AMR 2.1.1.9125__py3-none-any.whl → 2.1.1.9127__py3-none-any.whl

AMR/__init__.py

@@ -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

AMR/datasets.py

@@ -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")
@@ -18,11 +19,16 @@ r_lib_path = os.path.join(venv_path, "R_libs")
 os.makedirs(r_lib_path, exist_ok=True)
 # Set the R library path in .libPaths
 base = importr('base')
+# Turn off warnings
+base.options(warn = -1)
+
 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
@@ -37,12 +43,15 @@ 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:
         print(f"{BLUE}AMR:{RESET} Could not update: {e}{RESET}", flush=True)
 
+# Restore warnings to default
+base.options(warn = 0)
+
 print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
 
 # Activate the automatic conversion between R and pandas DataFrames

AMR/functions.py

@@ -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))

{AMR-2.1.1.9125.dist-info → AMR-2.1.1.9127.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9125
+Version: 2.1.1.9127
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends
@@ -98,48 +98,6 @@ print(df)
 
 * **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     |
-
-
 ## Calculating AMR
 
 ```python
@@ -190,6 +148,47 @@ print(result2b)
 
 In this example, we generate an antibiogram by selecting various antibiotics.
 
+## Taxonomic Data Sets Now in Python!
+
+As a Python user, you might like that the most important data sets of the `AMR` R package, `microorganisms`, `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     |
+
+
 # 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.

AMR-2.1.1.9127.dist-info/RECORD

@@ -0,0 +1,7 @@
+AMR/__init__.py,sha256=-3zoWVuhybnYkXePzljDrtcxxaAQscPpCPP75EiqLfQ,7540
+AMR/datasets.py,sha256=tNLt7ERRxR-HYWD_gY6NwkMjdTIkg0bqtdi98U7sCyQ,2673
+AMR/functions.py,sha256=JSh-0_mfrAj7ajpazlv2KFyEtRAglj7oQV9Iiaux7eo,45557
+AMR-2.1.1.9127.dist-info/METADATA,sha256=sYrsK-qr05-Yn2pxCyIyna4NKGIBZ_ZCvWI0lHUeVQE,9624
+AMR-2.1.1.9127.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+AMR-2.1.1.9127.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
+AMR-2.1.1.9127.dist-info/RECORD,,

AMR-2.1.1.9125.dist-info/RECORD

@@ -1,7 +0,0 @@
-AMR/__init__.py,sha256=cSUa6bz_aXEUR5o0D3dh8opo6XdlgS10hoIgYH1r_mY,7467
-AMR/datasets.py,sha256=IDeqfVGjzvhMhKZRlS6Pc3xIO4HBlRDvPdQjDQ8qVTc,2426
-AMR/functions.py,sha256=FmEKlH-hCyJBaJIU6dCX6WAKjYhhpGAo4qSwHP_XkzE,44231
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