AMR 2.1.1.9094__py3-none-any.whl

AMR/__init__.py

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+from .datasets import example_isolates
+from .datasets import microorganisms
+from .datasets import antibiotics
+from .datasets import clinical_breakpoints
+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 ab_class
+from .functions import ab_selector
+from .functions import aminoglycosides
+from .functions import aminopenicillins
+from .functions import antifungals
+from .functions import antimycobacterials
+from .functions import betalactams
+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 lincosamides
+from .functions import lipoglycopeptides
+from .functions import macrolides
+from .functions import nitrofurans
+from .functions import oxazolidinones
+from .functions import penicillins
+from .functions import polymyxins
+from .functions import quinolones
+from .functions import rifamycins
+from .functions import streptogramins
+from .functions import tetracyclines
+from .functions import trimethoprims
+from .functions import ureidopenicillins
+from .functions import 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 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 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 theme_sir
+from .functions import labels_sir_count
+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 antimicrobials_equal
+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 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 reset_AMR_locale
+from .functions import translate_AMR

AMR/datasets.py

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+BLUE = '\033[94m'
+GREEN = '\033[32m'
+RESET = '\033[0m'
+
+print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
+
+from rpy2 import robjects
+from rpy2.robjects import pandas2ri
+from rpy2.robjects.packages import importr, isinstalled
+import pandas as pd
+
+# Check if the R package is installed
+if not isinstalled('AMR'):
+    utils = importr('utils')
+    utils.install_packages('AMR')
+
+# 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
+'''))
+example_isolates['date'] = pd.to_datetime(example_isolates['date'])
+
+# microorganisms
+microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]'))
+antibiotics = pandas2ri.rpy2py(robjects.r('AMR::antibiotics[, !sapply(AMR::antibiotics, is.list)]'))
+clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints'))
+
+print(f"{BLUE}AMR:{RESET} {GREEN}Done.{RESET}", flush=True)

AMR/functions.py

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+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_from_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(*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(*args, **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(*args, **kwargs))
+def ab_class(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(ab_class, *args, **kwargs))
+def ab_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.ab_selector(filter, *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 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 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 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 polymyxins(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
+def quinolones(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.quinolones(only_sir_columns = False, *args, **kwargs))
+def rifamycins(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.rifamycins(only_sir_columns = False, *args, **kwargs))
+def streptogramins(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.streptogramins(only_sir_columns = False, *args, **kwargs))
+def tetracyclines(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.tetracyclines(only_sir_columns = False, *args, **kwargs))
+def trimethoprims(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.trimethoprims(only_sir_columns = False, *args, **kwargs))
+def ureidopenicillins(only_sir_columns = False, *args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.ureidopenicillins(only_sir_columns = False, *args, **kwargs))
+def 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(*args, **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(*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 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 as_mo(*args, **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(*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(*args, **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(*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(*args, **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(*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(*args, **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(*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(*args, **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(*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(*args, **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(*args, **kwargs))
+def first_isolate(*args, **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(*args, **kwargs))
+def filter_first_isolate(*args, **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(*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(*args, **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(*args, **kwargs))
+def ggplot_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.ggplot_sir(*args, **kwargs))
+def geom_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.geom_sir(*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(*args, **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(*args, **kwargs))
+def guess_ab_col(*args, **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(*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(*args, **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(*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 antimicrobials_equal(*args, **kwargs):
+    """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
+    return convert_to_python(amr_r.antimicrobials_equal(*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(*args, **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(*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(*args, **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(*args, **kwargs))
+def mo_fullname(*args, **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(*args, **kwargs))
+def mo_shortname(*args, **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(*args, **kwargs))
+def mo_subspecies(*args, **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(*args, **kwargs))
+def mo_species(*args, **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(*args, **kwargs))
+def mo_genus(*args, **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(*args, **kwargs))
+def mo_family(*args, **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(*args, **kwargs))
+def mo_order(*args, **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(*args, **kwargs))
+def mo_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.mo_class(*args, **kwargs))
+def mo_phylum(*args, **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(*args, **kwargs))
+def mo_kingdom(*args, **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(*args, **kwargs))
+def mo_domain(*args, **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(*args, **kwargs))
+def mo_type(*args, **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(*args, **kwargs))
+def mo_status(*args, **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(*args, **kwargs))
+def mo_pathogenicity(*args, **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(*args, **kwargs))
+def mo_gramstain(*args, **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(*args, **kwargs))
+def mo_is_gram_negative(*args, **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(*args, **kwargs))
+def mo_is_gram_positive(*args, **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(*args, **kwargs))
+def mo_is_yeast(*args, **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(*args, **kwargs))
+def mo_is_intrinsic_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.mo_is_intrinsic_resistant(*args, **kwargs))
+def mo_oxygen_tolerance(*args, **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(*args, **kwargs))
+def mo_is_anaerobic(*args, **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(*args, **kwargs))
+def mo_snomed(*args, **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(*args, **kwargs))
+def mo_ref(*args, **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(*args, **kwargs))
+def mo_authors(*args, **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(*args, **kwargs))
+def mo_year(*args, **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(*args, **kwargs))
+def mo_lpsn(*args, **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(*args, **kwargs))
+def mo_mycobank(*args, **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(*args, **kwargs))
+def mo_gbif(*args, **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(*args, **kwargs))
+def mo_rank(*args, **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(*args, **kwargs))
+def mo_taxonomy(*args, **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(*args, **kwargs))
+def mo_synonyms(*args, **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(*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(*args, **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(*args, **kwargs))
+def mo_info(*args, **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(*args, **kwargs))
+def mo_url(*args, **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(*args, **kwargs))
+def mo_property(*args, **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(*args, **kwargs))
+def pca(*args, **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(*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(*args, **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(*args, **kwargs))
+def sir_df(*args, **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(*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(*args, **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(*args, **kwargs))
+def sir_predict(*args, **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(*args, **kwargs))
+def ggplot_sir_predict(*args, **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(*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 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))

