commit 4f7764858c1f6c86024d24eeb3947cbd1209479b Author: github-actions[bot] Date: Thu Jul 9 19:08:11 2026 +0000 Python wrapper update diff --git a/AMR.egg-info/PKG-INFO b/AMR.egg-info/PKG-INFO new file mode 100644 index 000000000..764f023ba --- /dev/null +++ b/AMR.egg-info/PKG-INFO @@ -0,0 +1,254 @@ +Metadata-Version: 2.4 +Name: AMR +Version: 3.0.1.9085 +Summary: A Python wrapper for the AMR R package +Home-page: https://github.com/msberends/AMR +Author: Matthijs Berends +Author-email: m.s.berends@umcg.nl +License: GPL 2 +Project-URL: Bug Tracker, https://github.com/msberends/AMR/issues +Classifier: Programming Language :: Python :: 3 +Classifier: Operating System :: OS Independent +Requires-Python: >=3.6 +Description-Content-Type: text/markdown +Requires-Dist: rpy2 +Requires-Dist: numpy +Requires-Dist: pandas +Dynamic: author +Dynamic: author-email +Dynamic: classifier +Dynamic: description +Dynamic: description-content-type +Dynamic: home-page +Dynamic: license +Dynamic: project-url +Dynamic: requires-dist +Dynamic: requires-python +Dynamic: summary + + +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 | + + +# Installation Channels + +## Stable Release (CRAN) + +The default `AMR` Python package uses the latest stable version of the `AMR` R package, published on CRAN. After running `pip install AMR`, import it as usual: + +```python +import AMR + +AMR.example_isolates +``` + +## Development Version (GitHub) + +To use the latest development version of the `AMR` R package (sourced directly from GitHub), import the `beta` sub-package and alias it as `AMR`: + +```python +import AMR.beta as AMR + +AMR.example_isolates +``` + +Aliasing with `as AMR` keeps all downstream code identical to the stable import. Switching between the stable release and the development version requires changing only the import line — nothing else in your script needs to change. + +# SIR Classification with `as_sir()` + +## Using `enforce_method` + +The `as_sir()` function in R uses S3 method dispatch to select the correct calculation method based on the input class: `` for MIC values and `` for disk diffusion values. Because Python objects do not carry R class attributes through the `rpy2` bridge, this automatic dispatch may not resolve correctly. + +To explicitly specify the input type, use the `enforce_method` argument: + +```python +# Treat the column as MIC values — maps to R's as.sir.mic() +AMR.as_sir(df["MIC_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="mic") + +# Treat the column as disk diffusion values — maps to R's as.sir.disk() +AMR.as_sir(df["disk_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="disk") +``` + +Without `enforce_method`, R falls back to class-based dispatch on the raw Python input, which may fail or return unexpected results. Always supply `enforce_method` when calling `as_sir()` from Python. + +# 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. diff --git a/AMR.egg-info/SOURCES.txt b/AMR.egg-info/SOURCES.txt new file mode 100644 index 000000000..617d18f78 --- /dev/null +++ b/AMR.egg-info/SOURCES.txt @@ -0,0 +1,12 @@ +README.md +setup.py +AMR/__init__.py +AMR/_engine.py +AMR/beta.py +AMR/datasets.py +AMR/functions.py +AMR.egg-info/PKG-INFO +AMR.egg-info/SOURCES.txt +AMR.egg-info/dependency_links.txt +AMR.egg-info/requires.txt +AMR.egg-info/top_level.txt \ No newline at end of file diff --git a/AMR.egg-info/dependency_links.txt b/AMR.egg-info/dependency_links.txt new file mode 100644 index 000000000..8b1378917 --- /dev/null +++ b/AMR.egg-info/dependency_links.txt @@ -0,0 +1 @@ + diff --git a/AMR.egg-info/requires.txt b/AMR.egg-info/requires.txt new file mode 100644 index 000000000..fb2bcf682 --- /dev/null +++ b/AMR.egg-info/requires.txt @@ -0,0 +1,3 @@ +rpy2 +numpy +pandas diff --git a/AMR.egg-info/top_level.txt b/AMR.egg-info/top_level.txt new file mode 100644 index 000000000..18f3926f7 --- /dev/null +++ b/AMR.egg-info/top_level.txt @@ -0,0 +1 @@ +AMR diff --git a/AMR/__init__.py b/AMR/__init__.py new file mode 100644 index 000000000..741874607 --- /dev/null +++ b/AMR/__init__.py @@ -0,0 +1,249 @@ +import sys + +_DATASETS = frozenset({ + 'example_isolates', 'microorganisms', + 'antimicrobials', 'clinical_breakpoints' +}) + +class _AMRModule(type(sys.modules[__name__])): + """Lazy-loading module: nothing runs until an attribute is accessed.""" + + def __getattr__(self, name): + if name in _DATASETS: + from .datasets import get + return get(name, source="cran") + try: + from . import functions + return getattr(functions, name) + except AttributeError: + raise AttributeError( + f"module 'AMR' has no attribute '{name}'") + +sys.modules[__name__].__class__ = _AMRModule +from .functions import custom_eucast_rules +from .functions import ab_class +from .functions import ab_selector +from .functions import ab_from_text +from .functions import ab_name +from .functions import ab_cid +from .functions import ab_synonyms +from .functions import ab_tradenames +from .functions import ab_group +from .functions import ab_atc +from .functions import ab_atc_group1 +from .functions import ab_atc_group2 +from .functions import ab_loinc +from .functions import ab_ddd +from .functions import ab_ddd_units +from .functions import ab_info +from .functions import ab_url +from .functions import ab_property +from .functions import add_custom_antimicrobials +from .functions import clear_custom_antimicrobials +from .functions import add_custom_microorganisms +from .functions import clear_custom_microorganisms +from .functions import age +from .functions import age_groups +from .functions import all_sir +from .functions import all_sir_predictors +from .functions import all_mic +from .functions import all_mic_predictors +from .functions import all_disk +from .functions import all_disk_predictors +from .functions import step_mic_log2 +from .functions import step_sir_numeric +from .functions import amr_course +from .functions import wisca +from .functions import antibiogram +from .functions import retrieve_wisca_parameters +from .functions import wisca_plot +from .functions