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AMR.egg-info/PKG-INFO
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AMR.egg-info/PKG-INFO
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Metadata-Version: 2.4
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Name: AMR
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Version: 2.1.1.9268
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Summary: A Python wrapper for the AMR R package
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Home-page: https://github.com/msberends/AMR
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Author: Matthijs Berends
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Author-email: m.s.berends@umcg.nl
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License: GPL 2
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Project-URL: Bug Tracker, https://github.com/msberends/AMR/issues
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Classifier: Programming Language :: Python :: 3
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Classifier: Operating System :: OS Independent
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Requires-Python: >=3.6
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Description-Content-Type: text/markdown
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Requires-Dist: rpy2
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Requires-Dist: numpy
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Requires-Dist: pandas
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Dynamic: author
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Dynamic: author-email
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Dynamic: classifier
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Dynamic: description
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Dynamic: description-content-type
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Dynamic: home-page
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Dynamic: license
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Dynamic: project-url
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Dynamic: requires-dist
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Dynamic: requires-python
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Dynamic: summary
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The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) analysis. It provides extensive features for handling microbial and antimicrobial data. However, for those who work primarily in Python, we now have a more intuitive option available: the [`AMR` Python package](https://pypi.org/project/AMR/).
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This Python package is a wrapper around the `AMR` R package. It uses the `rpy2` package internally. Despite the need to have R installed, Python users can now easily work with AMR data directly through Python code.
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# Prerequisites
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This package was only tested with a [virtual environment (venv)](https://docs.python.org/3/library/venv.html). You can set up such an environment by running:
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```python
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# linux and macOS:
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python -m venv /path/to/new/virtual/environment
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# Windows:
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python -m venv C:\path\to\new\virtual\environment
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```
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Then you can [activate the environment](https://docs.python.org/3/library/venv.html#how-venvs-work), after which the venv is ready to work with.
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# Install AMR
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1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
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```bash
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pip install AMR
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```
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2. Make sure you have R installed. There is **no need to install the `AMR` R package**, as it will be installed automatically.
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For Linux:
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```bash
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# Ubuntu / Debian
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sudo apt install r-base
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# Fedora:
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sudo dnf install R
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# CentOS/RHEL
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sudo yum install R
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```
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For macOS (using [Homebrew](https://brew.sh)):
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```bash
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brew install r
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```
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For Windows, visit the [CRAN download page](https://cran.r-project.org) to download and install R.
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# Examples of Usage
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## Cleaning Taxonomy
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Here’s an example that demonstrates how to clean microorganism and drug names using the `AMR` Python package:
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```python
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import pandas as pd
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import AMR
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# Sample data
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data = {
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"MOs": ['E. coli', 'ESCCOL', 'esco', 'Esche coli'],
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"Drug": ['Cipro', 'CIP', 'J01MA02', 'Ciproxin']
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}
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df = pd.DataFrame(data)
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# Use AMR functions to clean microorganism and drug names
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df['MO_clean'] = AMR.mo_name(df['MOs'])
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df['Drug_clean'] = AMR.ab_name(df['Drug'])
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# Display the results
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print(df)
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```
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| MOs | Drug | MO_clean | Drug_clean |
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|-------------|-----------|--------------------|---------------|
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| E. coli | Cipro | Escherichia coli | Ciprofloxacin |
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| ESCCOL | CIP | Escherichia coli | Ciprofloxacin |
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| esco | J01MA02 | Escherichia coli | Ciprofloxacin |
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| Esche coli | Ciproxin | Escherichia coli | Ciprofloxacin |
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### Explanation
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* **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".
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* **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".
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## Calculating AMR
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```python
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import AMR
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import pandas as pd
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df = AMR.example_isolates
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result = AMR.resistance(df["AMX"])
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print(result)
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```
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```
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[0.59555556]
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```
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## Generating Antibiograms
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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:
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```python
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result2a = AMR.antibiogram(df[["mo", "AMX", "CIP", "TZP"]])
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print(result2a)
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```
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| Pathogen | Amoxicillin | Ciprofloxacin | Piperacillin/tazobactam |
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|-----------------|-----------------|-----------------|--------------------------|
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| CoNS | 7% (10/142) | 73% (183/252) | 30% (10/33) |
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| E. coli | 50% (196/392) | 88% (399/456) | 94% (393/416) |
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| K. pneumoniae | 0% (0/58) | 96% (53/55) | 89% (47/53) |
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| P. aeruginosa | 0% (0/30) | 100% (30/30) | None |
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| P. mirabilis | None | 94% (34/36) | None |
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| S. aureus | 6% (8/131) | 90% (171/191) | None |
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| S. epidermidis | 1% (1/91) | 64% (87/136) | None |
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| S. hominis | None | 80% (56/70) | None |
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| S. pneumoniae | 100% (112/112) | None | 100% (112/112) |
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```python
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result2b = AMR.antibiogram(df[["mo", "AMX", "CIP", "TZP"]], mo_transform = "gramstain")
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print(result2b)
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```
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| Pathogen | Amoxicillin | Ciprofloxacin | Piperacillin/tazobactam |
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|----------------|-----------------|------------------|--------------------------|
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| Gram-negative | 36% (226/631) | 91% (621/684) | 88% (565/641) |
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| Gram-positive | 43% (305/703) | 77% (560/724) | 86% (296/345) |
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In this example, we generate an antibiogram by selecting various antibiotics.
