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Code Releases Activity

(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-01-26 23:01:17 +01:00
parent 92c4fc0f94
commit 66833b4f5a
46 changed files with 1786 additions and 1842 deletions
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2
PythonPackage/AMR/AMR.egg-info/PKG-INFO
View File

@ -1,6 +1,6 @@
Metadata-Version: 2.2
Name: AMR
Version: 2.1.1.9125
Version: 2.1.1.9126
Summary: A Python wrapper for the AMR R package
Home-page: https://github.com/msberends/AMR
Author: Matthijs Berends

2
PythonPackage/AMR/AMR/__init__.py
View File

@ -26,6 +26,7 @@ from .functions import clear_custom_microorganisms
from .functions import age
from .functions import age_groups
from .functions import antibiogram
from .functions import wisca
from .functions import amr_class
from .functions import amr_selector
from .functions import aminoglycosides
@ -201,5 +202,6 @@ from .functions import resistance_predict
from .functions import sir_predict
from .functions import ggplot_sir_predict
from .functions import skewness
from .functions import top_n_microorganisms
from .functions import reset_AMR_locale
from .functions import translate_AMR

9
PythonPackage/AMR/AMR/datasets.py
View File

@ -3,6 +3,7 @@ GREEN = '\033[32m'
RESET = '\033[0m'
import os
import sys
from rpy2 import robjects
from rpy2.robjects import pandas2ri
from rpy2.robjects.packages import importr, isinstalled
@ -10,7 +11,7 @@ import pandas as pd
import importlib.metadata as metadata
# Get the path to the virtual environment
venv_path = os.getenv('VIRTUAL_ENV') # Path to the active virtual environment
venv_path = sys.prefix
# Define R library path within the venv
r_lib_path = os.path.join(venv_path, "R_libs")
@ -19,10 +20,12 @@ os.makedirs(r_lib_path, exist_ok=True)
# Set the R library path in .libPaths
base = importr('base')
base._libPaths(r_lib_path)
r_amr_lib_path = base._libPaths()[0]
# Check if the AMR package is installed in R
if not isinstalled('AMR'):
if not isinstalled('AMR', lib_loc = r_amr_lib_path):
utils = importr('utils')
print(f"{BLUE}AMR:{RESET} Installing AMR package to {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
# Python package version of AMR
@ -37,7 +40,7 @@ r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_li
# Compare R and Python package versions
if r_amr_version != python_amr_version:
try:
print(f"{BLUE}AMR:{RESET} Updating package version{RESET}", flush=True)
print(f"{BLUE}AMR:{RESET} Updating AMR package in {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
utils = importr('utils')
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
except Exception as e:

