AMR 2.1.1.9125__py3-none-any.whl → 2.1.1.9126__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
AMR/__init__.py CHANGED
@@ -26,6 +26,7 @@ from .functions import clear_custom_microorganisms
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  from .functions import age
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  from .functions import age_groups
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  from .functions import antibiogram
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+ from .functions import wisca
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  from .functions import amr_class
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  from .functions import amr_selector
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  from .functions import aminoglycosides
@@ -201,5 +202,6 @@ from .functions import resistance_predict
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  from .functions import sir_predict
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  from .functions import ggplot_sir_predict
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  from .functions import skewness
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+ from .functions import top_n_microorganisms
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  from .functions import reset_AMR_locale
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  from .functions import translate_AMR
AMR/datasets.py CHANGED
@@ -3,6 +3,7 @@ GREEN = '\033[32m'
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  RESET = '\033[0m'
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  import os
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+ import sys
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  from rpy2 import robjects
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  from rpy2.robjects import pandas2ri
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  from rpy2.robjects.packages import importr, isinstalled
@@ -10,7 +11,7 @@ import pandas as pd
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  import importlib.metadata as metadata
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  # Get the path to the virtual environment
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- venv_path = os.getenv('VIRTUAL_ENV') # Path to the active virtual environment
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+ venv_path = sys.prefix
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  # Define R library path within the venv
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  r_lib_path = os.path.join(venv_path, "R_libs")
@@ -19,10 +20,12 @@ os.makedirs(r_lib_path, exist_ok=True)
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  # Set the R library path in .libPaths
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  base = importr('base')
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  base._libPaths(r_lib_path)
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+ r_amr_lib_path = base._libPaths()[0]
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  # Check if the AMR package is installed in R
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- if not isinstalled('AMR'):
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+ if not isinstalled('AMR', lib_loc = r_amr_lib_path):
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  utils = importr('utils')
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+ print(f"{BLUE}AMR:{RESET} Installing AMR package to {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
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  utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
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  # Python package version of AMR
@@ -37,7 +40,7 @@ r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_li
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  # Compare R and Python package versions
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  if r_amr_version != python_amr_version:
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  try:
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- print(f"{BLUE}AMR:{RESET} Updating package version{RESET}", flush=True)
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+ print(f"{BLUE}AMR:{RESET} Updating AMR package in {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
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  utils = importr('utils')
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  utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
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  except Exception as e:
AMR/functions.py CHANGED
@@ -42,9 +42,9 @@ def ab_class(*args, **kwargs):
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  def ab_selector(*args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.ab_selector(*args, **kwargs))
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- def ab_from_text(*args, **kwargs):
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+ def ab_from_text(text, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.ab_from_text(*args, **kwargs))
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+ return convert_to_python(amr_r.ab_from_text(text, *args, **kwargs))
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  def ab_name(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.ab_name(x, *args, **kwargs))
@@ -105,18 +105,21 @@ def age(x, *args, **kwargs):
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  def age_groups(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.age_groups(x, *args, **kwargs))
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- def antibiogram(*args, **kwargs):
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+ def antibiogram(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.antibiogram(*args, **kwargs))
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- def amr_class(*args, **kwargs):
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+ return convert_to_python(amr_r.antibiogram(x, *args, **kwargs))
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+ def wisca(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.amr_class(*args, **kwargs))
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- def amr_selector(*args, **kwargs):
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+ return convert_to_python(amr_r.wisca(x, *args, **kwargs))
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+ def amr_class(amr_class, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.amr_selector(*args, **kwargs))
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- def aminoglycosides(*args, **kwargs):
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+ return convert_to_python(amr_r.amr_class(amr_class, *args, **kwargs))
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+ def amr_selector(filter, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.aminoglycosides(*args, **kwargs))
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+ return convert_to_python(amr_r.amr_selector(filter, *args, **kwargs))
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+ def aminoglycosides(only_sir_columns = False, *args, **kwargs):