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## Taxonomic Data Sets Now in Python!
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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:
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```python
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AMR.microorganisms
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```
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| mo | fullname | status | kingdom | gbif | gbif_parent | gbif_renamed_to | prevalence |
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|--------------|------------------------------------|----------|----------|-----------|-------------|-----------------|------------|
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| B_GRAMN | (unknown Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
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| B_GRAMP | (unknown Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
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| B_ANAER-NEG | (unknown anaerobic Gram-negatives) | unknown | Bacteria | None | None | None | 2.0 |
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| B_ANAER-POS | (unknown anaerobic Gram-positives) | unknown | Bacteria | None | None | None | 2.0 |
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| B_ANAER | (unknown anaerobic bacteria) | unknown | Bacteria | None | None | None | 2.0 |
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| ... | ... | ... | ... | ... | ... | ... | ... |
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| B_ZYMMN_POMC | Zymomonas pomaceae | accepted | Bacteria | 10744418 | 3221412 | None | 2.0 |
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| B_ZYMPH | Zymophilus | synonym | Bacteria | None | 9475166 | None | 2.0 |
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| B_ZYMPH_PCVR | Zymophilus paucivorans | synonym | Bacteria | None | None | None | 2.0 |
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| B_ZYMPH_RFFN | Zymophilus raffinosivorans | synonym | Bacteria | None | None | None | 2.0 |
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| F_ZYZYG | Zyzygomyces | unknown | Fungi | None | 7581 | None | 2.0 |
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```python
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AMR.antimicrobials
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```
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| ab | cid | name | group | oral_ddd | oral_units | iv_ddd | iv_units |
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|-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
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| AMA | 4649.0 | 4-aminosalicylic acid| Antimycobacterials | 12.00 | g | NaN | None |
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| ACM | 6450012.0 | Acetylmidecamycin | Macrolides/lincosamides | NaN | None | NaN | None |
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| ASP | 49787020.0 | Acetylspiramycin | Macrolides/lincosamides | NaN | None | NaN | None |
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| ALS | 8954.0 | Aldesulfone sodium | Other antibacterials | 0.33 | g | NaN | None |
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| AMK | 37768.0 | Amikacin | Aminoglycosides | NaN | None | 1.0 | g |
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| ... | ... | ... | ... | ... | ... | ... | ... |
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| VIR | 11979535.0 | Virginiamycine | Other antibacterials | NaN | None | NaN | None |
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| VOR | 71616.0 | Voriconazole | Antifungals/antimycotics | 0.40 | g | 0.4 | g |
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| XBR | 72144.0 | Xibornol | Other antibacterials | NaN | None | NaN | None |
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| ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
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| ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
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# Conclusion
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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.
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By just running `import AMR`, users can seamlessly integrate the robust features of the R `AMR` package into Python workflows.
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Whether you're cleaning data or analysing resistance patterns, the `AMR` Python package makes it easy to work with AMR data in Python.
