AMR 3.0.0.9010__py3-none-any.whl → 3.0.0.9012__py3-none-any.whl

AMR/datasets.py

@@ -12,7 +12,8 @@ os.makedirs(r_lib_path, exist_ok=True)
 os.environ['R_LIBS_SITE'] = r_lib_path
 
 from rpy2 import robjects
-from rpy2.robjects import pandas2ri
+from rpy2.robjects.conversion import localconverter
+from rpy2.robjects import default_converter, numpy2ri, pandas2ri
 from rpy2.robjects.packages import importr, isinstalled
 
 # Import base and utils
@@ -50,27 +51,26 @@ if r_amr_version != python_amr_version:
 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)]'))
+with localconverter(default_converter + numpy2ri.converter + pandas2ri.converter):
+    # example_isolates
+    example_isolates = 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 = robjects.r('AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]')
+    antimicrobials = robjects.r('AMR::antimicrobials[, !sapply(AMR::antimicrobials, is.list)]')
+    clinical_breakpoints = robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]')
 
 base.options(warn = 0)
 

AMR/functions.py

@@ -1,13 +1,12 @@
+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 import pandas2ri
+from rpy2.robjects.conversion import localconverter
+from rpy2.robjects import default_converter, numpy2ri, 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')
 
@@ -25,10 +24,8 @@ def convert_to_python(r_output):
         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):
+    elif isinstance(r_output, (pd.DataFrame, 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_):
@@ -36,648 +33,872 @@ def convert_to_python(r_output):
     