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+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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+ return convert_to_python(amr_r.aminoglycosides(only_sir_columns = False, *args, **kwargs))
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  def aminopenicillins(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  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):
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  def antimycobacterials(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.antimycobacterials(only_sir_columns = False, *args, **kwargs))
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- def betalactams(*args, **kwargs):
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+ def betalactams(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.betalactams(*args, **kwargs))
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+ return convert_to_python(amr_r.betalactams(only_sir_columns = False, *args, **kwargs))
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  def betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.betalactams_with_inhibitor(only_sir_columns = False, *args, **kwargs))
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- def carbapenems(*args, **kwargs):
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+ def carbapenems(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.carbapenems(*args, **kwargs))
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+ return convert_to_python(amr_r.carbapenems(only_sir_columns = False, *args, **kwargs))
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  def cephalosporins(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  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):
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  def glycopeptides(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.glycopeptides(only_sir_columns = False, *args, **kwargs))
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- def lincosamides(*args, **kwargs):
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+ def lincosamides(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.lincosamides(*args, **kwargs))
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+ return convert_to_python(amr_r.lincosamides(only_sir_columns = False, *args, **kwargs))
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  def lipoglycopeptides(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  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):
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  def phenicols(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.phenicols(only_sir_columns = False, *args, **kwargs))
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- def polymyxins(*args, **kwargs):
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+ def polymyxins(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.polymyxins(*args, **kwargs))
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+ return convert_to_python(amr_r.polymyxins(only_sir_columns = False, *args, **kwargs))
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  def quinolones(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  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):
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  def administrable_iv(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.administrable_iv(only_sir_columns = False, *args, **kwargs))
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- def not_intrinsic_resistant(*args, **kwargs):
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+ def not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.not_intrinsic_resistant(*args, **kwargs))
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+ return convert_to_python(amr_r.not_intrinsic_resistant(only_sir_columns = False, *args, **kwargs))
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  def as_ab(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.as_ab(x, *args, **kwargs))
@@ -237,9 +240,9 @@ def is_mic(x):
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  def rescale_mic(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.rescale_mic(x, *args, **kwargs))
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- def as_mo(*args, **kwargs):
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+ def as_mo(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.as_mo(*args, **kwargs))
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+ return convert_to_python(amr_r.as_mo(x, *args, **kwargs))
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  def is_mo(x):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.is_mo(x))
@@ -270,9 +273,9 @@ def is_sir_eligible(x, *args, **kwargs):
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  def sir_interpretation_history(clean):
271
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.sir_interpretation_history(clean))
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- def atc_online_property(*args, **kwargs):
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+ def atc_online_property(atc_code, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.atc_online_property(*args, **kwargs))
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+ return convert_to_python(amr_r.atc_online_property(atc_code, *args, **kwargs))
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  def atc_online_groups(atc_code, *args, **kwargs):
277
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  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):
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  def atc_online_ddd_units(atc_code, *args, **kwargs):
283
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.atc_online_ddd_units(atc_code, *args, **kwargs))
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- def av_from_text(*args, **kwargs):
288
+ def av_from_text(text, *args, **kwargs):
286
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.av_from_text(*args, **kwargs))
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+ return convert_to_python(amr_r.av_from_text(text, *args, **kwargs))
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  def av_name(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.av_name(x, *args, **kwargs))
@@ -354,45 +357,45 @@ def count_all(*args, **kwargs):
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  def n_sir(*args, **kwargs):
355
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.n_sir(*args, **kwargs))
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- def count_df(*args, **kwargs):
360
+ def count_df(data, *args, **kwargs):
358
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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- return convert_to_python(amr_r.count_df(*args, **kwargs))
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+ return convert_to_python(amr_r.count_df(data, *args, **kwargs))
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  def custom_eucast_rules(*args, **kwargs):
361
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
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  return convert_to_python(amr_r.custom_eucast_rules(*args, **kwargs))
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- def eucast_rules(*args, **kwargs):
366