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10
AMR.egg-info/SOURCES.txt
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AMR.egg-info/SOURCES.txt
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README.md
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setup.py
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AMR/__init__.py
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AMR/datasets.py
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AMR/functions.py
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AMR.egg-info/PKG-INFO
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AMR.egg-info/SOURCES.txt
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AMR.egg-info/dependency_links.txt
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AMR.egg-info/requires.txt
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AMR.egg-info/top_level.txt
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1
AMR.egg-info/dependency_links.txt
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AMR.egg-info/dependency_links.txt
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3
AMR.egg-info/requires.txt
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AMR.egg-info/requires.txt
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rpy2
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numpy
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pandas
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AMR.egg-info/top_level.txt
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AMR.egg-info/top_level.txt
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AMR
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AMR/__init__.py
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AMR/__init__.py
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from .datasets import example_isolates
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from .datasets import microorganisms
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from .datasets import antimicrobials
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from .datasets import clinical_breakpoints
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from .functions import ab_class
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from .functions import ab_selector
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from .functions import ab_from_text
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from .functions import ab_name
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from .functions import ab_cid
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from .functions import ab_synonyms
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from .functions import ab_tradenames
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from .functions import ab_group
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from .functions import ab_atc
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from .functions import ab_atc_group1
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from .functions import ab_atc_group2
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from .functions import ab_loinc
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from .functions import ab_ddd
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from .functions import ab_ddd_units
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from .functions import ab_info
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from .functions import ab_url
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from .functions import ab_property
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from .functions import add_custom_antimicrobials
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from .functions import clear_custom_antimicrobials
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from .functions import add_custom_microorganisms
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from .functions import clear_custom_microorganisms
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from .functions import age
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from .functions import age_groups
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from .functions import antibiogram
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from .functions import wisca
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from .functions import retrieve_wisca_parameters
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from .functions import aminoglycosides
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from .functions import aminopenicillins
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from .functions import antifungals
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from .functions import antimycobacterials
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from .functions import betalactams
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from .functions import betalactams_with_inhibitor
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from .functions import carbapenems
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from .functions import cephalosporins
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from .functions import cephalosporins_1st
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from .functions import cephalosporins_2nd
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from .functions import cephalosporins_3rd
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from .functions import cephalosporins_4th
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from .functions import cephalosporins_5th
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from .functions import fluoroquinolones
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from .functions import glycopeptides
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from .functions import isoxazolylpenicillins
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from .functions import lincosamides
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from .functions import lipoglycopeptides
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from .functions import macrolides
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from .functions import monobactams
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from .functions import nitrofurans
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from .functions import oxazolidinones
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from .functions import penicillins
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from .functions import phenicols
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from .functions import polymyxins
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from .functions import quinolones
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from .functions import rifamycins
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from .functions import streptogramins
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from .functions import sulfonamides
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from .functions import tetracyclines
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from .functions import trimethoprims
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from .functions import ureidopenicillins
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from .functions import amr_class
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from .functions import amr_selector
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from .functions import administrable_per_os