     # Fall-back
     return r_output
+
+def r_to_python(r_func):
+    """Decorator that runs an rpy2 function under a localconverter
+    and then applies convert_to_python to its output."""
+    @functools.wraps(r_func)
+    def wrapper(*args, **kwargs):
+        with localconverter(default_converter + numpy2ri.converter + pandas2ri.converter):
+            return convert_to_python(r_func(*args, **kwargs))
+    return wrapper
+@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 convert_to_python(amr_r.ab_class(*args, **kwargs))
+    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 convert_to_python(amr_r.ab_selector(*args, **kwargs))
+    return amr_r.ab_selector(*args, **kwargs)
+@r_to_python
 def ab_from_text(text, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.ab_from_text(text, *args, **kwargs))
+    return amr_r.ab_from_text(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 convert_to_python(amr_r.ab_name(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_cid(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_synonyms(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_tradenames(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_group(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_atc(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_atc_group1(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_atc_group2(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_loinc(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_ddd(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_ddd_units(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_info(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_url(x, *args, **kwargs))
+    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 convert_to_python(amr_r.ab_property(x, *args, **kwargs))
+    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 convert_to_python(amr_r.add_custom_antimicrobials(x))
+    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 convert_to_python(amr_r.clear_custom_antimicrobials(*args, **kwargs))
+    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 convert_to_python(amr_r.add_custom_microorganisms(x))
+    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 convert_to_python(amr_r.clear_custom_microorganisms(*args, **kwargs))
+    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 convert_to_python(amr_r.age(x, *args, **kwargs))
+    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 convert_to_python(amr_r.age_groups(x, *args, **kwargs))
+    return amr_r.age_groups(x, *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 convert_to_python(amr_r.all_mic(*args, **kwargs))
+    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 convert_to_python(amr_r.all_mic_predictors(*args, **kwargs))
+    return amr_r.all_mic_predictors(*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 convert_to_python(amr_r.all_sir(*args, **kwargs))
+    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 convert_to_python(amr_r.all_sir_predictors(*args, **kwargs))
+    return amr_r.all_sir_predictors(*args, **kwargs)
+@r_to_python
 def step_mic_log2(recipe, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.step_mic_log2(recipe, *args, **kwargs))
+    return amr_r.step_mic_log2(recipe, *args, **kwargs)
+@r_to_python
 def step_sir_numeric(recipe, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.step_sir_numeric(recipe, *args, **kwargs))
+    return amr_r.step_sir_numeric(recipe, *args, **kwargs)
+@r_to_python
 def antibiogram(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.antibiogram(x, *args, **kwargs))
+    return amr_r.antibiogram(x, *args, **kwargs)
+@r_to_python
 def wisca(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.wisca(x, *args, **kwargs))
+    return amr_r.wisca(x, *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 convert_to_python(amr_r.retrieve_wisca_parameters(wisca_model, *args, **kwargs))
+    return amr_r.retrieve_wisca_parameters(wisca_model, *args, **kwargs)
+@r_to_python
 def aminoglycosides(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.aminoglycosides(only_sir_columns = False, *args, **kwargs))
+    return amr_r.aminoglycosides(only_sir_columns = False, *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 convert_to_python(amr_r.aminopenicillins(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.antifungals(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs))
+    return amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def betalactams(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
+    return amr_r.betalactams(only_sir_columns = False, *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 convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
+    return amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def carbapenems(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))
+    return amr_r.carbapenems(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def cephalosporins(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.cephalosporins(only_sir_columns = False, *args, **kwargs))
+    return amr_r.cephalosporins(only_sir_columns = False, *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 convert_to_python(amr_r.cephalosporins_1st(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.cephalosporins_2nd(only_sir_columns = False, *args, **kwargs))
+    return amr_r.cephalosporins_2nd(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def cephalosporins_3rd(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.cephalosporins_3rd(only_sir_columns = False, *args, **kwargs))
+    return amr_r.cephalosporins_3rd(only_sir_columns = False, *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 convert_to_python(amr_r.cephalosporins_4th(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.cephalosporins_5th(only_sir_columns = False, *args, **kwargs))
+    return amr_r.cephalosporins_5th(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def fluoroquinolones(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.fluoroquinolones(only_sir_columns = False, *args, **kwargs))
