjects import pandas2ri
|
|
||||||
from rpy2.robjects.packages import importr, isinstalled
|
|
||||||
import pandas as pd
|
|
||||||
import importlib.metadata as metadata
|
|
||||||
|
|
||||||
# Get the path to the virtual environment
|
|
||||||
venv_path = sys.prefix
|
|
||||||
|
|
||||||
# Define R library path within the venv
|
|
||||||
r_lib_path = os.path.join(venv_path, "R_libs")
|
|
||||||
# Ensure the R library path exists
|
|
||||||
os.makedirs(r_lib_path, exist_ok=True)
|
|
||||||
|
|
||||||
# Import base and utils
|
|
||||||
base = importr('base')
|
|
||||||
utils = importr('utils')
|
|
||||||
|
|
||||||
base.options(warn = -1)
|
|
||||||
|
|
||||||
# Override R library paths globally for the session
|
|
||||||
robjects.r(f'.Library.site <- "{r_lib_path}"') # Replace site-specific library
|
|
||||||
base._libPaths(r_lib_path) # Override .libPaths() as well
|
|
||||||
|
|
||||||
# Get the effective library path
|
|
||||||
r_amr_lib_path = base._libPaths()[0]
|
|
||||||
|
|
||||||
# Check if the AMR package is installed in R
|
|
||||||
if not isinstalled('AMR', lib_loc=r_amr_lib_path):
|
|
||||||
print(f"AMR: Installing latest AMR R package to {r_amr_lib_path}...", flush=True)
|
|
||||||
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
|
|
||||||
|
|
||||||
# Python package version of AMR
|
|
||||||
try:
|
|
||||||
python_amr_version = metadata.version('AMR')
|
|
||||||
except metadata.PackageNotFoundError:
|
|
||||||
python_amr_version = ''
|
|
||||||
|
|
||||||
# R package version of AMR
|
|
||||||
r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')[0]
|
|
||||||
|
|
||||||
# Compare R and Python package versions
|
|
||||||
if r_amr_version != python_amr_version:
|
|
||||||
try:
|
|
||||||
print(f"AMR: Updating AMR package in {r_amr_lib_path}...", flush=True)
|
|
||||||
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
|
|
||||||
except Exception as e:
|
|
||||||
print(f"AMR: Could not update: {e}", flush=True)
|
|
||||||
|
|
||||||
print(f"AMR: Setting up R environment and AMR datasets...", flush=True)
|
|
||||||
|
|
||||||
# Activate the automatic conversion between R and pandas DataFrames
|
|
||||||
pandas2ri.activate()
|
|
||||||
|
|
||||||
# example_isolates
|
|
||||||
example_isolates = pandas2ri.rpy2py(robjects.r('''
|
|
||||||
df <- AMR::example_isolates
|
|
||||||
df[] <- lapply(df, function(x) {
|
|
||||||
if (inherits(x, c("Date", "POSIXt", "factor"))) {
|
|
||||||
as.character(x)
|
|
||||||
} else {
|
|
||||||
x
|
|
||||||
}
|
|
||||||
})
|
|
||||||
df <- df[, !sapply(df, is.list)]
|
|
||||||
df
|
|
||||||
'''))
|
|
||||||
example_isolates['date'] = pd.to_datetime(example_isolates['date'])
|
|
||||||
|
|
||||||
# microorganisms
|
|
||||||
microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]'))
|
|
||||||
antimicrobials = pandas2ri.rpy2py(robjects.r('AMR::antimicrobials[, !sapply(AMR::antimicrobials, is.list)]'))
|
|
||||||
clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
|
|
||||||
|
|
||||||
base.options(warn = 0)
|
|
||||||
|
|
||||||
print(f"AMR: Done.", flush=True)
|
|
||||||
@ -1,662 +0,0 @@
|
|||||||
import rpy2.robjects as robjects
|
|
||||||
from rpy2.robjects.packages import importr
|
|
||||||
from rpy2.robjects.vectors import StrVector, FactorVector, IntVector, FloatVector, DataFrame
|
|
||||||
from rpy2.robjects import pandas2ri
|
|
||||||
import pandas as pd
|
|
||||||
import numpy as np
|
|
||||||
|
|
||||||
# Activate automatic conversion between R data frames and pandas data frames
|
|
||||||
pandas2ri.activate()
|
|
||||||
|
|
||||||
# Import the AMR R package
|
|
||||||
amr_r = importr('AMR')
|
|
||||||
|
|
||||||
def convert_to_python(r_output):
|
|
||||||
# Check if it's a StrVector (R character vector)
|
|
||||||
if isinstance(r_output, StrVector):
|
|
||||||
return list(r_output) # Convert to a Python list of strings
|
|
||||||
|
|
||||||
# Check if it's a FactorVector (R factor)
|
|
||||||
elif isinstance(r_output, FactorVector):
|
|
||||||
return list(r_output) # Convert to a list of integers (factor levels)
|
|
||||||
|
|
||||||
# Check if it's an IntVector or FloatVector (numeric R vectors)
|
|
||||||
elif isinstance(r_output, (IntVector, FloatVector)):
|
|
||||||
return list(r_output) # Convert to a Python list of integers or floats
|
|
||||||
|
|
||||||
# Check if it's a pandas-compatible R data frame
|
|
||||||
elif isinstance(r_output, pd.DataFrame):
|
|
||||||
return r_output # Return as pandas DataFrame (already converted by pandas2ri)
|
|
||||||
elif isinstance(r_output, DataFrame):
|
|
||||||
return pandas2ri.rpy2py(r_output) # Return as pandas DataFrame
|
|
||||||
|
|
||||||
# Check if the input is a NumPy array and has a string data type
|
|
||||||
if isinstance(r_output, np.ndarray) and np.issubdtype(r_output.dtype, np.str_):
|
|
||||||
return r_output.tolist() # Convert to a regular Python list
|
|
||||||
|
|
||||||
# Fall-back
|
|
||||||
return r_output
|
|
||||||
def ab_class(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_class(*args, **kwargs))
|
|
||||||
def ab_selector(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_selector(*args, **kwargs))
|
|
||||||
def ab_from_text(text, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_from_text(text, *args, **kwargs))
|
|
||||||
def ab_name(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_name(x, *args, **kwargs))
|
|
||||||
def ab_cid(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_cid(x, *args, **kwargs))
|
|
||||||
def ab_synonyms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_synonyms(x, *args, **kwargs))
|
|
||||||
def ab_tradenames(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_tradenames(x, *args, **kwargs))
|
|
||||||
def ab_group(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_group(x, *args, **kwargs))
|
|
||||||
def ab_atc(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_atc(x, *args, **kwargs))
|
|
||||||