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from .functions import administrable_iv
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from .functions import not_intrinsic_resistant
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from .functions import as_ab
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from .functions import is_ab
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from .functions import ab_reset_session
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from .functions import as_av
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from .functions import is_av
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from .functions import as_disk
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from .functions import is_disk
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from .functions import as_mic
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from .functions import is_mic
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from .functions import rescale_mic
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from .functions import mic_p50
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from .functions import mic_p90
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from .functions import as_mo
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from .functions import is_mo
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from .functions import mo_uncertainties
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from .functions import mo_renamed
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from .functions import mo_failures
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from .functions import mo_reset_session
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from .functions import mo_cleaning_regex
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from .functions import as_sir
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from .functions import is_sir
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from .functions import is_sir_eligible
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from .functions import sir_interpretation_history
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from .functions import atc_online_property
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from .functions import atc_online_groups
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from .functions import atc_online_ddd
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from .functions import atc_online_ddd_units
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from .functions import av_from_text
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from .functions import av_name
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from .functions import av_cid
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from .functions import av_synonyms
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from .functions import av_tradenames
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from .functions import av_group
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from .functions import av_atc
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from .functions import av_loinc
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from .functions import av_ddd
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from .functions import av_ddd_units
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from .functions import av_info
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from .functions import av_url
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from .functions import av_property
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from .functions import availability
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from .functions import bug_drug_combinations
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from .functions import count_resistant
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from .functions import count_susceptible
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from .functions import count_S
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from .functions import count_SI
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from .functions import count_I
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from .functions import count_IR
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from .functions import count_R
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from .functions import count_all
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from .functions import n_sir
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from .functions import count_df
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from .functions import custom_eucast_rules
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from .functions import eucast_rules
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from .functions import eucast_dosage
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from .functions import export_ncbi_biosample
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from .functions import first_isolate
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from .functions import filter_first_isolate
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from .functions import g_test
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from .functions import is_new_episode
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from .functions import ggplot_pca
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from .functions import ggplot_sir
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from .functions import geom_sir
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from .functions import guess_ab_col
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from .functions import italicise_taxonomy
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from .functions import italicize_taxonomy
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from .functions import inner_join_microorganisms
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from .functions import left_join_microorganisms
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from .functions import right_join_microorganisms
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from .functions import full_join_microorganisms
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from .functions import semi_join_microorganisms
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from .functions import anti_join_microorganisms
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from .functions import key_antimicrobials
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from .functions import all_antimicrobials
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from .functions import kurtosis
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from .functions import like
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from .functions import mdro
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from .functions import custom_mdro_guideline
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from .functions import brmo
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from .functions import mrgn
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from .functions import mdr_tb
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from .functions import mdr_cmi2012
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from .functions import eucast_exceptional_phenotypes
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from .functions import mean_amr_distance