+    return amr_r.fluoroquinolones(only_sir_columns = False, *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 convert_to_python(amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs))
+    return amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs))
+    return amr_r.isoxazolylpenicillins(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def lincosamides(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.lincosamides(only_sir_columns = False, *args, **kwargs))
+    return amr_r.lincosamides(only_sir_columns = False, *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 convert_to_python(amr_r.lipoglycopeptides(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.macrolides(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.monobactams(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.nitrofurans(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.oxazolidinones(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.penicillins(only_sir_columns = False, *args, **kwargs))
+    return amr_r.penicillins(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 convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
+    return amr_r.phenicols(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def polymyxins(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
+    return amr_r.polymyxins(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def quinolones(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.quinolones(only_sir_columns = False, *args, **kwargs))
+    return amr_r.quinolones(only_sir_columns = False, *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 convert_to_python(amr_r.rifamycins(only_sir_columns = False, *args, **kwargs))
+    return amr_r.rifamycins(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 convert_to_python(amr_r.streptogramins(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.sulfonamides(only_sir_columns = False, *args, **kwargs))
+    return amr_r.sulfonamides(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def tetracyclines(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.tetracyclines(only_sir_columns = False, *args, **kwargs))
+    return amr_r.tetracyclines(only_sir_columns = False, *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 convert_to_python(amr_r.trimethoprims(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs))
+    return amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def amr_class(amr_class, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.amr_class(amr_class, *args, **kwargs))
+    return amr_r.amr_class(amr_class, *args, **kwargs)
+@r_to_python
 def amr_selector(filter, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.amr_selector(filter, *args, **kwargs))
+    return amr_r.amr_selector(filter, *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 convert_to_python(amr_r.administrable_per_os(only_sir_columns = False, *args, **kwargs))
+    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 convert_to_python(amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs))
+    return amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs))
+    return amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs)
+@r_to_python
 def as_ab(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.as_ab(x, *args, **kwargs))
+    return amr_r.as_ab(x, *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 convert_to_python(amr_r.is_ab(x))
+    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 convert_to_python(amr_r.ab_reset_session(*args, **kwargs))
+    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 convert_to_python(amr_r.as_av(x, *args, **kwargs))
+    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 convert_to_python(amr_r.is_av(x))
+    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 convert_to_python(amr_r.as_disk(x, *args, **kwargs))
+    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 convert_to_python(amr_r.is_disk(x))
+    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 convert_to_python(amr_r.as_mic(x, *args, **kwargs))
+    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 convert_to_python(amr_r.is_mic(x))
+    return amr_r.is_mic(x)
+@r_to_python
 def rescale_mic(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.rescale_mic(x, *args, **kwargs))
+    return amr_r.rescale_mic(x, *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 convert_to_python(amr_r.mic_p50(x, *args, **kwargs))
+    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 convert_to_python(amr_r.mic_p90(x, *args, **kwargs))
+    return amr_r.mic_p90(x, *args, **kwargs)
+@r_to_python
 def as_mo(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.as_mo(x, *args, **kwargs))
+    return amr_r.as_mo(x, *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 convert_to_python(amr_r.is_mo(x))
+    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 convert_to_python(amr_r.mo_uncertainties(*args, **kwargs))
+    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 convert_to_python(amr_r.mo_renamed(*args, **kwargs))
+    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 convert_to_python(amr_r.mo_failures(*args, **kwargs))
+    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 convert_to_python(amr_r.mo_reset_session(*args, **kwargs))
+    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 convert_to_python(amr_r.mo_cleaning_regex(*args, **kwargs))
+    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 convert_to_python(amr_r.as_sir(x, *args, **kwargs))
+    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 convert_to_python(amr_r.is_sir(x))
+    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 convert_to_python(amr_r.is_sir_eligible(x, *args, **kwargs))
+    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 convert_to_python(amr_r.sir_interpretation_history(clean))
+    return amr_r.sir_interpretation_history(clean)
+@r_to_python