def ab_atc_group1(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_atc_group1(x, *args, **kwargs))
|
|
||||||
def ab_atc_group2(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_atc_group2(x, *args, **kwargs))
|
|
||||||
def ab_loinc(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_loinc(x, *args, **kwargs))
|
|
||||||
def ab_ddd(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_ddd(x, *args, **kwargs))
|
|
||||||
def ab_ddd_units(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_ddd_units(x, *args, **kwargs))
|
|
||||||
def ab_info(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_info(x, *args, **kwargs))
|
|
||||||
def ab_url(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_url(x, *args, **kwargs))
|
|
||||||
def ab_property(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_property(x, *args, **kwargs))
|
|
||||||
def add_custom_antimicrobials(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.add_custom_antimicrobials(x))
|
|
||||||
def clear_custom_antimicrobials(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.clear_custom_antimicrobials(*args, **kwargs))
|
|
||||||
def add_custom_microorganisms(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.add_custom_microorganisms(x))
|
|
||||||
def clear_custom_microorganisms(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.clear_custom_microorganisms(*args, **kwargs))
|
|
||||||
def age(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.age(x, *args, **kwargs))
|
|
||||||
def age_groups(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.age_groups(x, *args, **kwargs))
|
|
||||||
def antibiogram(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.antibiogram(x, *args, **kwargs))
|
|
||||||
def wisca(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.wisca(x, *args, **kwargs))
|
|
||||||
def retrieve_wisca_parameters(wisca_model, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.retrieve_wisca_parameters(wisca_model, *args, **kwargs))
|
|
||||||
def aminoglycosides(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.aminoglycosides(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def aminopenicillins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.aminopenicillins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def antifungals(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.antifungals(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def antimycobacterials(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def betalactams(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def carbapenems(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def cephalosporins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.cephalosporins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def cephalosporins_1st(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.cephalosporins_1st(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def cephalosporins_2nd(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.cephalosporins_2nd(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def cephalosporins_3rd(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.cephalosporins_3rd(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def cephalosporins_4th(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.cephalosporins_4th(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def cephalosporins_5th(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.cephalosporins_5th(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def fluoroquinolones(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.fluoroquinolones(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def glycopeptides(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def lincosamides(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.lincosamides(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def lipoglycopeptides(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.lipoglycopeptides(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def macrolides(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.macrolides(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def monobactams(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.monobactams(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def nitrofurans(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.nitrofurans(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def oxazolidinones(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.oxazolidinones(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def penicillins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.penicillins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def phenicols(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def polymyxins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def quinolones(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.quinolones(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def rifamycins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.rifamycins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def streptogramins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.streptogramins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def tetracyclines(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.tetracyclines(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def trimethoprims(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.trimethoprims(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def ureidopenicillins(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def amr_class(amr_class, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.amr_class(amr_class, *args, **kwargs))
|
|
||||||
def amr_selector(filter, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.amr_selector(filter, *args, **kwargs))
|
|
||||||
def administrable_per_os(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.administrable_per_os(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def administrable_iv(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs))