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from .functions import amr_distance_from_row
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from .functions import mo_matching_score
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from .functions import mo_name
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from .functions import mo_fullname
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from .functions import mo_shortname
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from .functions import mo_subspecies
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from .functions import mo_species
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from .functions import mo_genus
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from .functions import mo_family
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from .functions import mo_order
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from .functions import mo_class
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from .functions import mo_phylum
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from .functions import mo_kingdom
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from .functions import mo_domain
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from .functions import mo_type
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from .functions import mo_status
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from .functions import mo_pathogenicity
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||||
from .functions import mo_gramstain
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from .functions import mo_is_gram_negative
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from .functions import mo_is_gram_positive
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from .functions import mo_is_yeast
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||||
from .functions import mo_is_intrinsic_resistant
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||||
from .functions import mo_oxygen_tolerance
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||||
from .functions import mo_is_anaerobic
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from .functions import mo_snomed
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from .functions import mo_ref
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||||
from .functions import mo_authors
|
||||
from .functions import mo_year
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||||
from .functions import mo_lpsn
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||||
from .functions import mo_mycobank
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from .functions import mo_gbif
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||||
from .functions import mo_rank
|
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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
|
||||
82
AMR/datasets.py
Normal file
82
AMR/datasets.py
Normal file
@ -0,0 +1,82 @@
|
||||
import os
|
||||
import sys
|
||||
import pandas as pd
|
||||
import importlib.metadata as metadata
|
||||
|
||||
# Get the path to the virtual environment
|
||||
venv_path = sys.prefix
|
||||
r_lib_path = os.path.join(venv_path, "R_libs")
|
||||
os.makedirs(r_lib_path, exist_ok=True)
|
||||
|
||||
# Set environment variable before importing rpy2
|
||||
os.environ['R_LIBS_SITE'] = r_lib_path
|
||||
|
||||
from rpy2 import robjects
|
||||
from rpy2.robjects import pandas2ri
|
||||
from rpy2.robjects.packages import importr, isinstalled
|
||||
|
||||
# Import base and utils
|
||||
base = importr('base')
|
||||
utils = importr('utils')
|
||||
|
||||
base.options(warn=-1)
|
||||
|
||||
# Ensure library paths explicitly
|
||||
base._libPaths(r_lib_path)
|
||||
|
||||
# Check if the AMR package is installed in R
|
||||
if not isinstalled('AMR', lib_loc=r_lib_path):
|
||||
print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True)
|
||||
utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True)
|
||||
|
||||
# Retrieve Python AMR version
|
||||
try:
|
||||
python_amr_version = str(metadata.version('AMR'))
|
||||
except metadata.PackageNotFoundError:
|
||||
python_amr_version = str('')
|
||||
|
||||
# Retrieve R AMR version
|
||||
r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')
|
||||
r_amr_version = str(r_amr_version[0])
|
||||
|
||||
print(python_amr_version, flush=True)
|
||||
print(r_amr_version, flush=True)
|
||||
|
||||
print(r_amr_version != python_amr_version, flush=True)
|
||||
|
||||
# # Compare R and Python package versions
|
||||
# if r_amr_version != python_amr_version:
|
||||
# try:
|
||||
# print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True)
|
||||
# utils.install_packages('AMR', repos='beta.amr-for-r.org', 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)
|
||||
665
AMR/functions.py
Normal file
665
AMR/functions.py
Normal file
@ -0,0 +1,665 @@
|
||||
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):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_class(*args, **kwargs))
|
||||
def ab_selector(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_selector(*args, **kwargs))
|
||||
def ab_from_text(text, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_from_text(text, *args, **kwargs))
|
||||
def ab_name(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_name(x, *args, **kwargs))
|
||||
def ab_cid(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_cid(x, *args, **kwargs))
|
||||
def ab_synonyms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_synonyms(x, *args, **kwargs))
|
||||
def ab_tradenames(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_tradenames(x, *args, **kwargs))
|
||||
def ab_group(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_group(x, *args, **kwargs))
|
||||
def ab_atc(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_atc(x, *args, **kwargs))
|
||||
def ab_atc_group1(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_atc_group1(x, *args, **kwargs))
|
||||
def ab_atc_group2(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_atc_group2(x, *args, **kwargs))
|
||||
def ab_loinc(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_loinc(x, *args, **kwargs))
|
||||
def ab_ddd(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_ddd(x, *args, **kwargs))
|
||||
def ab_ddd_units(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_ddd_units(x, *args, **kwargs))
|
||||
def ab_info(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_info(x, *args, **kwargs))
|
||||
def ab_url(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_url(x, *args, **kwargs))
|
||||
def ab_property(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_property(x, *args, **kwargs))
|
||||
def add_custom_antimicrobials(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.add_custom_antimicrobials(x))
|
||||
def clear_custom_antimicrobials(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.clear_custom_antimicrobials(*args, **kwargs))
|
||||
def add_custom_microorganisms(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.add_custom_microorganisms(x))
|
||||
def clear_custom_microorganisms(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.clear_custom_microorganisms(*args, **kwargs))
|
||||
def age(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.age(x, *args, **kwargs))
|
||||
def age_groups(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.age_groups(x, *args, **kwargs))
|
||||
def antibiogram(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.antibiogram(x, *args, **kwargs))
|
||||
def wisca(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.wisca(x, *args, **kwargs))