 def atc_online_property(atc_code, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.atc_online_property(atc_code, *args, **kwargs))
+    return amr_r.atc_online_property(atc_code, *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 convert_to_python(amr_r.atc_online_groups(atc_code, *args, **kwargs))
+    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 convert_to_python(amr_r.atc_online_ddd(atc_code, *args, **kwargs))
+    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 convert_to_python(amr_r.atc_online_ddd_units(atc_code, *args, **kwargs))
+    return amr_r.atc_online_ddd_units(atc_code, *args, **kwargs)
+@r_to_python
 def av_from_text(text, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.av_from_text(text, *args, **kwargs))
+    return amr_r.av_from_text(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 convert_to_python(amr_r.av_name(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_cid(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_synonyms(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_tradenames(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_group(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_atc(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_loinc(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_ddd(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_ddd_units(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_info(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_url(x, *args, **kwargs))
+    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 convert_to_python(amr_r.av_property(x, *args, **kwargs))
+    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 convert_to_python(amr_r.availability(tbl, *args, **kwargs))
+    return amr_r.availability(tbl, *args, **kwargs)
+@r_to_python
 def bug_drug_combinations(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.bug_drug_combinations(x, *args, **kwargs))
+    return amr_r.bug_drug_combinations(x, *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 convert_to_python(amr_r.count_resistant(*args, **kwargs))
+    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 convert_to_python(amr_r.count_susceptible(*args, **kwargs))
+    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 convert_to_python(amr_r.count_S(*args, **kwargs))
+    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 convert_to_python(amr_r.count_SI(*args, **kwargs))
+    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 convert_to_python(amr_r.count_I(*args, **kwargs))
+    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 convert_to_python(amr_r.count_IR(*args, **kwargs))
+    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 convert_to_python(amr_r.count_R(*args, **kwargs))
+    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 convert_to_python(amr_r.count_all(*args, **kwargs))
+    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 convert_to_python(amr_r.n_sir(*args, **kwargs))
+    return amr_r.n_sir(*args, **kwargs)
+@r_to_python
 def count_df(data, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.count_df(data, *args, **kwargs))
+    return amr_r.count_df(data, *args, **kwargs)
+@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 convert_to_python(amr_r.custom_eucast_rules(*args, **kwargs))
+    return amr_r.custom_eucast_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 convert_to_python(amr_r.custom_mdro_guideline(*args, **kwargs))
+    return amr_r.custom_mdro_guideline(*args, **kwargs)
+@r_to_python
 def eucast_rules(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.eucast_rules(x, *args, **kwargs))
+    return amr_r.eucast_rules(x, *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 convert_to_python(amr_r.eucast_dosage(ab, *args, **kwargs))
+    return amr_r.eucast_dosage(ab, *args, **kwargs)
+@r_to_python
 def export_ncbi_biosample(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.export_ncbi_biosample(x, *args, **kwargs))
+    return amr_r.export_ncbi_biosample(x, *args, **kwargs)
+@r_to_python
 def first_isolate(x = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.first_isolate(x = None, *args, **kwargs))
+    return amr_r.first_isolate(x = None, *args, **kwargs)
+@r_to_python
 def filter_first_isolate(x = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.filter_first_isolate(x = None, *args, **kwargs))
+    return amr_r.filter_first_isolate(x = None, *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 convert_to_python(amr_r.g_test(x, *args, **kwargs))
+    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 convert_to_python(amr_r.is_new_episode(x, *args, **kwargs))
+    return amr_r.is_new_episode(x, *args, **kwargs)
+@r_to_python
 def ggplot_pca(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.ggplot_pca(x, *args, **kwargs))
+    return amr_r.ggplot_pca(x, *args, **kwargs)
+@r_to_python
 def ggplot_sir(data, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.ggplot_sir(data, *args, **kwargs))
+    return amr_r.ggplot_sir(data, *args, **kwargs)
+@r_to_python
 def geom_sir(position = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.geom_sir(position = None, *args, **kwargs))
+    return amr_r.geom_sir(position = None, *args, **kwargs)
+@r_to_python
 def guess_ab_col(x = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.guess_ab_col(x = None, *args, **kwargs))
+    return amr_r.guess_ab_col(x = None, *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 convert_to_python(amr_r.italicise_taxonomy(string, *args, **kwargs))
+    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 convert_to_python(amr_r.italicize_taxonomy(string, *args, **kwargs))
+    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 convert_to_python(amr_r.inner_join_microorganisms(x, *args, **kwargs))
+    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 convert_to_python(amr_r.left_join_microorganisms(x, *args, **kwargs))
+    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 convert_to_python(amr_r.right_join_microorganisms(x, *args, **kwargs))