|
|
||||||
def as_ab(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.as_ab(x, *args, **kwargs))
|
|
||||||
def is_ab(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_ab(x))
|
|
||||||
def ab_reset_session(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ab_reset_session(*args, **kwargs))
|
|
||||||
def as_av(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.as_av(x, *args, **kwargs))
|
|
||||||
def is_av(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_av(x))
|
|
||||||
def as_disk(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.as_disk(x, *args, **kwargs))
|
|
||||||
def is_disk(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_disk(x))
|
|
||||||
def as_mic(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.as_mic(x, *args, **kwargs))
|
|
||||||
def is_mic(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_mic(x))
|
|
||||||
def rescale_mic(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.rescale_mic(x, *args, **kwargs))
|
|
||||||
def mic_p50(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mic_p50(x, *args, **kwargs))
|
|
||||||
def mic_p90(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mic_p90(x, *args, **kwargs))
|
|
||||||
def as_mo(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.as_mo(x, *args, **kwargs))
|
|
||||||
def is_mo(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_mo(x))
|
|
||||||
def mo_uncertainties(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_uncertainties(*args, **kwargs))
|
|
||||||
def mo_renamed(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_renamed(*args, **kwargs))
|
|
||||||
def mo_failures(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_failures(*args, **kwargs))
|
|
||||||
def mo_reset_session(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_reset_session(*args, **kwargs))
|
|
||||||
def mo_cleaning_regex(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_cleaning_regex(*args, **kwargs))
|
|
||||||
def as_sir(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.as_sir(x, *args, **kwargs))
|
|
||||||
def is_sir(x):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_sir(x))
|
|
||||||
def is_sir_eligible(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_sir_eligible(x, *args, **kwargs))
|
|
||||||
def sir_interpretation_history(clean):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.sir_interpretation_history(clean))
|
|
||||||
def atc_online_property(atc_code, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.atc_online_property(atc_code, *args, **kwargs))
|
|
||||||
def atc_online_groups(atc_code, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.atc_online_groups(atc_code, *args, **kwargs))
|
|
||||||
def atc_online_ddd(atc_code, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.atc_online_ddd(atc_code, *args, **kwargs))
|
|
||||||
def atc_online_ddd_units(atc_code, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.atc_online_ddd_units(atc_code, *args, **kwargs))
|
|
||||||
def av_from_text(text, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_from_text(text, *args, **kwargs))
|
|
||||||
def av_name(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_name(x, *args, **kwargs))
|
|
||||||
def av_cid(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_cid(x, *args, **kwargs))
|
|
||||||
def av_synonyms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_synonyms(x, *args, **kwargs))
|
|
||||||
def av_tradenames(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_tradenames(x, *args, **kwargs))
|
|
||||||
def av_group(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_group(x, *args, **kwargs))
|
|
||||||
def av_atc(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_atc(x, *args, **kwargs))
|
|
||||||
def av_loinc(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_loinc(x, *args, **kwargs))
|
|
||||||
def av_ddd(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_ddd(x, *args, **kwargs))
|
|
||||||
def av_ddd_units(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_ddd_units(x, *args, **kwargs))
|
|
||||||
def av_info(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_info(x, *args, **kwargs))
|
|
||||||
def av_url(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_url(x, *args, **kwargs))
|
|
||||||
def av_property(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.av_property(x, *args, **kwargs))
|
|
||||||
def availability(tbl, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.availability(tbl, *args, **kwargs))
|
|
||||||
def bug_drug_combinations(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.bug_drug_combinations(x, *args, **kwargs))
|
|
||||||
def count_resistant(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_resistant(*args, **kwargs))
|
|
||||||
def count_susceptible(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_susceptible(*args, **kwargs))
|
|
||||||
def count_S(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_S(*args, **kwargs))
|
|
||||||
def count_SI(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_SI(*args, **kwargs))
|
|
||||||
def count_I(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_I(*args, **kwargs))
|
|
||||||
def count_IR(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_IR(*args, **kwargs))
|
|
||||||
def count_R(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_R(*args, **kwargs))
|
|
||||||
def count_all(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_all(*args, **kwargs))
|
|
||||||
def n_sir(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.n_sir(*args, **kwargs))
|
|
||||||
def count_df(data, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.count_df(data, *args, **kwargs))
|
|
||||||
def custom_eucast_rules(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.custom_eucast_rules(*args, **kwargs))
|
|
||||||