282
PythonPackage/AMR/AMR/functions.py
View File

@ -42,9 +42,9 @@ def ab_class(*args, **kwargs):
def ab_selector(*args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.ab_selector(*args, **kwargs))
def ab_from_text(*args, **kwargs):
def ab_from_text(text, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.ab_from_text(*args, **kwargs))
return convert_to_python(amr_r.ab_from_text(text, *args, **kwargs))
def ab_name(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.ab_name(x, *args, **kwargs))
@ -105,18 +105,21 @@ def 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):
def antibiogram(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.antibiogram(*args, **kwargs))
def amr_class(*args, **kwargs):
return convert_to_python(amr_r.antibiogram(x, *args, **kwargs))
def wisca(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.amr_class(*args, **kwargs))
def amr_selector(*args, **kwargs):
return convert_to_python(amr_r.wisca(x, *args, **kwargs))
def amr_class(amr_class, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.amr_selector(*args, **kwargs))
def aminoglycosides(*args, **kwargs):
return convert_to_python(amr_r.amr_class(amr_class, *args, **kwargs))
def amr_selector(filter, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.aminoglycosides(*args, **kwargs))
return convert_to_python(amr_r.amr_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))
@ -126,15 +129,15 @@ def 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(*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(*args, **kwargs))
return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
def carbapenems(*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(*args, **kwargs))
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))
@ -159,9 +162,9 @@ def 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(*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(*args, **kwargs))
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))
@ -180,9 +183,9 @@ def penicillins(only_sir_columns = False, *args, **kwargs):
def phenicols(only_sir_columns = False, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
def polymyxins(*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(*args, **kwargs))
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))
@ -207,9 +210,9 @@ def 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):
def not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.not_intrinsic_resistant(*args, **kwargs))
return convert_to_python(amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs))
def as_ab(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.as_ab(x, *args, **kwargs))
@ -237,9 +240,9 @@ def 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):
def as_mo(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.as_mo(*args, **kwargs))
return convert_to_python(amr_r.as_mo(x, *args, **kwargs))
def is_mo(x):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.is_mo(x))
@ -270,9 +273,9 @@ def 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):
def atc_online_property(atc_code, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.atc_online_property(*args, **kwargs))
return convert_to_python(amr_r.atc_online_property(atc_code, *args, **kwargs))
def atc_online_groups(atc_code, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.atc_online_groups(atc_code, *args, **kwargs))
@ -282,9 +285,9 @@ def 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):
def av_from_text(text, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.av_from_text(*args, **kwargs))
return convert_to_python(amr_r.av_from_text(text, *args, **kwargs))
def av_name(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.av_name(x, *args, **kwargs))
@ -354,45 +357,45 @@ def 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):
def count_df(data, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.count_df(*args, **kwargs))
return convert_to_python(amr_r.count_df(data, *args, **kwargs))
def custom_eucast_rules(*args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.custom_eucast_rules(*args, **kwargs))
def eucast_rules(*args, **kwargs):
def eucast_rules(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.eucast_rules(*args, **kwargs))
return convert_to_python(amr_r.eucast_rules(x, *args, **kwargs))
def eucast_dosage(ab, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.eucast_dosage(ab, *args, **kwargs))
def export_ncbi_biosample(*args, **kwargs):
def export_ncbi_biosample(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.export_ncbi_biosample(*args, **kwargs))
def first_isolate(*args, **kwargs):
return convert_to_python(amr_r.export_ncbi_biosample(x, *args, **kwargs))
def first_isolate(x = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.first_isolate(*args, **kwargs))
def filter_first_isolate(*args, **kwargs):
return convert_to_python(amr_r.first_isolate(x = None, *args, **kwargs))
def filter_first_isolate(x = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.filter_first_isolate(*args, **kwargs))
return convert_to_python(amr_r.filter_first_isolate(x = None, *args, **kwargs))
def g_test(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.g_test(x, *args, **kwargs))
def is_new_episode(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.is_new_episode(x, *args, **kwargs))
def ggplot_pca(*args, **kwargs):
def ggplot_pca(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.ggplot_pca(*args, **kwargs))
def ggplot_sir(*args, **kwargs):
return convert_to_python(amr_r.ggplot_pca(x, *args, **kwargs))
def ggplot_sir(data, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.ggplot_sir(*args, **kwargs))
def geom_sir(*args, **kwargs):
return convert_to_python(amr_r.ggplot_sir(data, *args, **kwargs))
