From ba2f4e5ae00df4fe812dd918d69cc69761977a6f Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Mon, 7 Apr 2025 16:38:07 +0000
Subject: [PATCH] Python wrapper update
---
AMR.egg-info/PKG-INFO | 212 +++++++++
AMR.egg-info/SOURCES.txt | 10 +
AMR.egg-info/dependency_links.txt | 1 +
AMR.egg-info/requires.txt | 3 +
AMR.egg-info/top_level.txt | 1 +
AMR/__init__.py | 213 +++++++++
AMR/datasets.py | 77 ++++
AMR/functions.py | 665 +++++++++++++++++++++++++++
README.md | 184 ++++++++
dist/amr-2.1.1.9234-py3-none-any.whl | Bin 0 -> 10220 bytes
dist/amr-2.1.1.9234.tar.gz | Bin 0 -> 10058 bytes
setup.py | 27 ++
12 files changed, 1393 insertions(+)
create mode 100644 AMR.egg-info/PKG-INFO
create mode 100644 AMR.egg-info/SOURCES.txt
create mode 100644 AMR.egg-info/dependency_links.txt
create mode 100644 AMR.egg-info/requires.txt
create mode 100644 AMR.egg-info/top_level.txt
create mode 100644 AMR/__init__.py
create mode 100644 AMR/datasets.py
create mode 100644 AMR/functions.py
create mode 100755 README.md
create mode 100644 dist/amr-2.1.1.9234-py3-none-any.whl
create mode 100644 dist/amr-2.1.1.9234.tar.gz
create mode 100644 setup.py
diff --git a/AMR.egg-info/PKG-INFO b/AMR.egg-info/PKG-INFO
new file mode 100644
index 000000000..797390da9
--- /dev/null
+++ b/AMR.egg-info/PKG-INFO
@@ -0,0 +1,212 @@
+Metadata-Version: 2.4
+Name: AMR
+Version: 2.1.1.9234
+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 |
+
+
+# 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..f37c14848
--- /dev/null
+++ b/AMR.egg-info/SOURCES.txt
@@ -0,0 +1,10 @@
+README.md
+setup.py
+AMR/__init__.py
+AMR/datasets.py
+AMR/functions.py
+AMR.egg-info/PKG-INFO
+AMR.egg-info/SOURCES.txt
+AMR.egg-info/dependency_links.txt
+AMR.egg-info/requires.txt
+AMR.egg-info/top_level.txt
\ 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..0dd6e1f18
--- /dev/null
+++ b/AMR/__init__.py
@@ -0,0 +1,213 @@
+from .datasets import example_isolates
+from .datasets import microorganisms
+from .datasets import antimicrobials
+from .datasets import clinical_breakpoints
+from .functions import ab_class
+from .functions import ab_selector
+from .functions import ab_from_text
+from .functions import ab_name
+from .functions import ab_cid
+from .functions import ab_synonyms
+from .functions import ab_tradenames
+from .functions import ab_group
+from .functions import ab_atc
+from .functions import ab_atc_group1
+from .functions import ab_atc_group2
+from .functions import ab_loinc
+from .functions import ab_ddd
+from .functions import ab_ddd_units
+from .functions import ab_info
+from .functions import ab_url
+from .functions import ab_property
+from .functions import add_custom_antimicrobials
+from .functions import clear_custom_antimicrobials
+from .functions import add_custom_microorganisms
+from .functions import clear_custom_microorganisms
+from .functions import age
+from .functions import age_groups
+from .functions import antibiogram
+from .functions import wisca
+from .functions import retrieve_wisca_parameters
+from .functions import aminoglycosides
+from .functions import aminopenicillins
+from .functions import antifungals
+from .functions import antimycobacterials
+from .functions import betalactams
+from .functions import betalactams_with_inhibitor
+from .functions import carbapenems
+from .functions import cephalosporins
+from .functions import cephalosporins_1st
+from .functions import cephalosporins_2nd
+from .functions import cephalosporins_3rd
+from .functions import cephalosporins_4th
+from .functions import cephalosporins_5th
+from .functions import fluoroquinolones
+from .functions import glycopeptides
+from .functions import isoxazolylpenicillins
+from .functions import lincosamides
+from .functions import lipoglycopeptides
+from .functions import macrolides
+from .functions import monobactams
+from .functions import nitrofurans
+from .functions import oxazolidinones
+from .functions import penicillins
+from .functions import phenicols
+from .functions import polymyxins
+from .functions import quinolones
+from .functions import rifamycins
+from .functions import streptogramins
+from .functions import 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_eucast_rules
+from .functions import eucast_rules
+from .functions import eucast_dosage
+from .functions import export_ncbi_biosample
+from .functions import first_isolate
+from .functions import filter_first_isolate
+from .functions import g_test
+from .functions import is_new_episode
+from .functions import ggplot_pca
+from .functions import ggplot_sir
+from .functions import geom_sir
+from .functions import guess_ab_col
+from .functions import italicise_taxonomy
+from .functions import italicize_taxonomy
+from .functions import inner_join_microorganisms
+from .functions import left_join_microorganisms
+from .functions import right_join_microorganisms
+from .functions import full_join_microorganisms
+from .functions import semi_join_microorganisms
+from .functions import anti_join_microorganisms
+from .functions import key_antimicrobials
+from .functions import all_antimicrobials
+from .functions import kurtosis
+from .functions import like
+from .functions import mdro
+from .functions import custom_mdro_guideline
+from .functions import brmo
+from .functions import mrgn
+from .functions import mdr_tb
+from .functions import mdr_cmi2012