import aminoglycosides +from .functions import aminopenicillins +from .functions import antifungals +from .functions import antimycobacterials +from .functions import betalactams +from .functions import betalactams_with_inhibitor +from .functions import carbapenems +from .functions import cephalosporins +from .functions import cephalosporins_1st +from .functions import cephalosporins_2nd +from .functions import cephalosporins_3rd +from .functions import cephalosporins_4th +from .functions import cephalosporins_5th +from .functions import fluoroquinolones +from .functions import glycopeptides +from .functions import ionophores +from .functions import isoxazolylpenicillins +from .functions import lincosamides +from .functions import lipoglycopeptides +from .functions import macrolides +from .functions import monobactams +from .functions import nitrofurans +from .functions import oxazolidinones +from .functions import penicillins +from .functions import peptides +from .functions import phenicols +from .functions import phosphonics +from .functions import polymyxins +from .functions import quinolones +from .functions import rifamycins +from .functions import spiropyrimidinetriones +from .functions import streptogramins +from .functions import sulfonamides +from .functions import tetracyclines +from .functions import trimethoprims +from .functions import ureidopenicillins +from .functions import amr_class +from .functions import amr_selector +from .functions import administrable_per_os +from .functions import administrable_iv +from .functions import not_intrinsic_resistant +from .functions import as_ab +from .functions import is_ab +from .functions import ab_reset_session +from .functions import as_av +from .functions import is_av +from .functions import as_disk +from .functions import is_disk +from .functions import as_mic +from .functions import is_mic +from .functions import rescale_mic +from .functions import mic_p50 +from .functions import mic_p90 +from .functions import as_mo +from .functions import is_mo +from .functions import mo_uncertainties +from .functions import mo_renamed +from .functions import mo_failures +from .functions import mo_reset_session +from .functions import mo_cleaning_regex +from .functions import as_sir +from .functions import is_sir +from .functions import is_sir_eligible +from .functions import sir_interpretation_history +from .functions import atc_online_property +from .functions import atc_online_groups +from .functions import atc_online_ddd +from .functions import atc_online_ddd_units +from .functions import av_from_text +from .functions import av_name +from .functions import av_cid +from .functions import av_synonyms +from .functions import av_tradenames +from .functions import av_group +from .functions import av_atc +from .functions import av_loinc +from .functions import av_ddd +from .functions import av_ddd_units +from .functions import av_info +from .functions import av_url +from .functions import av_property +from .functions import availability +from .functions import bug_drug_combinations +from .functions import count_resistant +from .functions import count_susceptible +from .functions import count_S +from .functions import count_SI +from .functions import count_I +from .functions import count_IR +from .functions import count_R +from .functions import count_all +from .functions import n_sir +from .functions import count_df +from .functions import custom_interpretive_rules +from .functions import custom_mdro_guideline +from .functions import export_ncbi_biosample +from .functions import first_isolate +from .functions import filter_first_isolate +from .functions import g_test +from .functions import is_new_episode +from .functions import ggplot_pca +from .functions import ggplot_sir +from .functions import geom_sir +from .functions import guess_ab_col +from .functions import interpretive_rules +from .functions import eucast_rules +from .functions import clsi_rules +from .functions import eucast_dosage +from .functions import italicise_taxonomy +from .functions import italicize_taxonomy +from .functions import inner_join_microorganisms +from .functions import left_join_microorganisms +from .functions import right_join_microorganisms +from .functions import full_join_microorganisms +from .functions import semi_join_microorganisms +from .functions import anti_join_microorganisms +from .functions import key_antimicrobials +from .functions import all_antimicrobials +from .functions import kurtosis +from .functions import like +from .functions import mdro +from .functions import brmo +from .functions import mrgn +from .functions import mdr_tb +from .functions import mdr_cmi2012 +from .functions import eucast_exceptional_phenotypes +from .functions import mean_amr_distance +from .functions import amr_distance_from_row +from .functions import mo_matching_score +from .functions import mo_name +from .functions import mo_fullname +from .functions import mo_shortname +from .functions import mo_subspecies +from .functions import mo_species +from .functions import mo_genus +from .functions import mo_family +from .functions import mo_order +from .functions import mo_class +from .functions import mo_phylum +from .functions import mo_kingdom +from .functions import mo_domain +from .functions import mo_type +from .functions import mo_status +from .functions import mo_pathogenicity +from .functions import mo_gramstain +from .functions import mo_is_gram_negative +from .functions import mo_is_gram_positive +from .functions import mo_is_yeast +from .functions import mo_is_intrinsic_resistant +from .functions import mo_oxygen_tolerance +from .functions import mo_is_anaerobic +from .functions import mo_morphology +from .functions import mo_snomed +from .functions import mo_ref +from .functions import mo_authors +from .functions import mo_year +from .functions import mo_lpsn +from .functions import mo_mycobank +from .functions import mo_gbif +from .functions import mo_rank +from .functions import mo_taxonomy +from .functions import mo_synonyms +from .functions