+    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 convert_to_python(amr_r.full_join_microorganisms(x, *args, **kwargs))
+    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 convert_to_python(amr_r.semi_join_microorganisms(x, *args, **kwargs))
+    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 convert_to_python(amr_r.anti_join_microorganisms(x, *args, **kwargs))
+    return amr_r.anti_join_microorganisms(x, *args, **kwargs)
+@r_to_python
 def key_antimicrobials(x = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.key_antimicrobials(x = None, *args, **kwargs))
+    return amr_r.key_antimicrobials(x = None, *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 convert_to_python(amr_r.all_antimicrobials(x = None, *args, **kwargs))
+    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 convert_to_python(amr_r.kurtosis(x, *args, **kwargs))
+    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 convert_to_python(amr_r.like(x, *args, **kwargs))
+    return amr_r.like(x, *args, **kwargs)
+@r_to_python
 def mdro(x = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mdro(x = None, *args, **kwargs))
+    return amr_r.mdro(x = None, *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 convert_to_python(amr_r.brmo(x = None, *args, **kwargs))
+    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 convert_to_python(amr_r.mrgn(x = None, *args, **kwargs))
+    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 convert_to_python(amr_r.mdr_tb(x = None, *args, **kwargs))
+    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 convert_to_python(amr_r.mdr_cmi2012(x = None, *args, **kwargs))
+    return amr_r.mdr_cmi2012(x = None, *args, **kwargs)
+@r_to_python
 def eucast_exceptional_phenotypes(x = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.eucast_exceptional_phenotypes(x = None, *args, **kwargs))
+    return amr_r.eucast_exceptional_phenotypes(x = None, *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 convert_to_python(amr_r.mean_amr_distance(x, *args, **kwargs))
+    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 convert_to_python(amr_r.amr_distance_from_row(amr_distance, *args, **kwargs))
+    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 convert_to_python(amr_r.mo_matching_score(x, *args, **kwargs))
+    return amr_r.mo_matching_score(x, *args, **kwargs)
+@r_to_python
 def mo_name(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_name(x, *args, **kwargs))
+    return amr_r.mo_name(x, *args, **kwargs)
+@r_to_python
 def mo_fullname(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_fullname(x, *args, **kwargs))
+    return amr_r.mo_fullname(x, *args, **kwargs)
+@r_to_python
 def mo_shortname(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_shortname(x, *args, **kwargs))
+    return amr_r.mo_shortname(x, *args, **kwargs)
+@r_to_python
 def mo_subspecies(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_subspecies(x, *args, **kwargs))
+    return amr_r.mo_subspecies(x, *args, **kwargs)
+@r_to_python
 def mo_species(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_species(x, *args, **kwargs))
+    return amr_r.mo_species(x, *args, **kwargs)
+@r_to_python
 def mo_genus(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_genus(x, *args, **kwargs))
+    return amr_r.mo_genus(x, *args, **kwargs)
+@r_to_python
 def mo_family(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_family(x, *args, **kwargs))
+    return amr_r.mo_family(x, *args, **kwargs)
+@r_to_python
 def mo_order(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_order(x, *args, **kwargs))
+    return amr_r.mo_order(x, *args, **kwargs)
+@r_to_python
 def mo_class(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_class(x, *args, **kwargs))
+    return amr_r.mo_class(x, *args, **kwargs)
+@r_to_python
 def mo_phylum(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_phylum(x, *args, **kwargs))
+    return amr_r.mo_phylum(x, *args, **kwargs)
+@r_to_python
 def mo_kingdom(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_kingdom(x, *args, **kwargs))
+    return amr_r.mo_kingdom(x, *args, **kwargs)
+@r_to_python
 def mo_domain(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_domain(x, *args, **kwargs))
+    return amr_r.mo_domain(x, *args, **kwargs)
+@r_to_python
 def mo_type(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_type(x, *args, **kwargs))
+    return amr_r.mo_type(x, *args, **kwargs)
+@r_to_python
 def mo_status(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_status(x, *args, **kwargs))
+    return amr_r.mo_status(x, *args, **kwargs)
+@r_to_python
 def mo_pathogenicity(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_pathogenicity(x, *args, **kwargs))
+    return amr_r.mo_pathogenicity(x, *args, **kwargs)
+@r_to_python
 def mo_gramstain(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_gramstain(x, *args, **kwargs))
+    return amr_r.mo_gramstain(x, *args, **kwargs)
+@r_to_python
 def mo_is_gram_negative(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_is_gram_negative(x, *args, **kwargs))
+    return amr_r.mo_is_gram_negative(x, *args, **kwargs)
+@r_to_python
 def mo_is_gram_positive(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_is_gram_positive(x, *args, **kwargs))
+    return amr_r.mo_is_gram_positive(x, *args, **kwargs)
+@r_to_python
 def mo_is_yeast(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_is_yeast(x, *args, **kwargs))
+    return amr_r.mo_is_yeast(x, *args, **kwargs)
+@r_to_python
 def mo_is_intrinsic_resistant(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs))
+    return amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs)
+@r_to_python
 def mo_oxygen_tolerance(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_oxygen_tolerance(x, *args, **kwargs))
+    return amr_r.mo_oxygen_tolerance(x, *args, **kwargs)
+@r_to_python
 def mo_is_anaerobic(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_is_anaerobic(x, *args, **kwargs))