+from .functions import eucast_exceptional_phenotypes
+from .functions import mean_amr_distance
+from .functions import amr_distance_from_row
+from .functions import mo_matching_score
+from .functions import mo_name
+from .functions import mo_fullname
+from .functions import mo_shortname
+from .functions import mo_subspecies
+from .functions import mo_species
+from .functions import mo_genus
+from .functions import mo_family
+from .functions import mo_order
+from .functions import mo_class
+from .functions import mo_phylum
+from .functions import mo_kingdom
+from .functions import mo_domain
+from .functions import mo_type
+from .functions import mo_status
+from .functions import mo_pathogenicity
+from .functions import mo_gramstain
+from .functions import mo_is_gram_negative
+from .functions import mo_is_gram_positive
+from .functions import mo_is_yeast
+from .functions import mo_is_intrinsic_resistant
+from .functions import mo_oxygen_tolerance
+from .functions import mo_is_anaerobic
+from .functions import mo_snomed
+from .functions import mo_ref
+from .functions import mo_authors
+from .functions import mo_year
+from .functions import mo_lpsn
+from .functions import mo_mycobank
+from .functions import mo_gbif
+from .functions import mo_rank
+from .functions import mo_taxonomy
+from .functions import mo_synonyms
+from .functions import mo_current
+from .functions import mo_group_members
+from .functions import mo_info
+from .functions import mo_url
+from .functions import mo_property
+from .functions import pca
+from .functions import theme_sir
+from .functions import labels_sir_count
+from .functions import resistance
+from .functions import susceptibility
+from .functions import sir_confidence_interval
+from .functions import proportion_R
+from .functions import proportion_IR
+from .functions import proportion_I
+from .functions import proportion_SI
+from .functions import proportion_S
+from .functions import proportion_df
+from .functions import sir_df
+from .functions import random_mic
+from .functions import random_disk
+from .functions import random_sir
+from .functions import resistance_predict
+from .functions import sir_predict
+from .functions import ggplot_sir_predict
+from .functions import skewness
+from .functions import top_n_microorganisms
+from .functions import reset_AMR_locale
+from .functions import translate_AMR
diff --git a/AMR/datasets.py b/AMR/datasets.py
new file mode 100644
index 000000000..348bbc339
--- /dev/null
+++ b/AMR/datasets.py
@@ -0,0 +1,77 @@
+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='https://msberends.r-universe.dev', quiet=True)
+
+# # Retrieve Python AMR version
+# try:
+# python_amr_version = metadata.version('AMR')
+# except metadata.PackageNotFoundError:
+# python_amr_version = ''
+#
+# # 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])
+#
+# # 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='https://msberends.r-universe.dev', quiet=True)
+# except Exception as e:
+# print(f"AMR: Could not update: {e}", flush=True)
+
+print(f"AMR: Setting up R environment and AMR datasets...", flush=True)
+
+# Activate the automatic conversion between R and pandas DataFrames
+pandas2ri.activate()
+
+# example_isolates
+example_isolates = pandas2ri.rpy2py(robjects.r('''
+df <- AMR::example_isolates
+df[] <- lapply(df, function(x) {
+ if (inherits(x, c("Date", "POSIXt", "factor"))) {
+ as.character(x)
+ } else {
+ x
+ }
+})
+df <- df[, !sapply(df, is.list)]
+df
+'''))
+example_isolates['date'] = pd.to_datetime(example_isolates['date'])
+
+# microorganisms
+microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]'))
+antimicrobials = pandas2ri.rpy2py(robjects.r('AMR::antimicrobials[, !sapply(AMR::antimicrobials, is.list)]'))
+clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
+
+base.options(warn = 0)
+
+print(f"AMR: Done.", flush=True)
diff --git a/AMR/functions.py b/AMR/functions.py
new file mode 100644
index 000000000..fd4987d69
--- /dev/null
+++ b/AMR/functions.py
@@ -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):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_class(*args, **kwargs))
+def ab_selector(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_selector(*args, **kwargs))
+def ab_from_text(text, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_from_text(text, *args, **kwargs))
+def ab_name(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_name(x, *args, **kwargs))
+def ab_cid(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_cid(x, *args, **kwargs))
+def ab_synonyms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_synonyms(x, *args, **kwargs))
+def ab_tradenames(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_tradenames(x, *args, **kwargs))
+def ab_group(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_group(x, *args, **kwargs))
+def ab_atc(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_atc(x, *args, **kwargs))
+def ab_atc_group1(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_atc_group1(x, *args, **kwargs))
+def ab_atc_group2(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_atc_group2(x, *args, **kwargs))
+def ab_loinc(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_loinc(x, *args, **kwargs))
+def ab_ddd(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_ddd(x, *args, **kwargs))
+def ab_ddd_units(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_ddd_units(x, *args, **kwargs))