def geom_sir(position = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.geom_sir(*args, **kwargs))
def guess_ab_col(*args, **kwargs):
return convert_to_python(amr_r.geom_sir(position = None, *args, **kwargs))
def guess_ab_col(x = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.guess_ab_col(*args, **kwargs))
return convert_to_python(amr_r.guess_ab_col(x = None, *args, **kwargs))
def italicise_taxonomy(string, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.italicise_taxonomy(string, *args, **kwargs))
@ -417,24 +420,24 @@ def 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):
def key_antimicrobials(x = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.key_antimicrobials(*args, **kwargs))
return convert_to_python(amr_r.key_antimicrobials(x = None, *args, **kwargs))
def all_antimicrobials(x = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.all_antimicrobials(x = None, *args, **kwargs))
def antimicrobials_equal(*args, **kwargs):
def antimicrobials_equal(y, *args, **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))
return convert_to_python(amr_r.antimicrobials_equal(y, *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):
def mdro(x = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mdro(*args, **kwargs))
return convert_to_python(amr_r.mdro(x = None, *args, **kwargs))
def custom_mdro_guideline(*args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.custom_mdro_guideline(*args, **kwargs))
@ -450,9 +453,9 @@ def 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(*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(*args, **kwargs))
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))
@ -462,126 +465,126 @@ def 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):
def mo_name(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_name(*args, **kwargs))
def mo_fullname(*args, **kwargs):
return convert_to_python(amr_r.mo_name(x, *args, **kwargs))
def mo_fullname(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_fullname(*args, **kwargs))
def mo_shortname(*args, **kwargs):
return convert_to_python(amr_r.mo_fullname(x, *args, **kwargs))
def mo_shortname(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_shortname(*args, **kwargs))
def mo_subspecies(*args, **kwargs):
return convert_to_python(amr_r.mo_shortname(x, *args, **kwargs))
def mo_subspecies(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_subspecies(*args, **kwargs))
def mo_species(*args, **kwargs):
return convert_to_python(amr_r.mo_subspecies(x, *args, **kwargs))
def mo_species(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_species(*args, **kwargs))
def mo_genus(*args, **kwargs):
return convert_to_python(amr_r.mo_species(x, *args, **kwargs))
def mo_genus(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_genus(*args, **kwargs))
def mo_family(*args, **kwargs):
return convert_to_python(amr_r.mo_genus(x, *args, **kwargs))
def mo_family(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_family(*args, **kwargs))
def mo_order(*args, **kwargs):
return convert_to_python(amr_r.mo_family(x, *args, **kwargs))
def mo_order(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_order(*args, **kwargs))
def mo_class(*args, **kwargs):
return convert_to_python(amr_r.mo_order(x, *args, **kwargs))
def mo_class(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_class(*args, **kwargs))
def mo_phylum(*args, **kwargs):
return convert_to_python(amr_r.mo_class(x, *args, **kwargs))
def mo_phylum(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_phylum(*args, **kwargs))
def mo_kingdom(*args, **kwargs):
return convert_to_python(amr_r.mo_phylum(x, *args, **kwargs))
def mo_kingdom(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_kingdom(*args, **kwargs))
def mo_domain(*args, **kwargs):
return convert_to_python(amr_r.mo_kingdom(x, *args, **kwargs))
def mo_domain(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_domain(*args, **kwargs))
def mo_type(*args, **kwargs):
return convert_to_python(amr_r.mo_domain(x, *args, **kwargs))
def mo_type(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_type(*args, **kwargs))
def mo_status(*args, **kwargs):
return convert_to_python(amr_r.mo_type(x, *args, **kwargs))
def mo_status(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_status(*args, **kwargs))
def mo_pathogenicity(*args, **kwargs):
return convert_to_python(amr_r.mo_status(x, *args, **kwargs))
def mo_pathogenicity(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_pathogenicity(*args, **kwargs))
def mo_gramstain(*args, **kwargs):
return convert_to_python(amr_r.mo_pathogenicity(x, *args, **kwargs))
def mo_gramstain(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_gramstain(*args, **kwargs))
def mo_is_gram_negative(*args, **kwargs):
return convert_to_python(amr_r.mo_gramstain(x, *args, **kwargs))
def mo_is_gram_negative(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_is_gram_negative(*args, **kwargs))
def mo_is_gram_positive(*args, **kwargs):
return convert_to_python(amr_r.mo_is_gram_negative(x, *args, **kwargs))
def mo_is_gram_positive(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_is_gram_positive(*args, **kwargs))
def mo_is_yeast(*args, **kwargs):
return convert_to_python(amr_r.mo_is_gram_positive(x, *args, **kwargs))
def mo_is_yeast(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_is_yeast(*args, **kwargs))
def mo_is_intrinsic_resistant(*args, **kwargs):
return convert_to_python(amr_r.mo_is_yeast(x, *args, **kwargs))
def mo_is_intrinsic_resistant(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_is_intrinsic_resistant(*args, **kwargs))
def mo_oxygen_tolerance(*args, **kwargs):
return convert_to_python(amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs))