import mo_current +from .functions import mo_group_members +from .functions import mo_info +from .functions import mo_url +from .functions import mo_property +from .functions import pca +from .functions import theme_sir +from .functions import labels_sir_count +from .functions import resistance +from .functions import susceptibility +from .functions import sir_confidence_interval +from .functions import proportion_R +from .functions import proportion_IR +from .functions import proportion_I +from .functions import proportion_SI +from .functions import proportion_S +from .functions import proportion_df +from .functions import sir_df +from .functions import random_mic +from .functions import random_disk +from .functions import random_sir +from .functions import resistance_predict +from .functions import sir_predict +from .functions import ggplot_sir_predict +from .functions import skewness +from .functions import top_n_microorganisms +from .functions import reset_AMR_locale +from .functions import translate_AMR diff --git a/AMR/_engine.py b/AMR/_engine.py new file mode 100644 index 000000000..cc6c5d9ff --- /dev/null +++ b/AMR/_engine.py @@ -0,0 +1,93 @@ +import os +import sys +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.vectors import StrVector +from rpy2.robjects.packages import importr, isinstalled + +# Import base and utils once +base = importr('base') +utils = importr('utils') + +# Silence R console output entirely +robjects.r('suppressMessages(suppressWarnings(sink(tempfile())))') +base._libPaths(r_lib_path) + +_installed_source = None + +def _r_version(): + """Return the currently installed AMR R package version, or None.""" + try: + return str(robjects.r( + f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')[0]) + except Exception: + return None + +def _py_version(): + """Return the Python AMR package version from metadata, or empty string.""" + try: + return str(metadata.version('AMR')) + except metadata.PackageNotFoundError: + return '' + +def _install_cran(): + """Install AMR from CRAN into the isolated library.""" + print("AMR: Installing from CRAN...", flush=True) + utils.install_packages( + 'AMR', + repos='https://cloud.r-project.org', + lib=r_lib_path, + quiet=True + ) + +def _install_github(): + """Install AMR development version from GitHub into the isolated library.""" + print("AMR: Installing development version from GitHub...", flush=True) + utils.install_packages( + StrVector(['remotes', 'desc']), + repos='https://cloud.r-project.org', + lib=r_lib_path, + quiet=True + ) + remotes = importr('remotes', lib_loc=r_lib_path) + remotes.install_github('msberends/AMR', lib=r_lib_path, quiet=True) + +def ensure_amr(source="cran"): + """Ensure AMR is installed from the requested source. Idempotent per source.""" + global _installed_source + + if _installed_source == source: + return + + install_fn = _install_github if source == "github" else _install_cran + + if not isinstalled('AMR', lib_loc=r_lib_path): + install_fn() + else: + # Check for version mismatch and update if needed + r_ver = _r_version() + py_ver = _py_version() + if r_ver != py_ver: + try: + install_fn() + except Exception as e: + print(f"AMR: Could not update ({e})", flush=True) + + print(f"AMR: R package version {_r_version()} ready.", flush=True) + _installed_source = source + +def restore_sink(): + """Restore R console output after setup is complete.""" + try: + robjects.r('sink()') + except Exception: + pass diff --git a/AMR/beta.py b/AMR/beta.py new file mode 100644 index 000000000..df55d4f81 --- /dev/null +++ b/AMR/beta.py @@ -0,0 +1,22 @@ +import sys + +_DATASETS = frozenset({ + 'example_isolates', 'microorganisms', + 'antimicrobials', 'clinical_breakpoints' +}) + +class _BetaModule(type(sys.modules[__name__])): + """Lazy-loading module: installs AMR from GitHub on first access.""" + + def __getattr__(self, name): + if name in _DATASETS: + from .datasets import get + return get(name, source="github") + try: + from . import functions + return getattr(functions, name) + except AttributeError: + raise AttributeError( + f"module 'AMR.beta' has no attribute '{name}'") + +sys.modules[__name__].__class__ = _BetaModule diff --git a/AMR/datasets.py b/AMR/datasets.py new file mode 100644 index 000000000..1c84065e7 --- /dev/null +++ b/AMR/datasets.py @@ -0,0 +1,54 @@ +import pandas as pd +from rpy2 import robjects +from rpy2.robjects.conversion import localconverter +from rpy2.robjects import default_converter, numpy2ri, pandas2ri + +from ._engine import ensure_amr, restore_sink + +_cache = {} +_loaded_source = None + +def _load_datasets(source="cran"): + """Load all AMR datasets into the module cache.""" + global _loaded_source + + if _cache and _loaded_source == source: + return + + if _cache and _loaded_source != source: + _cache.clear() + + ensure_amr(source) + + with localconverter(default_converter + numpy2ri.converter + pandas2ri.converter): + _cache['example_isolates'] = _load_example_isolates() + _cache['microorganisms'] = robjects.r( + 'AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]') + _cache['antimicrobials'] = robjects.r( + 'AMR::antimicrobials[, !sapply(AMR::antimicrobials, is.list)]') + _cache['clinical_breakpoints'] = robjects.r( + 'AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]') + + restore_sink() + _loaded_source = source + +def _load_example_isolates(): + df = 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 + ''') + df['date'] = pd.to_datetime(df['date']) + return df + +def get(name, source="cran"): + """Retrieve a dataset by name, installing AMR if needed.""" + _load_datasets(source) + return _cache[name] diff --git a/AMR/functions.py b/AMR/functions.py new file mode 100644 index 000000000..d8eef8f9b --- /dev/null +++ b/AMR/functions.py @@ -0,0 +1,984 @@ +import functools +import rpy2.robjects as robjects +from rpy2.robjects.packages import importr +from rpy2.robjects.vectors import StrVector, FactorVector, IntVector, FloatVector, DataFrame +from rpy2.robjects.conversion import localconverter +from rpy2.robjects import