+def ab_info(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_info(x, *args, **kwargs))
+def ab_url(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_url(x, *args, **kwargs))
+def ab_property(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_property(x, *args, **kwargs))
+def add_custom_antimicrobials(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.add_custom_antimicrobials(x))
+def clear_custom_antimicrobials(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.clear_custom_antimicrobials(*args, **kwargs))
+def add_custom_microorganisms(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.add_custom_microorganisms(x))
+def clear_custom_microorganisms(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.clear_custom_microorganisms(*args, **kwargs))
+def age(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.age(x, *args, **kwargs))
+def age_groups(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.age_groups(x, *args, **kwargs))
+def antibiogram(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.antibiogram(x, *args, **kwargs))
+def wisca(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.wisca(x, *args, **kwargs))
+def retrieve_wisca_parameters(wisca_model, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.retrieve_wisca_parameters(wisca_model, *args, **kwargs))
+def aminoglycosides(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.aminoglycosides(only_sir_columns = False, *args, **kwargs))
+def aminopenicillins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.aminopenicillins(only_sir_columns = False, *args, **kwargs))
+def antifungals(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.antifungals(only_sir_columns = False, *args, **kwargs))
+def antimycobacterials(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs))
+def betalactams(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
+def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
+def carbapenems(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))
+def cephalosporins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.cephalosporins(only_sir_columns = False, *args, **kwargs))
+def cephalosporins_1st(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.cephalosporins_1st(only_sir_columns = False, *args, **kwargs))
+def cephalosporins_2nd(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.cephalosporins_2nd(only_sir_columns = False, *args, **kwargs))
+def cephalosporins_3rd(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.cephalosporins_3rd(only_sir_columns = False, *args, **kwargs))
+def cephalosporins_4th(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.cephalosporins_4th(only_sir_columns = False, *args, **kwargs))
+def cephalosporins_5th(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.cephalosporins_5th(only_sir_columns = False, *args, **kwargs))
+def fluoroquinolones(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.fluoroquinolones(only_sir_columns = False, *args, **kwargs))
+def glycopeptides(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs))
+def isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs))
+def lincosamides(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.lincosamides(only_sir_columns = False, *args, **kwargs))
+def lipoglycopeptides(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.lipoglycopeptides(only_sir_columns = False, *args, **kwargs))
+def macrolides(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.macrolides(only_sir_columns = False, *args, **kwargs))
+def monobactams(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.monobactams(only_sir_columns = False, *args, **kwargs))
+def nitrofurans(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.nitrofurans(only_sir_columns = False, *args, **kwargs))
+def oxazolidinones(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.oxazolidinones(only_sir_columns = False, *args, **kwargs))
+def penicillins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.penicillins(only_sir_columns = False, *args, **kwargs))
+def phenicols(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
+def polymyxins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
+def quinolones(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.quinolones(only_sir_columns = False, *args, **kwargs))
+def rifamycins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.rifamycins(only_sir_columns = False, *args, **kwargs))
+def streptogramins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.streptogramins(only_sir_columns = False, *args, **kwargs))
+def sulfonamides(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.sulfonamides(only_sir_columns = False, *args, **kwargs))
+def tetracyclines(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.tetracyclines(only_sir_columns = False, *args, **kwargs))
+def trimethoprims(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.trimethoprims(only_sir_columns = False, *args, **kwargs))
+def ureidopenicillins(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs))
+def amr_class(amr_class, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.amr_class(amr_class, *args, **kwargs))
+def amr_selector(filter, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.amr_selector(filter, *args, **kwargs))
+def administrable_per_os(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.administrable_per_os(only_sir_columns = False, *args, **kwargs))