def eucast_rules(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.eucast_rules(x, *args, **kwargs))
|
|
||||||
def eucast_dosage(ab, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.eucast_dosage(ab, *args, **kwargs))
|
|
||||||
def export_ncbi_biosample(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.export_ncbi_biosample(x, *args, **kwargs))
|
|
||||||
def first_isolate(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.first_isolate(x = None, *args, **kwargs))
|
|
||||||
def filter_first_isolate(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.filter_first_isolate(x = None, *args, **kwargs))
|
|
||||||
def g_test(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.g_test(x, *args, **kwargs))
|
|
||||||
def is_new_episode(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.is_new_episode(x, *args, **kwargs))
|
|
||||||
def ggplot_pca(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ggplot_pca(x, *args, **kwargs))
|
|
||||||
def ggplot_sir(data, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ggplot_sir(data, *args, **kwargs))
|
|
||||||
def geom_sir(position = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.geom_sir(position = None, *args, **kwargs))
|
|
||||||
def guess_ab_col(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.guess_ab_col(x = None, *args, **kwargs))
|
|
||||||
def italicise_taxonomy(string, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.italicise_taxonomy(string, *args, **kwargs))
|
|
||||||
def italicize_taxonomy(string, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.italicize_taxonomy(string, *args, **kwargs))
|
|
||||||
def inner_join_microorganisms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.inner_join_microorganisms(x, *args, **kwargs))
|
|
||||||
def left_join_microorganisms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.left_join_microorganisms(x, *args, **kwargs))
|
|
||||||
def right_join_microorganisms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.right_join_microorganisms(x, *args, **kwargs))
|
|
||||||
def full_join_microorganisms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.full_join_microorganisms(x, *args, **kwargs))
|
|
||||||
def semi_join_microorganisms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.semi_join_microorganisms(x, *args, **kwargs))
|
|
||||||
def anti_join_microorganisms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.anti_join_microorganisms(x, *args, **kwargs))
|
|
||||||
def key_antimicrobials(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.key_antimicrobials(x = None, *args, **kwargs))
|
|
||||||
def all_antimicrobials(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.all_antimicrobials(x = None, *args, **kwargs))
|
|
||||||
def kurtosis(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.kurtosis(x, *args, **kwargs))
|
|
||||||
def like(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.like(x, *args, **kwargs))
|
|
||||||
def mdro(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mdro(x = None, *args, **kwargs))
|
|
||||||
def custom_mdro_guideline(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.custom_mdro_guideline(*args, **kwargs))
|
|
||||||
def brmo(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.brmo(x = None, *args, **kwargs))
|
|
||||||
def mrgn(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mrgn(x = None, *args, **kwargs))
|
|
||||||
def mdr_tb(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mdr_tb(x = None, *args, **kwargs))
|
|
||||||
def mdr_cmi2012(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mdr_cmi2012(x = None, *args, **kwargs))
|
|
||||||
def eucast_exceptional_phenotypes(x = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.eucast_exceptional_phenotypes(x = None, *args, **kwargs))
|
|
||||||
def mean_amr_distance(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mean_amr_distance(x, *args, **kwargs))
|
|
||||||
def amr_distance_from_row(amr_distance, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.amr_distance_from_row(amr_distance, *args, **kwargs))
|
|
||||||
def mo_matching_score(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_matching_score(x, *args, **kwargs))
|
|
||||||
def mo_name(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_name(x, *args, **kwargs))
|
|
||||||
def mo_fullname(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_fullname(x, *args, **kwargs))
|
|
||||||
def mo_shortname(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_shortname(x, *args, **kwargs))
|
|
||||||
def mo_subspecies(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_subspecies(x, *args, **kwargs))
|
|
||||||
def mo_species(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_species(x, *args, **kwargs))
|
|
||||||
def mo_genus(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_genus(x, *args, **kwargs))
|
|
||||||
def mo_family(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_family(x, *args, **kwargs))
|
|
||||||
def mo_order(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_order(x, *args, **kwargs))
|
|
||||||
def mo_class(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_class(x, *args, **kwargs))
|
|
||||||
def mo_phylum(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_phylum(x, *args, **kwargs))
|
|
||||||
def mo_kingdom(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_kingdom(x, *args, **kwargs))
|
|
||||||
def mo_domain(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_domain(x, *args, **kwargs))
|
|
||||||
def mo_type(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_type(x, *args, **kwargs))
|
|
||||||
def mo_status(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_status(x, *args, **kwargs))
|
|
||||||
def mo_pathogenicity(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_pathogenicity(x, *args, **kwargs))
|
|
||||||
def mo_gramstain(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_gramstain(x, *args, **kwargs))
|
|
||||||