def mo_oxygen_tolerance(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_oxygen_tolerance(*args, **kwargs))
def mo_is_anaerobic(*args, **kwargs):
return convert_to_python(amr_r.mo_oxygen_tolerance(x, *args, **kwargs))
def mo_is_anaerobic(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_is_anaerobic(*args, **kwargs))
def mo_snomed(*args, **kwargs):
return convert_to_python(amr_r.mo_is_anaerobic(x, *args, **kwargs))
def mo_snomed(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_snomed(*args, **kwargs))
def mo_ref(*args, **kwargs):
return convert_to_python(amr_r.mo_snomed(x, *args, **kwargs))
def mo_ref(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_ref(*args, **kwargs))
def mo_authors(*args, **kwargs):
return convert_to_python(amr_r.mo_ref(x, *args, **kwargs))
def mo_authors(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_authors(*args, **kwargs))
def mo_year(*args, **kwargs):
return convert_to_python(amr_r.mo_authors(x, *args, **kwargs))
def mo_year(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_year(*args, **kwargs))
def mo_lpsn(*args, **kwargs):
return convert_to_python(amr_r.mo_year(x, *args, **kwargs))
def mo_lpsn(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_lpsn(*args, **kwargs))
def mo_mycobank(*args, **kwargs):
return convert_to_python(amr_r.mo_lpsn(x, *args, **kwargs))
def mo_mycobank(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_mycobank(*args, **kwargs))
def mo_gbif(*args, **kwargs):
return convert_to_python(amr_r.mo_mycobank(x, *args, **kwargs))
def mo_gbif(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_gbif(*args, **kwargs))
def mo_rank(*args, **kwargs):
return convert_to_python(amr_r.mo_gbif(x, *args, **kwargs))
def mo_rank(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_rank(*args, **kwargs))
def mo_taxonomy(*args, **kwargs):
return convert_to_python(amr_r.mo_rank(x, *args, **kwargs))
def mo_taxonomy(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_taxonomy(*args, **kwargs))
def mo_synonyms(*args, **kwargs):
return convert_to_python(amr_r.mo_taxonomy(x, *args, **kwargs))
def mo_synonyms(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_synonyms(*args, **kwargs))
return convert_to_python(amr_r.mo_synonyms(x, *args, **kwargs))
def mo_current(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_current(x, *args, **kwargs))
def mo_group_members(*args, **kwargs):
def mo_group_members(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_group_members(*args, **kwargs))
def mo_info(*args, **kwargs):
return convert_to_python(amr_r.mo_group_members(x, *args, **kwargs))
def mo_info(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_info(*args, **kwargs))
def mo_url(*args, **kwargs):
return convert_to_python(amr_r.mo_info(x, *args, **kwargs))
def mo_url(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_url(*args, **kwargs))
def mo_property(*args, **kwargs):
return convert_to_python(amr_r.mo_url(x, *args, **kwargs))
def mo_property(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.mo_property(*args, **kwargs))
def pca(*args, **kwargs):
return convert_to_python(amr_r.mo_property(x, *args, **kwargs))
def pca(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.pca(*args, **kwargs))
return convert_to_python(amr_r.pca(x, *args, **kwargs))
def theme_sir(*args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.theme_sir(*args, **kwargs))
def labels_sir_count(*args, **kwargs):
def labels_sir_count(position = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.labels_sir_count(*args, **kwargs))
return convert_to_python(amr_r.labels_sir_count(position = None, *args, **kwargs))
def resistance(*args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.resistance(*args, **kwargs))
@ -606,12 +609,12 @@ def 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):
def proportion_df(data, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.proportion_df(*args, **kwargs))
def sir_df(*args, **kwargs):
return convert_to_python(amr_r.proportion_df(data, *args, **kwargs))
def sir_df(data, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.sir_df(*args, **kwargs))
return convert_to_python(amr_r.sir_df(data, *args, **kwargs))
def random_mic(size = None, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.random_mic(size = None, *args, **kwargs))
@ -621,18 +624,21 @@ def 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):
def resistance_predict(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.resistance_predict(*args, **kwargs))
def sir_predict(*args, **kwargs):
return convert_to_python(amr_r.resistance_predict(x, *args, **kwargs))
def sir_predict(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.sir_predict(*args, **kwargs))
def ggplot_sir_predict(*args, **kwargs):
return convert_to_python(amr_r.sir_predict(x, *args, **kwargs))
def ggplot_sir_predict(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.ggplot_sir_predict(*args, **kwargs))
return convert_to_python(amr_r.ggplot_sir_predict(x, *args, **kwargs))
def skewness(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.skewness(x, *args, **kwargs))
def top_n_microorganisms(x, *args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.top_n_microorganisms(x, *args, **kwargs))
def reset_AMR_locale(*args, **kwargs):
"""See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
return convert_to_python(amr_r.reset_AMR_locale(*args, **kwargs))

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PythonPackage/AMR/setup.py
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@ -2,7 +2,7 @@ from setuptools import setup, find_packages
setup(
name='AMR',
version='2.1.1.9125',
version='2.1.1.9126',
packages=find_packages(),
install_requires=[
'rpy2',