+    return amr_r.mo_is_anaerobic(x, *args, **kwargs)
+@r_to_python
 def mo_snomed(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_snomed(x, *args, **kwargs))
+    return amr_r.mo_snomed(x, *args, **kwargs)
+@r_to_python
 def mo_ref(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_ref(x, *args, **kwargs))
+    return amr_r.mo_ref(x, *args, **kwargs)
+@r_to_python
 def mo_authors(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_authors(x, *args, **kwargs))
+    return amr_r.mo_authors(x, *args, **kwargs)
+@r_to_python
 def mo_year(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_year(x, *args, **kwargs))
+    return amr_r.mo_year(x, *args, **kwargs)
+@r_to_python
 def mo_lpsn(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_lpsn(x, *args, **kwargs))
+    return amr_r.mo_lpsn(x, *args, **kwargs)
+@r_to_python
 def mo_mycobank(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_mycobank(x, *args, **kwargs))
+    return amr_r.mo_mycobank(x, *args, **kwargs)
+@r_to_python
 def mo_gbif(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_gbif(x, *args, **kwargs))
+    return amr_r.mo_gbif(x, *args, **kwargs)
+@r_to_python
 def mo_rank(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_rank(x, *args, **kwargs))
+    return amr_r.mo_rank(x, *args, **kwargs)
+@r_to_python
 def mo_taxonomy(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_taxonomy(x, *args, **kwargs))
+    return amr_r.mo_taxonomy(x, *args, **kwargs)
+@r_to_python
 def mo_synonyms(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_synonyms(x, *args, **kwargs))
+    return amr_r.mo_synonyms(x, *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 convert_to_python(amr_r.mo_current(x, *args, **kwargs))
+    return amr_r.mo_current(x, *args, **kwargs)
+@r_to_python
 def mo_group_members(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_group_members(x, *args, **kwargs))
+    return amr_r.mo_group_members(x, *args, **kwargs)
+@r_to_python
 def mo_info(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_info(x, *args, **kwargs))
+    return amr_r.mo_info(x, *args, **kwargs)
+@r_to_python
 def mo_url(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_url(x, *args, **kwargs))
+    return amr_r.mo_url(x, *args, **kwargs)
+@r_to_python
 def mo_property(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.mo_property(x, *args, **kwargs))
+    return amr_r.mo_property(x, *args, **kwargs)
+@r_to_python
 def pca(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.pca(x, *args, **kwargs))
+    return amr_r.pca(x, *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 convert_to_python(amr_r.theme_sir(*args, **kwargs))
+    return amr_r.theme_sir(*args, **kwargs)
+@r_to_python
 def labels_sir_count(position = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.labels_sir_count(position = None, *args, **kwargs))
+    return amr_r.labels_sir_count(position = None, *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 convert_to_python(amr_r.resistance(*args, **kwargs))
+    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 convert_to_python(amr_r.susceptibility(*args, **kwargs))
+    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 convert_to_python(amr_r.sir_confidence_interval(*args, **kwargs))
+    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 convert_to_python(amr_r.proportion_R(*args, **kwargs))
+    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 convert_to_python(amr_r.proportion_IR(*args, **kwargs))
+    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 convert_to_python(amr_r.proportion_I(*args, **kwargs))
+    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 convert_to_python(amr_r.proportion_SI(*args, **kwargs))
+    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 convert_to_python(amr_r.proportion_S(*args, **kwargs))
+    return amr_r.proportion_S(*args, **kwargs)
+@r_to_python
 def proportion_df(data, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.proportion_df(data, *args, **kwargs))
+    return amr_r.proportion_df(data, *args, **kwargs)
+@r_to_python
 def sir_df(data, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.sir_df(data, *args, **kwargs))
+    return amr_r.sir_df(data, *args, **kwargs)
+@r_to_python
 def random_mic(size = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.random_mic(size = None, *args, **kwargs))
+    return amr_r.random_mic(size = None, *args, **kwargs)
+@r_to_python
 def random_disk(size = None, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.random_disk(size = None, *args, **kwargs))
+    return amr_r.random_disk(size = None, *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 convert_to_python(amr_r.random_sir(size = None, *args, **kwargs))
+    return amr_r.random_sir(size = None, *args, **kwargs)
+@r_to_python
 def resistance_predict(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.resistance_predict(x, *args, **kwargs))
+    return amr_r.resistance_predict(x, *args, **kwargs)
+@r_to_python
 def sir_predict(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.sir_predict(x, *args, **kwargs))
+    return amr_r.sir_predict(x, *args, **kwargs)
+@r_to_python
 def ggplot_sir_predict(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.ggplot_sir_predict(x, *args, **kwargs))
+    return amr_r.ggplot_sir_predict(x, *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 convert_to_python(amr_r.skewness(x, *args, **kwargs))
+    return amr_r.skewness(x, *args, **kwargs)
+@r_to_python
 def top_n_microorganisms(x, *args, **kwargs):
     """Please see our website of the R package for the full manual: https://amr-for-r.org"""
-    return convert_to_python(amr_r.top_n_microorganisms(x, *args, **kwargs))
+    return amr_r.top_n_microorganisms(x, *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 convert_to_python(amr_r.reset_AMR_locale(*args, **kwargs))
+    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 convert_to_python(amr_r.translate_AMR(x, *args, **kwargs))
+    return amr_r.translate_AMR(x, *args, **kwargs)