default_converter, numpy2ri, pandas2ri +import pandas as pd +import numpy as np + +from ._engine import ensure_amr + +# Ensure AMR is available before importing it in R +ensure_amr("cran") +amr_r = importr('AMR') + +def convert_to_r(value): + """Convert Python lists/tuples to typed R vectors. + + rpy2's default_converter passes Python lists to R as R lists, not as + character/numeric vectors. This causes element-wise type-check functions + such as is.mic(), is.sir(), and is.disk() to return a logical vector + rather than a single logical, breaking R's scalar && operator. + + This helper converts Python lists and tuples to the appropriate R vector + type based on the element types, so R always receives a proper vector.""" + if isinstance(value, (list, tuple)): + if len(value) == 0: + return StrVector([]) + # bool must be checked before int because bool is a subclass of int + if all(isinstance(v, bool) for v in value): + return robjects.vectors.BoolVector(value) + if all(isinstance(v, int) for v in value): + return IntVector(value) + if all(isinstance(v, float) for v in value): + return FloatVector(value) + if all(isinstance(v, str) for v in value): + return StrVector(value) + # Mixed types: coerce all to string + return StrVector([str(v) for v in value]) + return value + +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, DataFrame)): + return r_output # Return as pandas DataFrame (already converted by pandas2ri) + + # 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 r_to_python(r_func): + """Decorator that converts Python list/tuple inputs to typed R vectors, + runs the rpy2 function under a localconverter, and converts the output + to a Python type.""" + @functools.wraps(r_func) + def wrapper(*args, **kwargs): + args = tuple(convert_to_r(a) for a in args) + kwargs = {k: convert_to_r(v) for k, v in kwargs.items()} + with localconverter(default_converter + numpy2ri.converter + pandas2ri.converter): + return convert_to_python(r_func(*args, **kwargs)) + return wrapper +@r_to_python +def custom_eucast_rules(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.custom_eucast_rules(*args, **kwargs) +@r_to_python +def ab_class(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_class(*args, **kwargs) +@r_to_python +def ab_selector(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_selector(*args, **kwargs) +@r_to_python +def ab_from_text(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_from_text(*args, **kwargs) +@r_to_python +def ab_name(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_name(x, *args, **kwargs) +@r_to_python +def ab_cid(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_cid(x, *args, **kwargs) +@r_to_python +def ab_synonyms(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_synonyms(x, *args, **kwargs) +@r_to_python +def ab_tradenames(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_tradenames(x, *args, **kwargs) +@r_to_python +def ab_group(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_group(x, *args, **kwargs) +@r_to_python +def ab_atc(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_atc(x, *args, **kwargs) +@r_to_python +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 amr_r.ab_atc_group1(x, *args, **kwargs) +@r_to_python +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 amr_r.ab_atc_group2(x, *args, **kwargs) +@r_to_python +def ab_loinc(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_loinc(x, *args, **kwargs) +@r_to_python +def ab_ddd(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_ddd(x, *args, **kwargs) +@r_to_python +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 amr_r.ab_ddd_units(x, *args, **kwargs) +@r_to_python +def ab_info(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_info(x, *args, **kwargs) +@r_to_python +def ab_url(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_url(x, *args, **kwargs) +@r_to_python +def ab_property(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_property(x, *args, **kwargs) +@r_to_python +def add_custom_antimicrobials(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.add_custom_antimicrobials(x) +@r_to_python +def clear_custom_antimicrobials(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.clear_custom_antimicrobials(*args, **kwargs) +@r_to_python +def add_custom_microorganisms(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.add_custom_microorganisms(x) +@r_to_python +def clear_custom_microorganisms(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.clear_custom_microorganisms(*args, **kwargs) +@r_to_python +def age(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.age(x, *args, **kwargs) +@r_to_python +def age_groups(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.age_groups(x, *args, **kwargs) +@r_to_python +def all_sir(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.all_sir(*args, **kwargs) +@r_to_python +def all_sir_predictors(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.all_sir_predictors(*args, **kwargs) +@r_to_python +def all_mic(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.all_mic(*args, **kwargs) +@r_to_python +def all_mic_predictors(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.all_mic_predictors(*args, **kwargs) +@r_to_python +def all_disk(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.all_disk(*args, **kwargs) +@r_to_python +def all_disk_predictors(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.all_disk_predictors(*args, **kwargs) +@r_to_python +def step_mic_log2(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.step_mic_log2(*args, **kwargs) +@r_to_python +def step_sir_numeric(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.step_sir_numeric(*args, **kwargs) +@r_to_python +def amr_course(github_repo, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.amr_course(github_repo, *args, **kwargs) +@r_to_python +def wisca(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.wisca(*args, **kwargs) +@r_to_python +def antibiogram(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.antibiogram(*args, **kwargs) +@r_to_python +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 