def mo_is_gram_negative(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_is_gram_negative(x, *args, **kwargs))
|
|
||||||
def mo_is_gram_positive(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_is_gram_positive(x, *args, **kwargs))
|
|
||||||
def mo_is_yeast(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_is_yeast(x, *args, **kwargs))
|
|
||||||
def mo_is_intrinsic_resistant(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs))
|
|
||||||
def mo_oxygen_tolerance(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_oxygen_tolerance(x, *args, **kwargs))
|
|
||||||
def mo_is_anaerobic(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_is_anaerobic(x, *args, **kwargs))
|
|
||||||
def mo_snomed(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_snomed(x, *args, **kwargs))
|
|
||||||
def mo_ref(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_ref(x, *args, **kwargs))
|
|
||||||
def mo_authors(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_authors(x, *args, **kwargs))
|
|
||||||
def mo_year(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_year(x, *args, **kwargs))
|
|
||||||
def mo_lpsn(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_lpsn(x, *args, **kwargs))
|
|
||||||
def mo_mycobank(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_mycobank(x, *args, **kwargs))
|
|
||||||
def mo_gbif(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_gbif(x, *args, **kwargs))
|
|
||||||
def mo_rank(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_rank(x, *args, **kwargs))
|
|
||||||
def mo_taxonomy(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_taxonomy(x, *args, **kwargs))
|
|
||||||
def mo_synonyms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_synonyms(x, *args, **kwargs))
|
|
||||||
def mo_current(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_current(x, *args, **kwargs))
|
|
||||||
def mo_group_members(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_group_members(x, *args, **kwargs))
|
|
||||||
def mo_info(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_info(x, *args, **kwargs))
|
|
||||||
def mo_url(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_url(x, *args, **kwargs))
|
|
||||||
def mo_property(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.mo_property(x, *args, **kwargs))
|
|
||||||
def pca(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.pca(x, *args, **kwargs))
|
|
||||||
def theme_sir(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.theme_sir(*args, **kwargs))
|
|
||||||
def labels_sir_count(position = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.labels_sir_count(position = None, *args, **kwargs))
|
|
||||||
def resistance(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.resistance(*args, **kwargs))
|
|
||||||
def susceptibility(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.susceptibility(*args, **kwargs))
|
|
||||||
def sir_confidence_interval(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.sir_confidence_interval(*args, **kwargs))
|
|
||||||
def proportion_R(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.proportion_R(*args, **kwargs))
|
|
||||||
def proportion_IR(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.proportion_IR(*args, **kwargs))
|
|
||||||
def proportion_I(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.proportion_I(*args, **kwargs))
|
|
||||||
def proportion_SI(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.proportion_SI(*args, **kwargs))
|
|
||||||
def proportion_S(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.proportion_S(*args, **kwargs))
|
|
||||||
def proportion_df(data, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.proportion_df(data, *args, **kwargs))
|
|
||||||
def sir_df(data, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.sir_df(data, *args, **kwargs))
|
|
||||||
def random_mic(size = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.random_mic(size = None, *args, **kwargs))
|
|
||||||
def random_disk(size = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.random_disk(size = None, *args, **kwargs))
|
|
||||||
def random_sir(size = None, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.random_sir(size = None, *args, **kwargs))
|
|
||||||
def resistance_predict(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.resistance_predict(x, *args, **kwargs))
|
|
||||||
def sir_predict(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.sir_predict(x, *args, **kwargs))
|
|
||||||
def ggplot_sir_predict(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.ggplot_sir_predict(x, *args, **kwargs))
|
|
||||||
def skewness(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.skewness(x, *args, **kwargs))
|
|
||||||
def top_n_microorganisms(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.top_n_microorganisms(x, *args, **kwargs))
|
|
||||||
def reset_AMR_locale(*args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.reset_AMR_locale(*args, **kwargs))
|
|
||||||
def translate_AMR(x, *args, **kwargs):
|
|
||||||
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
|
|
||||||
return convert_to_python(amr_r.translate_AMR(x, *args, **kwargs))
|
|
||||||
@ -1,195 +0,0 @@
|
|||||||
---
|
|
||||||
title: "AMR for Python"
|
|
||||||
output:
|
|
||||||
rmarkdown::html_vignette:
|
|
||||||
toc: true
|
|
||||||
toc_depth: 3
|
|
||||||
vignette: >
|
|
||||||
%\VignetteIndexEntry{AMR for Python}
|
|
||||||
%\VignetteEncoding{UTF-8}
|
|
||||||
%\VignetteEngine{knitr::rmarkdown}
|
|
||||||
editor_options:
|
|
||||||
chunk_output_type: console
|
|
||||||
---
|
|
||||||
|
|
||||||
```{r setup, include = FALSE, results = 'markup'}
|
|
||||||
knitr::opts_chunk$set(
|
|
||||||
warning = FALSE,
|
|
||||||
collapse = TRUE,
|
|
||||||
comment = "#>",
|
|
||||||
fig.width = 7.5,
|
|
||||||
fig.height = 5
|
|
||||||
)
|
|
||||||
```
|
|
||||||
|
|
||||||
# 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/).
|
|
||||||
|
|
||||||
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.