AMR-2.1.1.9094.dist-info/METADATA

@@ -0,0 +1,223 @@
+Metadata-Version: 2.1
+Name: AMR
+Version: 2.1.1.9094
+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
+Platform: UNKNOWN
+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
+
+---
+title: "AMR for Python"
+output: 
+  rmarkdown::html_vignette:
+    toc: true
+    toc_depth: 3
+vignette: >
+  %\VignetteIndexEntry{AMR for Python}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: console
+---
+
+```{r setup, include = FALSE, results = 'markup'}
+knitr::opts_chunk$set(
+  warning = FALSE,
+  collapse = TRUE,
+  comment = "#>",
+  fig.width = 7.5,
+  fig.height = 5
+)
+```
+
+# Introduction
+
+The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) analysis. It provides extensive features for handling microbial and antimicrobial data. However, for those who work primarily in Python, we now have a more intuitive option available: the `AMR` Python package, which uses `rpy2` internally. This package allows Python users to access all the functions from the R `AMR` package without the need to set up `rpy2` themselves. Since this Python package is not a true 'port' (which would require all R functions to be rewritten into Python), R and the AMR R package are still required to be installed. Yet, Python users can now easily work with AMR data directly through Python code.
+
+In this document, we explain how this works and provide simple examples of using the `AMR` Python package.
+
+## How It Works
+
+The `AMR` Python package acts as a wrapper around the functions in the `AMR` R package. The package simplifies the process of calling R functions in Python, eliminating the need to manually manage the `rpy2` setup, which Python uses internally to be able to work with the R package. By just using `import AMR`, Python users can directly use the functions from the `AMR` R package as if they were native Python functions.
+
+Internally, `rpy2` is still being used, but all complexity is hidden from the user. This approach keeps the Python code clean and Pythonic, while still leveraging the full power of the R `AMR` package.
+
+## Example of Usage
+
+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".
+
+### 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`, `antibiotics`, `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.antibiotics
+```
+
+| ab  | cid         | name                 | group                      | oral_ddd | oral_units | iv_ddd | iv_units |
+|-----|-------------|----------------------|----------------------------|----------|------------|--------|----------|
+| AMA | 4649.0      | 4-aminosalicylic acid| Antimycobacterials         | 12.00    | g          | NaN    | None     |
+| ACM | 6450012.0   | Acetylmidecamycin    | Macrolides/lincosamides    | NaN      | None       | NaN    | None     |
+| ASP | 49787020.0  | Acetylspiramycin     | Macrolides/lincosamides    | NaN      | None       | NaN    | None     |
+| ALS | 8954.0      | Aldesulfone sodium   | Other antibacterials       | 0.33     | g          | NaN    | None     |
+| AMK | 37768.0     | Amikacin             | Aminoglycosides            | NaN      | None       | 1.0    | g        |
+| ... | ...         | ...                  | ...                        | ...      | ...        | ...    | ...      |
+| VIR | 11979535.0  | Virginiamycine       | Other antibacterials       | NaN      | None       | NaN    | None     |
+| VOR | 71616.0     | Voriconazole         | Antifungals/antimycotics   | 0.40     | g          | 0.4    | g        |
+| XBR | 72144.0     | Xibornol             | Other antibacterials       | NaN      | None       | NaN    | None     |
+| ZID | 77846445.0  | Zidebactam           | Other antibacterials       | NaN      | None       | NaN    | None     |
+| ZFD | NaN         | Zoliflodacin         | None                       | NaN      | None       | NaN    | None     |
+
+
+# Installation
+
+To be able to use the `AMR` Python package, it is required to install both R and the `AMR` R package.
+
+### Preparation: Install R and `AMR` R package
+
+For Linux and macOS, this is just:
+
+```bash
+# Ubuntu / Debian
+sudo apt install r-base && Rscript -e 'install.packages("AMR")'
+# Fedora:
+sudo dnf install R && Rscript -e 'install.packages("AMR")'
+# CentOS/RHEL
+sudo yum install R && Rscript -e 'install.packages("AMR")'
+# Arch Linux
+sudo pacman -S r && Rscript -e 'install.packages("AMR")'
+# macOS
+brew install r && Rscript -e 'install.packages("AMR")'
+```
+
+For Windows, visit the [CRAN download page](https://cran.r-project.org) in install R, then afterwards install the 'AMR' package manually.
+
+### Install `AMR` Python Package
+
+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
+```
+
+# Working with `AMR` in Python
+
+Now that we have everything set up, let’s walk through some practical examples of using the `AMR` package within Python.
+
+## Example 1: Calculating AMR
+
+```python
+import AMR
+import pandas as pd
+
+df = AMR.example_isolates
+result = AMR.resistance(df["AMX"])
+print(result)
+```
+
+```
+[0.59555556]
+```
+
+## Example 2: 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.
+
+# 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 using `import AMR`, you can seamlessly integrate the robust features of the R `AMR` package into your 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.
+
+

AMR-2.1.1.9094.dist-info/RECORD

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AMR-2.1.1.9094.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.37.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

AMR-2.1.1.9094.dist-info/top_level.txt

@@ -0,0 +1 @@
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