amr_r.retrieve_wisca_parameters(wisca_model, *args, **kwargs) +@r_to_python +def wisca_plot(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.wisca_plot(*args, **kwargs) +@r_to_python +def aminoglycosides(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.aminoglycosides(*args, **kwargs) +@r_to_python +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 amr_r.aminopenicillins(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.antifungals(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs) +@r_to_python +def betalactams(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.betalactams(*args, **kwargs) +@r_to_python +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 amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs) +@r_to_python +def carbapenems(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.carbapenems(*args, **kwargs) +@r_to_python +def cephalosporins(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.cephalosporins(*args, **kwargs) +@r_to_python +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 amr_r.cephalosporins_1st(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.cephalosporins_2nd(only_sir_columns = False, *args, **kwargs) +@r_to_python +def cephalosporins_3rd(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.cephalosporins_3rd(*args, **kwargs) +@r_to_python +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 amr_r.cephalosporins_4th(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.cephalosporins_5th(only_sir_columns = False, *args, **kwargs) +@r_to_python +def fluoroquinolones(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.fluoroquinolones(*args, **kwargs) +@r_to_python +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 amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs) +@r_to_python +def ionophores(only_sir_columns = False, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ionophores(only_sir_columns = False, *args, **kwargs) +@r_to_python +def isoxazolylpenicillins(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.isoxazolylpenicillins(*args, **kwargs) +@r_to_python +def lincosamides(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.lincosamides(*args, **kwargs) +@r_to_python +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 amr_r.lipoglycopeptides(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.macrolides(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.monobactams(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.nitrofurans(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.oxazolidinones(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.penicillins(only_sir_columns = False, *args, **kwargs) +@r_to_python +def peptides(only_sir_columns = False, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.peptides(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.phenicols(only_sir_columns = False, *args, **kwargs) +@r_to_python +def phosphonics(only_sir_columns = False, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.phosphonics(only_sir_columns = False, *args, **kwargs) +@r_to_python +def polymyxins(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.polymyxins(*args, **kwargs) +@r_to_python +def quinolones(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.quinolones(*args, **kwargs) +@r_to_python +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 amr_r.rifamycins(only_sir_columns = False, *args, **kwargs) +@r_to_python +def spiropyrimidinetriones(only_sir_columns = False, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.spiropyrimidinetriones(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.streptogramins(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.sulfonamides(only_sir_columns = False, *args, **kwargs) +@r_to_python +def tetracyclines(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.tetracyclines(*args, **kwargs) +@r_to_python +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 amr_r.trimethoprims(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs) +@r_to_python +def amr_class(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.amr_class(*args, **kwargs) +@r_to_python +def amr_selector(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.amr_selector(*args, **kwargs) +@r_to_python +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 amr_r.administrable_per_os(only_sir_columns = False, *args, **kwargs) +@r_to_python +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 amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs) +@r_to_python +def not_intrinsic_resistant(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.not_intrinsic_resistant(*args, **kwargs) +@r_to_python +def as_ab(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.as_ab(*args, **kwargs) +@r_to_python +def is_ab(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.is_ab(x) +@r_to_python +def ab_reset_session(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ab_reset_session(*args, **kwargs) +@r_to_python +def as_av(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.as_av(x, *args, **kwargs) +@r_to_python +def is_av(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.is_av(x) +@r_to_python +def as_disk(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.as_disk(x, *args, **kwargs) +@r_to_python +def is_disk(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.is_disk(x) +@r_to_python +def as_mic(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.as_mic(x, *args, **kwargs) +@r_to_python +def is_mic(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.is_mic(x) +@r_to_python +def rescale_mic(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.rescale_mic(*args, **kwargs) +@r_to_python +def mic_p50(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mic_p50(x, *args, **kwargs) +@r_to_python +def mic_p90(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mic_p90(x, *args, **kwargs) +@r_to_python +def as_mo(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.as_mo(*args, **kwargs) +@r_to_python +def is_mo(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.is_mo(x) +@r_to_python +def mo_uncertainties(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_uncertainties(*args, **kwargs) +@r_to_python +def mo_renamed(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_renamed(*args, **kwargs) +@r_to_python +def mo_failures(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_failures(*args, **kwargs) +@r_to_python +def mo_reset_session(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_reset_session(*args, **kwargs) +@r_to_python +def mo_cleaning_regex(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_cleaning_regex(*args, **kwargs) +@r_to_python +def as_sir(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.as_sir(x, *args, **kwargs) +@r_to_python +def is_sir(x): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.is_sir(x) +@r_to_python +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 amr_r.is_sir_eligible(x, *args, **kwargs) +@r_to_python +def sir_interpretation_history(clean): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.sir_interpretation_history(clean) +@r_to_python +def atc_online_property(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.atc_online_property(*args, **kwargs) +@r_to_python +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 amr_r.atc_online_groups(atc_code, *args, **kwargs) +@r_to_python +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 amr_r.atc_online_ddd(atc_code, *args, **kwargs) +@r_to_python +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 amr_r.atc_online_ddd_units(atc_code, *args, **kwargs) +@r_to_python +def av_from_text(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_from_text(*args, **kwargs) +@r_to_python +def av_name(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_name(x, *args, **kwargs) +@r_to_python +def av_cid(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_cid(x, *args, **kwargs) +@r_to_python +def av_synonyms(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_synonyms(x, *args, **kwargs) +@r_to_python +def av_tradenames(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_tradenames(x, *args, **kwargs) +@r_to_python +def av_group(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_group(x, *args, **kwargs) +@r_to_python +def av_atc(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_atc(x, *args, **kwargs) +@r_to_python +def av_loinc(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_loinc(x, *args, **kwargs) +@r_to_python +def av_ddd(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_ddd(x, *args, **kwargs) +@r_to_python +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 amr_r.av_ddd_units(x, *args, **kwargs) +@r_to_python +def av_info(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_info(x, *args, **kwargs) +@r_to_python +def av_url(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_url(x, *args, **kwargs) +@r_to_python +def av_property(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.av_property(x, *args, **kwargs) +@r_to_python +def availability(tbl, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.availability(tbl, *args, **kwargs) +@r_to_python +def bug_drug_combinations(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.bug_drug_combinations(*args, **kwargs) +@r_to_python +def count_resistant(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_resistant(*args, **kwargs) +@r_to_python +def count_susceptible(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_susceptible(*args, **kwargs) +@r_to_python +def count_S(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_S(*args, **kwargs) +@r_to_python +def count_SI(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_SI(*args, **kwargs) +@r_to_python +def count_I(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_I(*args, **kwargs) +@r_to_python +def count_IR(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_IR(*args, **kwargs) +@r_to_python +def count_R(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_R(*args, **kwargs) +@r_to_python +def count_all(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_all(*args, **kwargs) +@r_to_python +def n_sir(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.n_sir(*args, **kwargs) +@r_to_python +def count_df(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.count_df(*args, **kwargs) +@r_to_python +def custom_interpretive_rules(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.custom_interpretive_rules(*args, **kwargs) +@r_to_python +def custom_mdro_guideline(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.custom_mdro_guideline(*args, **kwargs) +@r_to_python +def export_ncbi_biosample(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.export_ncbi_biosample(*args, **kwargs) +@r_to_python +def first_isolate(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.first_isolate(*args, **kwargs) +@r_to_python +def filter_first_isolate(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.filter_first_isolate(*args, **kwargs) +@r_to_python +def g_test(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.g_test(x, *args, **kwargs) +@r_to_python +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 amr_r.is_new_episode(x, *args, **kwargs) +@r_to_python +def ggplot_pca(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ggplot_pca(*args, **kwargs) +@r_to_python +def ggplot_sir(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ggplot_sir(*args, **kwargs) +@r_to_python +def geom_sir(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.geom_sir(*args, **kwargs) +@r_to_python +def guess_ab_col(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.guess_ab_col(*args, **kwargs) +@r_to_python +def interpretive_rules(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.interpretive_rules(*args, **kwargs) +@r_to_python +def eucast_rules(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.eucast_rules(*args, **kwargs) +@r_to_python +def clsi_rules(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.clsi_rules(*args, **kwargs) +@r_to_python +def eucast_dosage(ab, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.eucast_dosage(ab, *args, **kwargs) +@r_to_python +def