|
|
||||||
|
|
||||||
# Install
|
|
||||||
|
|
||||||
1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
|
|
||||||
|
|
||||||
```bash
|
|
||||||
pip install AMR
|
|
||||||
```
|
|
||||||
|
|
||||||
2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
|
|
||||||
|
|
||||||
For Linux:
|
|
||||||
|
|
||||||
```bash
|
|
||||||
# Ubuntu / Debian
|
|
||||||
sudo apt install r-base
|
|
||||||
# Fedora:
|
|
||||||
sudo dnf install R
|
|
||||||
# CentOS/RHEL
|
|
||||||
sudo yum install R
|
|
||||||
```
|
|
||||||
|
|
||||||
For macOS (using [Homebrew](https://brew.sh)):
|
|
||||||
|
|
||||||
```bash
|
|
||||||
brew install r
|
|
||||||
```
|
|
||||||
|
|
||||||
For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R.
|
|
||||||
|
|
||||||
# Examples of Usage
|
|
||||||
|
|
||||||
## Cleaning Taxonomy
|
|
||||||
|
|
||||||
Here’s an example that demonstrates how to clean microorganism and drug names using the `AMR` Python package:
|
|
||||||
|
|
||||||
```python
|
|
||||||
import pandas as pd
|
|
||||||
import AMR
|
|
||||||
|
|
||||||
# Sample data
|
|
||||||
data = {
|
|
||||||
"MOs": ['E. coli', 'ESCCOL', 'esco', 'Esche coli'],
|
|
||||||
"Drug": ['Cipro', 'CIP', 'J01MA02', 'Ciproxin']
|
|
||||||
}
|
|
||||||
df = pd.DataFrame(data)
|
|
||||||
|
|
||||||
# Use AMR functions to clean microorganism and drug names
|
|
||||||
df['MO_clean'] = AMR.mo_name(df['MOs'])
|
|
||||||
df['Drug_clean'] = AMR.ab_name(df['Drug'])
|
|
||||||
|
|
||||||
# Display the results
|
|
||||||
print(df)
|
|
||||||
```
|
|
||||||
|
|
||||||
| MOs | Drug | MO_clean | Drug_clean |
|
|
||||||
|-------------|-----------|--------------------|---------------|
|
|
||||||
| E. coli | Cipro | Escherichia coli | Ciprofloxacin |
|
|
||||||
| ESCCOL | CIP | Escherichia coli | Ciprofloxacin |
|
|
||||||
| esco | J01MA02 | Escherichia coli | Ciprofloxacin |
|
|
||||||
| Esche coli | Ciproxin | Escherichia coli | Ciprofloxacin |
|
|
||||||
|
|
||||||
### Explanation
|
|
||||||
|
|
||||||
* **mo_name:** This function standardises microorganism names. Here, different variations of *Escherichia coli* (such as "E. coli", "ESCCOL", "esco", and "Esche coli") are all converted into the correct, standardised form, "Escherichia coli".
|
|
||||||
|
|
||||||
* **ab_name**: Similarly, this function standardises antimicrobial names. The different representations of ciprofloxacin (e.g., "Cipro", "CIP", "J01MA02", and "Ciproxin") are all converted to the standard name, "Ciprofloxacin".