+def administrable_iv(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs))
+def not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs))
+def as_ab(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.as_ab(x, *args, **kwargs))
+def is_ab(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_ab(x))
+def ab_reset_session(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ab_reset_session(*args, **kwargs))
+def as_av(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.as_av(x, *args, **kwargs))
+def is_av(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_av(x))
+def as_disk(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.as_disk(x, *args, **kwargs))
+def is_disk(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_disk(x))
+def as_mic(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.as_mic(x, *args, **kwargs))
+def is_mic(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_mic(x))
+def rescale_mic(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.rescale_mic(x, *args, **kwargs))
+def mic_p50(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mic_p50(x, *args, **kwargs))
+def mic_p90(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mic_p90(x, *args, **kwargs))
+def as_mo(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.as_mo(x, *args, **kwargs))
+def is_mo(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_mo(x))
+def mo_uncertainties(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_uncertainties(*args, **kwargs))
+def mo_renamed(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_renamed(*args, **kwargs))
+def mo_failures(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_failures(*args, **kwargs))
+def mo_reset_session(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_reset_session(*args, **kwargs))
+def mo_cleaning_regex(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_cleaning_regex(*args, **kwargs))
+def as_sir(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.as_sir(x, *args, **kwargs))
+def is_sir(x):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_sir(x))
+def is_sir_eligible(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_sir_eligible(x, *args, **kwargs))
+def sir_interpretation_history(clean):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.sir_interpretation_history(clean))
+def atc_online_property(atc_code, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.atc_online_property(atc_code, *args, **kwargs))
+def atc_online_groups(atc_code, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.atc_online_groups(atc_code, *args, **kwargs))
+def atc_online_ddd(atc_code, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.atc_online_ddd(atc_code, *args, **kwargs))
+def atc_online_ddd_units(atc_code, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.atc_online_ddd_units(atc_code, *args, **kwargs))
+def av_from_text(text, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_from_text(text, *args, **kwargs))
+def av_name(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_name(x, *args, **kwargs))
+def av_cid(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_cid(x, *args, **kwargs))
+def av_synonyms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_synonyms(x, *args, **kwargs))
+def av_tradenames(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_tradenames(x, *args, **kwargs))
+def av_group(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_group(x, *args, **kwargs))
+def av_atc(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_atc(x, *args, **kwargs))
+def av_loinc(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_loinc(x, *args, **kwargs))
+def av_ddd(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_ddd(x, *args, **kwargs))
+def av_ddd_units(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_ddd_units(x, *args, **kwargs))
+def av_info(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_info(x, *args, **kwargs))
+def av_url(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_url(x, *args, **kwargs))
+def av_property(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.av_property(x, *args, **kwargs))
+def availability(tbl, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.availability(tbl, *args, **kwargs))
+def bug_drug_combinations(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.bug_drug_combinations(x, *args, **kwargs))
+def count_resistant(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_resistant(*args, **kwargs))
+def count_susceptible(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_susceptible(*args, **kwargs))
+def count_S(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_S(*args, **kwargs))
+def count_SI(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_SI(*args, **kwargs))
+def count_I(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_I(*args, **kwargs))
+def count_IR(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_IR(*args, **kwargs))
+def count_R(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_R(*args, **kwargs))
+def count_all(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_all(*args, **kwargs))
+def n_sir(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.n_sir(*args, **kwargs))
+def count_df(data, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.count_df(data, *args, **kwargs))