italicise_taxonomy(string, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.italicise_taxonomy(string, *args, **kwargs) +@r_to_python +def italicize_taxonomy(string, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.italicize_taxonomy(string, *args, **kwargs) +@r_to_python +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 amr_r.inner_join_microorganisms(x, *args, **kwargs) +@r_to_python +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 amr_r.left_join_microorganisms(x, *args, **kwargs) +@r_to_python +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 amr_r.right_join_microorganisms(x, *args, **kwargs) +@r_to_python +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 amr_r.full_join_microorganisms(x, *args, **kwargs) +@r_to_python +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 amr_r.semi_join_microorganisms(x, *args, **kwargs) +@r_to_python +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 amr_r.anti_join_microorganisms(x, *args, **kwargs) +@r_to_python +def key_antimicrobials(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.key_antimicrobials(*args, **kwargs) +@r_to_python +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 amr_r.all_antimicrobials(x = None, *args, **kwargs) +@r_to_python +def kurtosis(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.kurtosis(x, *args, **kwargs) +@r_to_python +def like(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.like(x, *args, **kwargs) +@r_to_python +def mdro(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mdro(*args, **kwargs) +@r_to_python +def brmo(x = None, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.brmo(x = None, *args, **kwargs) +@r_to_python +def mrgn(x = None, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mrgn(x = None, *args, **kwargs) +@r_to_python +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 amr_r.mdr_tb(x = None, *args, **kwargs) +@r_to_python +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 amr_r.mdr_cmi2012(x = None, *args, **kwargs) +@r_to_python +def eucast_exceptional_phenotypes(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.eucast_exceptional_phenotypes(*args, **kwargs) +@r_to_python +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 amr_r.mean_amr_distance(x, *args, **kwargs) +@r_to_python +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 amr_r.amr_distance_from_row(amr_distance, *args, **kwargs) +@r_to_python +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 amr_r.mo_matching_score(x, *args, **kwargs) +@r_to_python +def mo_name(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_name(*args, **kwargs) +@r_to_python +def mo_fullname(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_fullname(*args, **kwargs) +@r_to_python +def mo_shortname(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_shortname(*args, **kwargs) +@r_to_python +def mo_subspecies(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_subspecies(*args, **kwargs) +@r_to_python +def mo_species(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_species(*args, **kwargs) +@r_to_python +def mo_genus(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_genus(*args, **kwargs) +@r_to_python +def mo_family(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_family(*args, **kwargs) +@r_to_python +def mo_order(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_order(*args, **kwargs) +@r_to_python +def mo_class(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_class(*args, **kwargs) +@r_to_python +def mo_phylum(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_phylum(*args, **kwargs) +@r_to_python +def mo_kingdom(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_kingdom(*args, **kwargs) +@r_to_python +def mo_domain(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_domain(*args, **kwargs) +@r_to_python +def mo_type(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_type(*args, **kwargs) +@r_to_python +def mo_status(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_status(*args, **kwargs) +@r_to_python +def mo_pathogenicity(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_pathogenicity(*args, **kwargs) +@r_to_python +def mo_gramstain(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_gramstain(*args, **kwargs) +@r_to_python +def mo_is_gram_negative(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_is_gram_negative(*args, **kwargs) +@r_to_python +def mo_is_gram_positive(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_is_gram_positive(*args, **kwargs) +@r_to_python +def mo_is_yeast(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_is_yeast(*args, **kwargs) +@r_to_python +def mo_is_intrinsic_resistant(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_is_intrinsic_resistant(*args, **kwargs) +@r_to_python +def mo_oxygen_tolerance(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_oxygen_tolerance(*args, **kwargs) +@r_to_python +def mo_is_anaerobic(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_is_anaerobic(*args, **kwargs) +@r_to_python +def mo_morphology(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_morphology(*args, **kwargs) +@r_to_python +def mo_snomed(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_snomed(*args, **kwargs) +@r_to_python +def mo_ref(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_ref(*args, **kwargs) +@r_to_python +def mo_authors(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_authors(*args, **kwargs) +@r_to_python +def mo_year(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_year(*args, **kwargs) +@r_to_python +def mo_lpsn(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_lpsn(*args, **kwargs) +@r_to_python +def mo_mycobank(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_mycobank(*args, **kwargs) +@r_to_python +def mo_gbif(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_gbif(*args, **kwargs) +@r_to_python +def mo_rank(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_rank(*args, **kwargs) +@r_to_python +def mo_taxonomy(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_taxonomy(*args, **kwargs) +@r_to_python +def