|
|
||||||
|
|
||||||
## Calculating AMR
|
|
||||||
|
|
||||||
```python
|
|
||||||
import AMR
|
|
||||||
import pandas as pd
|
|
||||||
|
|
||||||
df = AMR.example_isolates
|
|
||||||
result = AMR.resistance(df["AMX"])
|
|
||||||
print(result)
|
|
||||||
```
|
|
||||||
|
|
||||||
```
|
|
||||||
[0.59555556]
|
|
||||||
```
|
|
||||||
|
|
||||||
## Generating Antibiograms
|
|
||||||
|
|
||||||
One of the core functions of the `AMR` package is generating an antibiogram, a table that summarises the antimicrobial susceptibility of bacterial isolates. Here’s how you can generate an antibiogram from Python:
|
|
||||||
|
|
||||||
```python
|
|
||||||
result2a = AMR.antibiogram(df[["mo", "AMX", "CIP", "TZP"]])
|
|
||||||
print(result2a)
|
|
||||||
```
|
|
||||||
|
|
||||||
| Pathogen | Amoxicillin | Ciprofloxacin | Piperacillin/tazobactam |
|
|
||||||
|-----------------|-----------------|-----------------|--------------------------|
|
|
||||||
| CoNS | 7% (10/142) | 73% (183/252) | 30% (10/33) |
|
|
||||||
| E. coli | 50% (196/392) | 88% (399/456) | 94% (393/416) |
|
|
||||||
| K. pneumoniae | 0% (0/58) | 96% (53/55) | 89% (47/53) |
|
|
||||||
| P. aeruginosa | 0% (0/30) | 100% (30/30) | None |
|
|
||||||
| P. mirabilis | None | 94% (34/36) | None |
|
|
||||||
| S. aureus | 6% (8/131) | 90% (171/191) | None |
|
|
||||||
| S. epidermidis | 1% (1/91) | 64% (87/136) | None |
|
|
||||||
| S. hominis | None | 80% (56/70) | None |
|
|
||||||
| S. pneumoniae | 100% (112/112) | None | 100% (112/112) |
|
|
||||||
|
|
||||||
|
|
||||||
```python
|
|
||||||
result2b = AMR.antibiogram(df[["mo", "AMX", "CIP", "TZP"]], mo_transform = "gramstain")
|
|
||||||
print(result2b)
|
|
||||||
```
|
|
||||||
|
|
||||||
| Pathogen | Amoxicillin | Ciprofloxacin | Piperacillin/tazobactam |
|
|
||||||
|----------------|-----------------|------------------|--------------------------|
|
|
||||||
| Gram-negative | 36% (226/631) | 91% (621/684) | 88% (565/641) |
|
|
||||||
| Gram-positive | 43% (305/703) | 77% (560/724) | 86% (296/345) |
|
|
||||||
|
|
||||||
|
|
||||||
In this example, we generate an antibiogram by selecting various antibiotics.
|
|
||||||
|
|
||||||
## Taxonomic Data Sets Now in Python!
|
|
||||||
|
|
||||||
As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `antimicrobials`, `clinical_breakpoints`, and `example_isolates`, are now available as regular Python data frames:
|
|
||||||
|
|
||||||
```python
|
|
||||||
AMR.microorganisms
|
|
||||||
```
|
|
||||||
|
|
||||||
| mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
|
|
||||||
|--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
|
|
||||||
| B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
|
|
||||||
| ... | ... | ... | ... | ... | ... | ... | ... |
|
|
||||||
| B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
|
|
||||||
| B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
|
|
||||||
| B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
|
|
||||||
| B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
|
|
||||||
| F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
|
|
||||||
|
|
||||||
```python
|
|
||||||
AMR.antimicrobials
|
|
||||||
```
|
|
||||||
|
|
||||||
| ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
|
|
||||||
|-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
|
|
||||||
| AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
|
|
||||||
| ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
|
|
||||||
| ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
|
|
||||||
| ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
|
|
||||||
| AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
|
|
||||||
| ... | ... | ... | ... | ... | ... | ... | ... |
|
|
||||||
| VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
|
|
||||||
| VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
|
|
||||||
| XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
|
|
||||||
| ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
|
|
||||||
| ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
|
|
||||||
|
|
||||||
|
|
||||||
# Conclusion
|
|
||||||
|
|
||||||
With the `AMR` Python package, Python users can now effortlessly call R functions from the `AMR` R package. This eliminates the need for complex `rpy2` configurations and provides a clean, easy-to-use interface for antimicrobial resistance analysis. The examples provided above demonstrate how this can be applied to typical workflows, such as standardising microorganism and antimicrobial names or calculating resistance.
|
|
||||||
|
|
||||||
By just running `import AMR`, users can seamlessly integrate the robust features of the R `AMR` package into Python workflows.
|
|
||||||
|
|
||||||
Whether you're cleaning data or analysing resistance patterns, the `AMR` Python package makes it easy to work with AMR data in Python.
|
|
||||||
Binary file not shown.
BIN
PythonPackage/AMR/dist/amr-2.1.1.9203.tar.gz
vendored
BIN
PythonPackage/AMR/dist/amr-2.1.1.9203.tar.gz
vendored
Binary file not shown.