|
||||
def retrieve_wisca_parameters(wisca_model, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.retrieve_wisca_parameters(wisca_model, *args, **kwargs))
|
||||
def aminoglycosides(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.aminoglycosides(only_sir_columns = False, *args, **kwargs))
|
||||
def aminopenicillins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.aminopenicillins(only_sir_columns = False, *args, **kwargs))
|
||||
def antifungals(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.antifungals(only_sir_columns = False, *args, **kwargs))
|
||||
def antimycobacterials(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs))
|
||||
def betalactams(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
|
||||
def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
|
||||
def carbapenems(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))
|
||||
def cephalosporins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.cephalosporins(only_sir_columns = False, *args, **kwargs))
|
||||
def cephalosporins_1st(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.cephalosporins_1st(only_sir_columns = False, *args, **kwargs))
|
||||
def cephalosporins_2nd(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.cephalosporins_2nd(only_sir_columns = False, *args, **kwargs))
|
||||
def cephalosporins_3rd(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.cephalosporins_3rd(only_sir_columns = False, *args, **kwargs))
|
||||
def cephalosporins_4th(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.cephalosporins_4th(only_sir_columns = False, *args, **kwargs))
|
||||
def cephalosporins_5th(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.cephalosporins_5th(only_sir_columns = False, *args, **kwargs))
|
||||
def fluoroquinolones(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.fluoroquinolones(only_sir_columns = False, *args, **kwargs))
|
||||
def glycopeptides(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs))
|
||||
def isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs))
|
||||
def lincosamides(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.lincosamides(only_sir_columns = False, *args, **kwargs))
|
||||
def lipoglycopeptides(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.lipoglycopeptides(only_sir_columns = False, *args, **kwargs))
|
||||
def macrolides(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.macrolides(only_sir_columns = False, *args, **kwargs))
|
||||
def monobactams(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.monobactams(only_sir_columns = False, *args, **kwargs))
|
||||
def nitrofurans(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.nitrofurans(only_sir_columns = False, *args, **kwargs))
|
||||
def oxazolidinones(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.oxazolidinones(only_sir_columns = False, *args, **kwargs))
|
||||
def penicillins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.penicillins(only_sir_columns = False, *args, **kwargs))
|
||||
def phenicols(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
|
||||
def polymyxins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
|
||||
def quinolones(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.quinolones(only_sir_columns = False, *args, **kwargs))
|
||||
def rifamycins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.rifamycins(only_sir_columns = False, *args, **kwargs))
|
||||
def streptogramins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.streptogramins(only_sir_columns = False, *args, **kwargs))
|
||||
def sulfonamides(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.sulfonamides(only_sir_columns = False, *args, **kwargs))
|
||||
def tetracyclines(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.tetracyclines(only_sir_columns = False, *args, **kwargs))
|
||||
def trimethoprims(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.trimethoprims(only_sir_columns = False, *args, **kwargs))
|
||||
def ureidopenicillins(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs))
|
||||
def amr_class(amr_class, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.amr_class(amr_class, *args, **kwargs))
|
||||
def amr_selector(filter, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.amr_selector(filter, *args, **kwargs))
|
||||
def administrable_per_os(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.administrable_per_os(only_sir_columns = False, *args, **kwargs))
|
||||
def administrable_iv(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs))
|
||||
def not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs))
|
||||
def as_ab(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.as_ab(x, *args, **kwargs))
|
||||
def is_ab(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_ab(x))
|
||||
def ab_reset_session(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ab_reset_session(*args, **kwargs))
|
||||
def as_av(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.as_av(x, *args, **kwargs))
|
||||
def is_av(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_av(x))
|
||||
def as_disk(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.as_disk(x, *args, **kwargs))
|
||||
def is_disk(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_disk(x))
|
||||
def as_mic(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.as_mic(x, *args, **kwargs))
|
||||
def is_mic(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_mic(x))
|
||||
def rescale_mic(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.rescale_mic(x, *args, **kwargs))
|
||||
def mic_p50(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mic_p50(x, *args, **kwargs))
|
||||
def mic_p90(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mic_p90(x, *args, **kwargs))
|
||||
def as_mo(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.as_mo(x, *args, **kwargs))
|
||||
def is_mo(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_mo(x))
|
||||
def mo_uncertainties(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_uncertainties(*args, **kwargs))
|
||||
def mo_renamed(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_renamed(*args, **kwargs))
|
||||
def mo_failures(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_failures(*args, **kwargs))
|
||||
def mo_reset_session(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_reset_session(*args, **kwargs))
|
||||
def mo_cleaning_regex(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_cleaning_regex(*args, **kwargs))
|
||||
def as_sir(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.as_sir(x, *args, **kwargs))
|
||||
def is_sir(x):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_sir(x))
|
||||
def is_sir_eligible(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_sir_eligible(x, *args, **kwargs))
|
||||
def sir_interpretation_history(clean):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.sir_interpretation_history(clean))
|
||||
def atc_online_property(atc_code, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.atc_online_property(atc_code, *args, **kwargs))
|
||||
def atc_online_groups(atc_code, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.atc_online_groups(atc_code, *args, **kwargs))
|
||||
def atc_online_ddd(atc_code, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.atc_online_ddd(atc_code, *args, **kwargs))
|
||||
def atc_online_ddd_units(atc_code, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.atc_online_ddd_units(atc_code, *args, **kwargs))
|
||||
def av_from_text(text, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_from_text(text, *args, **kwargs))
|
||||
def av_name(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_name(x, *args, **kwargs))