mo_synonyms(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_synonyms(*args, **kwargs) +@r_to_python +def mo_current(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_current(x, *args, **kwargs) +@r_to_python +def mo_group_members(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_group_members(*args, **kwargs) +@r_to_python +def mo_info(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_info(*args, **kwargs) +@r_to_python +def mo_url(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_url(*args, **kwargs) +@r_to_python +def mo_property(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.mo_property(*args, **kwargs) +@r_to_python +def pca(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.pca(*args, **kwargs) +@r_to_python +def theme_sir(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.theme_sir(*args, **kwargs) +@r_to_python +def labels_sir_count(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.labels_sir_count(*args, **kwargs) +@r_to_python +def resistance(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.resistance(*args, **kwargs) +@r_to_python +def susceptibility(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.susceptibility(*args, **kwargs) +@r_to_python +def sir_confidence_interval(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.sir_confidence_interval(*args, **kwargs) +@r_to_python +def proportion_R(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.proportion_R(*args, **kwargs) +@r_to_python +def proportion_IR(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.proportion_IR(*args, **kwargs) +@r_to_python +def proportion_I(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.proportion_I(*args, **kwargs) +@r_to_python +def proportion_SI(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.proportion_SI(*args, **kwargs) +@r_to_python +def proportion_S(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.proportion_S(*args, **kwargs) +@r_to_python +def proportion_df(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.proportion_df(*args, **kwargs) +@r_to_python +def sir_df(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.sir_df(*args, **kwargs) +@r_to_python +def random_mic(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.random_mic(*args, **kwargs) +@r_to_python +def random_disk(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.random_disk(*args, **kwargs) +@r_to_python +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 amr_r.random_sir(size = None, *args, **kwargs) +@r_to_python +def resistance_predict(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.resistance_predict(*args, **kwargs) +@r_to_python +def sir_predict(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.sir_predict(*args, **kwargs) +@r_to_python +def ggplot_sir_predict(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.ggplot_sir_predict(*args, **kwargs) +@r_to_python +def skewness(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.skewness(x, *args, **kwargs) +@r_to_python +def top_n_microorganisms(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.top_n_microorganisms(*args, **kwargs) +@r_to_python +def reset_AMR_locale(*args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.reset_AMR_locale(*args, **kwargs) +@r_to_python +def translate_AMR(x, *args, **kwargs): + """Please see our website of the R package for the full manual: https://amr-for-r.org""" + return amr_r.translate_AMR(x, *args, **kwargs) diff --git a/README.md b/README.md new file mode 100755 index 000000000..0e944d21f --- /dev/null +++ b/README.md @@ -0,0 +1,226 @@ + +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 | + + +# Installation Channels + +## Stable Release (CRAN) + +The default `AMR` Python package uses the latest stable version of the `AMR` R package, published on CRAN. After running `pip install AMR`, import it as usual: + +```python +import AMR + +AMR.example_isolates +``` + +## Development Version (GitHub) + +To use the latest development version of the `AMR` R package (sourced directly from GitHub), import the `beta` sub-package and alias it as `AMR`: + +```python +import AMR.beta as AMR + +AMR.example_isolates +``` + +Aliasing with `as AMR` keeps all downstream code identical to the stable import. Switching between the stable release and the development version requires changing only the import line — nothing else in your script needs to change. + +# SIR Classification with `as_sir()` + +## Using `enforce_method` + +The `as_sir()` function in R uses S3 method dispatch to select the correct calculation method based on the input class: `` for MIC values and `` for disk diffusion values. Because Python objects do not carry R class attributes through the `rpy2` bridge, this automatic dispatch may not resolve correctly. + +To explicitly specify the input type, use the `enforce_method` argument: + +```python +# Treat the column as MIC values — maps to R's as.sir.mic() +AMR.as_sir(df["MIC_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="mic") + +# Treat the column as disk diffusion values — maps to R's as.sir.disk() +AMR.as_sir(df["disk_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="disk") +``` + +Without `enforce_method`, R falls back to class-based dispatch on the raw Python input, which may fail or return unexpected results. Always supply `enforce_method` when calling `as_sir()` from Python. + +# 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. diff --git a/dist/amr-3.0.1.9085-py3-none-any.whl b/dist/amr-3.0.1.9085-py3-none-any.whl new file mode 100644 index 000000000..a70287a82 Binary files /dev/null and b/dist/amr-3.0.1.9085-py3-none-any.whl differ diff --git a/dist/amr-3.0.1.9085.tar.gz b/dist/amr-3.0.1.9085.tar.gz new file mode 100644 index 000000000..f70ab75fd Binary files /dev/null and b/dist/amr-3.0.1.9085.tar.gz differ diff --git a/setup.py b/setup.py new file mode 100644 index 000000000..6b9f42025 --- /dev/null +++ b/setup.py @@ -0,0 +1,27 @@ +from setuptools import setup, find_packages + +setup( + name='AMR', + version='3.0.1.9085', + 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', +)