@ -1,27 +0,0 @@
|
|||||||
from setuptools import setup, find_packages
|
|
||||||
|
|
||||||
setup(
|
|
||||||
name='AMR',
|
|
||||||
version='2.1.1.9203',
|
|
||||||
packages=find_packages(),
|
|
||||||
install_requires=[
|
|
||||||
'rpy2',
|
|
||||||
'numpy',
|
|
||||||
'pandas',
|
|
||||||
],
|
|
||||||
author='Matthijs Berends',
|
|
||||||
author_email='m.s.berends@umcg.nl',
|
|
||||||
description='A Python wrapper for the AMR R package',
|
|
||||||
long_description=open('README.md').read(),
|
|
||||||
long_description_content_type='text/markdown',
|
|
||||||
url='https://github.com/msberends/AMR',
|
|
||||||
project_urls={
|
|
||||||
'Bug Tracker': 'https://github.com/msberends/AMR/issues',
|
|
||||||
},
|
|
||||||
license='GPL 2',
|
|
||||||
classifiers=[
|
|
||||||
'Programming Language :: Python :: 3',
|
|
||||||
'Operating System :: OS Independent',
|
|
||||||
],
|
|
||||||
python_requires='>=3.6',
|
|
||||||
)
|
|
||||||
@ -17,7 +17,7 @@ echo "This knowledge base contains all context you must know about the AMR packa
|
|||||||
echo "" >> "$output_file"
|
echo "" >> "$output_file"
|
||||||
echo "First and foremost, you are trained on version ${version}. Remember this whenever someone asks which AMR package version you’re at." >> "$output_file"
|
echo "First and foremost, you are trained on version ${version}. Remember this whenever someone asks which AMR package version you’re at." >> "$output_file"
|
||||||
echo "" >> "$output_file"
|
echo "" >> "$output_file"
|
||||||
echo "Below are the contents of the `NAMESPACE` file, the `index.md` file, and all the `man/*.Rd` files (documentation) in the package. Every file content is split using 100 hypens." >> "$output_file"
|
echo "Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens." >> "$output_file"
|
||||||
echo "----------------------------------------------------------------------------------------------------" >> "$output_file"
|
echo "----------------------------------------------------------------------------------------------------" >> "$output_file"
|
||||||
echo "" >> "$output_file"
|
echo "" >> "$output_file"
|
||||||
|
|
||||||
|
|||||||
@ -626,19 +626,28 @@ suppressMessages(reset_AMR_locale())
|
|||||||
devtools::load_all(quiet = TRUE)
|
devtools::load_all(quiet = TRUE)
|
||||||
suppressMessages(set_AMR_locale("English"))
|
suppressMessages(set_AMR_locale("English"))
|
||||||
|
|
||||||
|
files_changed <- function(paths = "^(R|data)/") {
|
||||||
|
tryCatch({
|
||||||
|
changed_files <- system("git diff --name-only", intern = TRUE)
|
||||||
|
any(changed_files %like% paths)
|
||||||
|
}, error = function(e) TRUE)
|
||||||
|
}
|
||||||
|
|
||||||
# Update URLs -------------------------------------------------------------
|
# Update URLs -------------------------------------------------------------
|
||||||
usethis::ui_info("Checking URLs for redirects")
|
if (files_changed()) {
|
||||||
invisible(urlchecker::url_update("."))
|
usethis::ui_info("Checking URLs for redirects")
|
||||||
|
invisible(urlchecker::url_update("."))
|
||||||
|
}
|
||||||
|
|
||||||
# Style pkg ---------------------------------------------------------------
|
# Style pkg ---------------------------------------------------------------
|
||||||
usethis::ui_info("Styling package")
|
if (files_changed(paths = "^(R|tests)/")) {
|
||||||
styler::style_pkg(include_roxygen_examples = FALSE,
|
sethis::ui_info("Styling package")
|
||||||
exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")])
|
styler::style_pkg(include_roxygen_examples = FALSE,
|
||||||
|
exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")])
|
||||||
|
}
|
||||||
|
|
||||||
# Document pkg ------------------------------------------------------------
|
# Document pkg ------------------------------------------------------------
|
||||||
if (interactive()) {
|
if (files_changed()) {
|
||||||
message("Skipping document in interactive mode")
|
|
||||||
} else {
|
|
||||||
usethis::ui_info("Documenting package")
|
usethis::ui_info("Documenting package")
|
||||||
suppressMessages(devtools::document(quiet = TRUE))
|
suppressMessages(devtools::document(quiet = TRUE))
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1,8 +1,8 @@
|
|||||||
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.
|
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 2.1.1.9203. Remember this whenever someone asks which AMR package version you’re at.
|
First and foremost, you are trained on version 2.1.1.9207. 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.
|
Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens.
|
||||||
----------------------------------------------------------------------------------------------------
|
----------------------------------------------------------------------------------------------------
|
||||||
|
|
||||||
----------------------------------------------------------------------------------------------------
|
----------------------------------------------------------------------------------------------------
|
||||||
Loading…
x
Reference in New Issue
Block a user