+def custom_eucast_rules(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.custom_eucast_rules(*args, **kwargs))
+def eucast_rules(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.eucast_rules(x, *args, **kwargs))
+def eucast_dosage(ab, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.eucast_dosage(ab, *args, **kwargs))
+def export_ncbi_biosample(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.export_ncbi_biosample(x, *args, **kwargs))
+def first_isolate(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.first_isolate(x = None, *args, **kwargs))
+def filter_first_isolate(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.filter_first_isolate(x = None, *args, **kwargs))
+def g_test(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.g_test(x, *args, **kwargs))
+def is_new_episode(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.is_new_episode(x, *args, **kwargs))
+def ggplot_pca(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ggplot_pca(x, *args, **kwargs))
+def ggplot_sir(data, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ggplot_sir(data, *args, **kwargs))
+def geom_sir(position = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.geom_sir(position = None, *args, **kwargs))
+def guess_ab_col(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.guess_ab_col(x = None, *args, **kwargs))
+def italicise_taxonomy(string, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.italicise_taxonomy(string, *args, **kwargs))
+def italicize_taxonomy(string, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.italicize_taxonomy(string, *args, **kwargs))
+def inner_join_microorganisms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.inner_join_microorganisms(x, *args, **kwargs))
+def left_join_microorganisms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.left_join_microorganisms(x, *args, **kwargs))
+def right_join_microorganisms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.right_join_microorganisms(x, *args, **kwargs))
+def full_join_microorganisms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.full_join_microorganisms(x, *args, **kwargs))
+def semi_join_microorganisms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.semi_join_microorganisms(x, *args, **kwargs))
+def anti_join_microorganisms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.anti_join_microorganisms(x, *args, **kwargs))
+def key_antimicrobials(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.key_antimicrobials(x = None, *args, **kwargs))
+def all_antimicrobials(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.all_antimicrobials(x = None, *args, **kwargs))
+def kurtosis(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.kurtosis(x, *args, **kwargs))
+def like(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.like(x, *args, **kwargs))
+def mdro(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mdro(x = None, *args, **kwargs))
+def custom_mdro_guideline(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.custom_mdro_guideline(*args, **kwargs))
+def brmo(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.brmo(x = None, *args, **kwargs))
+def mrgn(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mrgn(x = None, *args, **kwargs))
+def mdr_tb(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mdr_tb(x = None, *args, **kwargs))
+def mdr_cmi2012(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mdr_cmi2012(x = None, *args, **kwargs))
+def eucast_exceptional_phenotypes(x = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.eucast_exceptional_phenotypes(x = None, *args, **kwargs))
+def mean_amr_distance(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mean_amr_distance(x, *args, **kwargs))
+def amr_distance_from_row(amr_distance, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.amr_distance_from_row(amr_distance, *args, **kwargs))
+def mo_matching_score(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_matching_score(x, *args, **kwargs))
+def mo_name(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_name(x, *args, **kwargs))
+def mo_fullname(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_fullname(x, *args, **kwargs))
+def mo_shortname(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_shortname(x, *args, **kwargs))
+def mo_subspecies(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_subspecies(x, *args, **kwargs))
+def mo_species(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_species(x, *args, **kwargs))
+def mo_genus(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_genus(x, *args, **kwargs))
+def mo_family(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_family(x, *args, **kwargs))
+def mo_order(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_order(x, *args, **kwargs))
+def mo_class(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_class(x, *args, **kwargs))
+def mo_phylum(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_phylum(x, *args, **kwargs))
+def mo_kingdom(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_kingdom(x, *args, **kwargs))
+def mo_domain(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_domain(x, *args, **kwargs))
+def mo_type(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_type(x, *args, **kwargs))
+def mo_status(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_status(x, *args, **kwargs))
+def mo_pathogenicity(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_pathogenicity(x, *args, **kwargs))