|
||||
def av_cid(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_cid(x, *args, **kwargs))
|
||||
def av_synonyms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_synonyms(x, *args, **kwargs))
|
||||
def av_tradenames(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_tradenames(x, *args, **kwargs))
|
||||
def av_group(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_group(x, *args, **kwargs))
|
||||
def av_atc(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_atc(x, *args, **kwargs))
|
||||
def av_loinc(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_loinc(x, *args, **kwargs))
|
||||
def av_ddd(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_ddd(x, *args, **kwargs))
|
||||
def av_ddd_units(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_ddd_units(x, *args, **kwargs))
|
||||
def av_info(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_info(x, *args, **kwargs))
|
||||
def av_url(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_url(x, *args, **kwargs))
|
||||
def av_property(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.av_property(x, *args, **kwargs))
|
||||
def availability(tbl, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.availability(tbl, *args, **kwargs))
|
||||
def bug_drug_combinations(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.bug_drug_combinations(x, *args, **kwargs))
|
||||
def count_resistant(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_resistant(*args, **kwargs))
|
||||
def count_susceptible(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_susceptible(*args, **kwargs))
|
||||
def count_S(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_S(*args, **kwargs))
|
||||
def count_SI(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_SI(*args, **kwargs))
|
||||
def count_I(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_I(*args, **kwargs))
|
||||
def count_IR(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_IR(*args, **kwargs))
|
||||
def count_R(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_R(*args, **kwargs))
|
||||
def count_all(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_all(*args, **kwargs))
|
||||
def n_sir(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.n_sir(*args, **kwargs))
|
||||
def count_df(data, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.count_df(data, *args, **kwargs))
|
||||
def custom_eucast_rules(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.custom_eucast_rules(*args, **kwargs))
|
||||
def eucast_rules(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.eucast_rules(x, *args, **kwargs))
|
||||
def eucast_dosage(ab, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.eucast_dosage(ab, *args, **kwargs))
|
||||
def export_ncbi_biosample(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.export_ncbi_biosample(x, *args, **kwargs))
|
||||
def first_isolate(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.first_isolate(x = None, *args, **kwargs))
|
||||
def filter_first_isolate(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.filter_first_isolate(x = None, *args, **kwargs))
|
||||
def g_test(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.g_test(x, *args, **kwargs))
|
||||
def is_new_episode(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.is_new_episode(x, *args, **kwargs))
|
||||
def ggplot_pca(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ggplot_pca(x, *args, **kwargs))
|
||||
def ggplot_sir(data, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ggplot_sir(data, *args, **kwargs))
|
||||
def geom_sir(position = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.geom_sir(position = None, *args, **kwargs))
|
||||
def guess_ab_col(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.guess_ab_col(x = None, *args, **kwargs))
|
||||
def italicise_taxonomy(string, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.italicise_taxonomy(string, *args, **kwargs))
|
||||
def italicize_taxonomy(string, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.italicize_taxonomy(string, *args, **kwargs))
|
||||
def inner_join_microorganisms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.inner_join_microorganisms(x, *args, **kwargs))
|
||||
def left_join_microorganisms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.left_join_microorganisms(x, *args, **kwargs))
|
||||
def right_join_microorganisms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.right_join_microorganisms(x, *args, **kwargs))
|
||||
def full_join_microorganisms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.full_join_microorganisms(x, *args, **kwargs))
|
||||
def semi_join_microorganisms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.semi_join_microorganisms(x, *args, **kwargs))
|
||||
def anti_join_microorganisms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.anti_join_microorganisms(x, *args, **kwargs))
|
||||
def key_antimicrobials(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.key_antimicrobials(x = None, *args, **kwargs))
|
||||
def all_antimicrobials(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.all_antimicrobials(x = None, *args, **kwargs))
|
||||
def kurtosis(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.kurtosis(x, *args, **kwargs))
|
||||
def like(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.like(x, *args, **kwargs))
|
||||
def mdro(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mdro(x = None, *args, **kwargs))
|
||||
def custom_mdro_guideline(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.custom_mdro_guideline(*args, **kwargs))
|
||||
def brmo(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.brmo(x = None, *args, **kwargs))
|
||||
def mrgn(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mrgn(x = None, *args, **kwargs))
|
||||
def mdr_tb(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mdr_tb(x = None, *args, **kwargs))
|
||||
def mdr_cmi2012(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mdr_cmi2012(x = None, *args, **kwargs))
|
||||
def eucast_exceptional_phenotypes(x = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.eucast_exceptional_phenotypes(x = None, *args, **kwargs))
|
||||
def mean_amr_distance(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mean_amr_distance(x, *args, **kwargs))
|
||||
def amr_distance_from_row(amr_distance, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.amr_distance_from_row(amr_distance, *args, **kwargs))
|
||||
def mo_matching_score(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_matching_score(x, *args, **kwargs))
|
||||
def mo_name(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_name(x, *args, **kwargs))
|
||||
def mo_fullname(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_fullname(x, *args, **kwargs))
|
||||
def mo_shortname(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_shortname(x, *args, **kwargs))
|
||||
def mo_subspecies(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_subspecies(x, *args, **kwargs))
|
||||
def mo_species(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_species(x, *args, **kwargs))
|
||||
def mo_genus(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_genus(x, *args, **kwargs))
|
||||
def mo_family(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_family(x, *args, **kwargs))
|
||||
def mo_order(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_order(x, *args, **kwargs))
|
||||
def mo_class(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_class(x, *args, **kwargs))
|
||||
def mo_phylum(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_phylum(x, *args, **kwargs))
|
||||