{amr-3.0.0.9010.dist-info → amr-3.0.0.9012.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMR
-Version: 3.0.0.9010
+Version: 3.0.0.9012
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

amr-3.0.0.9012.dist-info/RECORD

@@ -0,0 +1,7 @@
+AMR/__init__.py,sha256=ZNl9ZnfkNuZCBu7bcKs7y9_fp6-AOzuvJ8wNqzlPgTk,7989
+AMR/datasets.py,sha256=y_Iy1fLnl7KyTXg2QuiXyizQ3f0ivVOPHpPxmafttn8,2572
+AMR/functions.py,sha256=kVhO81MiXDvV9c0264W_RJAS9783XQQhTyRQh3RAd8Q,45300
+amr-3.0.0.9012.dist-info/METADATA,sha256=H_5aOq4mlply2p5svxLuJf8G0asXHkPgf_PraEryxuk,10095
+amr-3.0.0.9012.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+amr-3.0.0.9012.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
+amr-3.0.0.9012.dist-info/RECORD,,

amr-3.0.0.9010.dist-info/RECORD

@@ -1,7 +0,0 @@
-AMR/__init__.py,sha256=ZNl9ZnfkNuZCBu7bcKs7y9_fp6-AOzuvJ8wNqzlPgTk,7989
-AMR/datasets.py,sha256=zNOGHIBZvcAx2Z2QF9gIccSkQkWW0CX9pEVBOVR-7gs,2430
-AMR/functions.py,sha256=goXl_k5v2SCI15zHpyU8CA1MCYi_l_cYx5_19FG7VTM,46306
-amr-3.0.0.9010.dist-info/METADATA,sha256=tv9ZABiqPi9SPrRdYC9w5YDu4TRBLmeqrJ-SwTNajj4,10095
-amr-3.0.0.9010.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-amr-3.0.0.9010.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
-amr-3.0.0.9010.dist-info/RECORD,,