+def mo_gramstain(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_gramstain(x, *args, **kwargs))
+def mo_is_gram_negative(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_is_gram_negative(x, *args, **kwargs))
+def mo_is_gram_positive(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_is_gram_positive(x, *args, **kwargs))
+def mo_is_yeast(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_is_yeast(x, *args, **kwargs))
+def mo_is_intrinsic_resistant(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs))
+def mo_oxygen_tolerance(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_oxygen_tolerance(x, *args, **kwargs))
+def mo_is_anaerobic(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_is_anaerobic(x, *args, **kwargs))
+def mo_snomed(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_snomed(x, *args, **kwargs))
+def mo_ref(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_ref(x, *args, **kwargs))
+def mo_authors(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_authors(x, *args, **kwargs))
+def mo_year(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_year(x, *args, **kwargs))
+def mo_lpsn(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_lpsn(x, *args, **kwargs))
+def mo_mycobank(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_mycobank(x, *args, **kwargs))
+def mo_gbif(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_gbif(x, *args, **kwargs))
+def mo_rank(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_rank(x, *args, **kwargs))
+def mo_taxonomy(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_taxonomy(x, *args, **kwargs))
+def mo_synonyms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_synonyms(x, *args, **kwargs))
+def mo_current(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_current(x, *args, **kwargs))
+def mo_group_members(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_group_members(x, *args, **kwargs))
+def mo_info(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_info(x, *args, **kwargs))
+def mo_url(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_url(x, *args, **kwargs))
+def mo_property(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.mo_property(x, *args, **kwargs))
+def pca(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.pca(x, *args, **kwargs))
+def theme_sir(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.theme_sir(*args, **kwargs))
+def labels_sir_count(position = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.labels_sir_count(position = None, *args, **kwargs))
+def resistance(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.resistance(*args, **kwargs))
+def susceptibility(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.susceptibility(*args, **kwargs))
+def sir_confidence_interval(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.sir_confidence_interval(*args, **kwargs))
+def proportion_R(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.proportion_R(*args, **kwargs))
+def proportion_IR(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.proportion_IR(*args, **kwargs))
+def proportion_I(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.proportion_I(*args, **kwargs))
+def proportion_SI(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.proportion_SI(*args, **kwargs))
+def proportion_S(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.proportion_S(*args, **kwargs))
+def proportion_df(data, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.proportion_df(data, *args, **kwargs))
+def sir_df(data, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.sir_df(data, *args, **kwargs))
+def random_mic(size = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.random_mic(size = None, *args, **kwargs))
+def random_disk(size = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.random_disk(size = None, *args, **kwargs))
+def random_sir(size = None, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.random_sir(size = None, *args, **kwargs))
+def resistance_predict(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.resistance_predict(x, *args, **kwargs))
+def sir_predict(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.sir_predict(x, *args, **kwargs))
+def ggplot_sir_predict(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.ggplot_sir_predict(x, *args, **kwargs))
+def skewness(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.skewness(x, *args, **kwargs))
+def top_n_microorganisms(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.top_n_microorganisms(x, *args, **kwargs))
+def reset_AMR_locale(*args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.reset_AMR_locale(*args, **kwargs))
+def translate_AMR(x, *args, **kwargs):
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+ return convert_to_python(amr_r.translate_AMR(x, *args, **kwargs))
diff --git a/README.md b/README.md
new file mode 100755
index 000000000..43aa015bd
--- /dev/null
+++ b/README.md
@@ -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.
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diff --git a/setup.py b/setup.py
new file mode 100644
index 000000000..b5a5a128a
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,27 @@
+from setuptools import setup, find_packages
+
+setup(
+ name='AMR',
+ version='2.1.1.9234',
+ 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',
+)