def mo_kingdom(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_kingdom(x, *args, **kwargs))
|
||||
def mo_domain(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_domain(x, *args, **kwargs))
|
||||
def mo_type(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_type(x, *args, **kwargs))
|
||||
def mo_status(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_status(x, *args, **kwargs))
|
||||
def mo_pathogenicity(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_pathogenicity(x, *args, **kwargs))
|
||||
def mo_gramstain(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_gramstain(x, *args, **kwargs))
|
||||
def mo_is_gram_negative(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_is_gram_negative(x, *args, **kwargs))
|
||||
def mo_is_gram_positive(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_is_gram_positive(x, *args, **kwargs))
|
||||
def mo_is_yeast(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_is_yeast(x, *args, **kwargs))
|
||||
def mo_is_intrinsic_resistant(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs))
|
||||
def mo_oxygen_tolerance(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_oxygen_tolerance(x, *args, **kwargs))
|
||||
def mo_is_anaerobic(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_is_anaerobic(x, *args, **kwargs))
|
||||
def mo_snomed(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_snomed(x, *args, **kwargs))
|
||||
def mo_ref(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_ref(x, *args, **kwargs))
|
||||
def mo_authors(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_authors(x, *args, **kwargs))
|
||||
def mo_year(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_year(x, *args, **kwargs))
|
||||
def mo_lpsn(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_lpsn(x, *args, **kwargs))
|
||||
def mo_mycobank(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_mycobank(x, *args, **kwargs))
|
||||
def mo_gbif(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_gbif(x, *args, **kwargs))
|
||||
def mo_rank(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_rank(x, *args, **kwargs))
|
||||
def mo_taxonomy(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_taxonomy(x, *args, **kwargs))
|
||||
def mo_synonyms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_synonyms(x, *args, **kwargs))
|
||||
def mo_current(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_current(x, *args, **kwargs))
|
||||
def mo_group_members(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_group_members(x, *args, **kwargs))
|
||||
def mo_info(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_info(x, *args, **kwargs))
|
||||
def mo_url(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_url(x, *args, **kwargs))
|
||||
def mo_property(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.mo_property(x, *args, **kwargs))
|
||||
def pca(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.pca(x, *args, **kwargs))
|
||||
def theme_sir(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.theme_sir(*args, **kwargs))
|
||||
def labels_sir_count(position = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.labels_sir_count(position = None, *args, **kwargs))
|
||||
def resistance(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.resistance(*args, **kwargs))
|
||||
def susceptibility(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.susceptibility(*args, **kwargs))
|
||||
def sir_confidence_interval(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.sir_confidence_interval(*args, **kwargs))
|
||||
def proportion_R(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.proportion_R(*args, **kwargs))
|
||||
def proportion_IR(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.proportion_IR(*args, **kwargs))
|
||||
def proportion_I(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.proportion_I(*args, **kwargs))
|
||||
def proportion_SI(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.proportion_SI(*args, **kwargs))
|
||||
def proportion_S(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.proportion_S(*args, **kwargs))
|
||||
def proportion_df(data, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.proportion_df(data, *args, **kwargs))
|
||||
def sir_df(data, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.sir_df(data, *args, **kwargs))
|
||||
def random_mic(size = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.random_mic(size = None, *args, **kwargs))
|
||||
def random_disk(size = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.random_disk(size = None, *args, **kwargs))
|
||||
def random_sir(size = None, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.random_sir(size = None, *args, **kwargs))
|
||||
def resistance_predict(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.resistance_predict(x, *args, **kwargs))
|
||||
def sir_predict(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.sir_predict(x, *args, **kwargs))
|
||||
def ggplot_sir_predict(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.ggplot_sir_predict(x, *args, **kwargs))
|
||||
def skewness(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.skewness(x, *args, **kwargs))
|
||||
def top_n_microorganisms(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.top_n_microorganisms(x, *args, **kwargs))
|
||||
def reset_AMR_locale(*args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.reset_AMR_locale(*args, **kwargs))
|
||||
def translate_AMR(x, *args, **kwargs):
|
||||
"""Please see our website of the R package for the full manual: https://amr-for-r.org"""
|
||||
return convert_to_python(amr_r.translate_AMR(x, *args, **kwargs))
|
||||
184
README.md
Executable file
184
README.md
Executable file
@ -0,0 +1,184 @@
|
||||
|
||||
The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) analysis. It provides extensive features for handling microbial and antimicrobial data. However, for those who work primarily in Python, we now have a more intuitive option available: the [`AMR` Python package](https://pypi.org/project/AMR/).
|
||||
|
||||
This Python package is a wrapper around the `AMR` R package. It uses the `rpy2` package internally. Despite the need to have R installed, Python users can now easily work with AMR data directly through Python code.
|
||||
|
||||
# Prerequisites
|
||||
|
||||
This package was only tested with a [virtual environment (venv)](https://docs.python.org/3/library/venv.html). You can set up such an environment by running:
|
||||
|
||||
```python
|
||||
# linux and macOS:
|
||||
python -m venv /path/to/new/virtual/environment
|
||||
|
||||
# Windows:
|
||||
python -m venv C:\path\to\new\virtual\environment
|
||||
```
|
||||
|
||||
Then you can [activate the environment](https://docs.python.org/3/library/venv.html#how-venvs-work), after which the venv is ready to work with.
|
||||
|
||||
# Install AMR
|
||||
|
||||
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.
|
||||
BIN
dist/amr-2.1.1.9268-py3-none-any.whl
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BIN
dist/amr-2.1.1.9268-py3-none-any.whl
vendored
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BIN
dist/amr-2.1.1.9268.tar.gz
vendored
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dist/amr-2.1.1.9268.tar.gz
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27
setup.py
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27
setup.py
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@ -0,0 +1,27 @@
|
||||
from setuptools import setup, find_packages
|
||||
|
||||
setup(
|
||||
name='AMR',
|
||||
version='2.1.1.9268',
|
||||
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',
|
||||
)
|
||||
Loading…
x
Reference in New Issue
Block a user