+ def eucast_rules(x, *args, **kwargs):
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
365
- return convert_to_python(amr_r.eucast_rules(*args, **kwargs))
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+ return convert_to_python(amr_r.eucast_rules(x, *args, **kwargs))
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  def eucast_dosage(ab, *args, **kwargs):
367
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
368
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  return convert_to_python(amr_r.eucast_dosage(ab, *args, **kwargs))
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- def export_ncbi_biosample(*args, **kwargs):
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+ def export_ncbi_biosample(x, *args, **kwargs):
370
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
371
- return convert_to_python(amr_r.export_ncbi_biosample(*args, **kwargs))
372
- def first_isolate(*args, **kwargs):
374
+ return convert_to_python(amr_r.export_ncbi_biosample(x, *args, **kwargs))
375
+ def first_isolate(x = None, *args, **kwargs):
373
376
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
374
- return convert_to_python(amr_r.first_isolate(*args, **kwargs))
375
- def filter_first_isolate(*args, **kwargs):
377
+ return convert_to_python(amr_r.first_isolate(x = None, *args, **kwargs))
378
+ def filter_first_isolate(x = None, *args, **kwargs):
376
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
377
- return convert_to_python(amr_r.filter_first_isolate(*args, **kwargs))
380
+ return convert_to_python(amr_r.filter_first_isolate(x = None, *args, **kwargs))
378
381
  def g_test(x, *args, **kwargs):
379
382
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
380
383
  return convert_to_python(amr_r.g_test(x, *args, **kwargs))
381
384
  def is_new_episode(x, *args, **kwargs):
382
385
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
383
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  return convert_to_python(amr_r.is_new_episode(x, *args, **kwargs))
384
- def ggplot_pca(*args, **kwargs):
387
+ def ggplot_pca(x, *args, **kwargs):
385
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
386
- return convert_to_python(amr_r.ggplot_pca(*args, **kwargs))
387
- def ggplot_sir(*args, **kwargs):
389
+ return convert_to_python(amr_r.ggplot_pca(x, *args, **kwargs))
390
+ def ggplot_sir(data, *args, **kwargs):
388
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
389
- return convert_to_python(amr_r.ggplot_sir(*args, **kwargs))
390
- def geom_sir(*args, **kwargs):
392
+ return convert_to_python(amr_r.ggplot_sir(data, *args, **kwargs))
393
+ def geom_sir(position = None, *args, **kwargs):
391
394
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
392
- return convert_to_python(amr_r.geom_sir(*args, **kwargs))
393
- def guess_ab_col(*args, **kwargs):
395
+ return convert_to_python(amr_r.geom_sir(position = None, *args, **kwargs))
396
+ def guess_ab_col(x = None, *args, **kwargs):
394
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
395
- return convert_to_python(amr_r.guess_ab_col(*args, **kwargs))
398
+ return convert_to_python(amr_r.guess_ab_col(x = None, *args, **kwargs))
396
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  def italicise_taxonomy(string, *args, **kwargs):
397
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
398
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  return convert_to_python(amr_r.italicise_taxonomy(string, *args, **kwargs))
@@ -417,24 +420,24 @@ def semi_join_microorganisms(x, *args, **kwargs):
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  def anti_join_microorganisms(x, *args, **kwargs):
418
421
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
419
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  return convert_to_python(amr_r.anti_join_microorganisms(x, *args, **kwargs))
420
- def key_antimicrobials(*args, **kwargs):
423
+ def key_antimicrobials(x = None, *args, **kwargs):
421
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  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
422
- return convert_to_python(amr_r.key_antimicrobials(*args, **kwargs))
425
+ return convert_to_python(amr_r.key_antimicrobials(x = None, *args, **kwargs))
423
426
  def all_antimicrobials(x = None, *args, **kwargs):
424
427
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
425
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  return convert_to_python(amr_r.all_antimicrobials(x = None, *args, **kwargs))
426
- def antimicrobials_equal(*args, **kwargs):
429
+ def antimicrobials_equal(y, *args, **kwargs):
427
430
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
428
- return convert_to_python(amr_r.antimicrobials_equal(*args, **kwargs))
431
+ return convert_to_python(amr_r.antimicrobials_equal(y, *args, **kwargs))
429
432
  def kurtosis(x, *args, **kwargs):
430
433
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
431
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  return convert_to_python(amr_r.kurtosis(x, *args, **kwargs))
432
435
  def like(x, *args, **kwargs):
433
436
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
434
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  return convert_to_python(amr_r.like(x, *args, **kwargs))
435
- def mdro(*args, **kwargs):
438
+ def mdro(x = None, *args, **kwargs):
436
439
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
437
- return convert_to_python(amr_r.mdro(*args, **kwargs))
440
+ return convert_to_python(amr_r.mdro(x = None, *args, **kwargs))
438
441
  def custom_mdro_guideline(*args, **kwargs):
439
442
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
440
443
  return convert_to_python(amr_r.custom_mdro_guideline(*args, **kwargs))
@@ -450,9 +453,9 @@ def mdr_tb(x = None, *args, **kwargs):
450
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  def mdr_cmi2012(x = None, *args, **kwargs):
451
454
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
452
455
  return convert_to_python(amr_r.mdr_cmi2012(x = None, *args, **kwargs))
453
- def eucast_exceptional_phenotypes(*args, **kwargs):
456
+ def eucast_exceptional_phenotypes(x = None, *args, **kwargs):
454
457
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
455
- return convert_to_python(amr_r.eucast_exceptional_phenotypes(*args, **kwargs))
458
+ return convert_to_python(amr_r.eucast_exceptional_phenotypes(x = None, *args, **kwargs))
456
459
  def mean_amr_distance(x, *args, **kwargs):
457
460
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
458
461
  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):
462
465
  def mo_matching_score(x, *args, **kwargs):
463
466
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
464
467
  return convert_to_python(amr_r.mo_matching_score(x, *args, **kwargs))
465
- def mo_name(*args, **kwargs):
468
+ def mo_name(x, *args, **kwargs):
466
469
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
467
- return convert_to_python(amr_r.mo_name(*args, **kwargs))
468
- def mo_fullname(*args, **kwargs):
470
+ return convert_to_python(amr_r.mo_name(x, *args, **kwargs))
471
+ def mo_fullname(x, *args, **kwargs):
469
472
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
470
- return convert_to_python(amr_r.mo_fullname(*args, **kwargs))
471
- def mo_shortname(*args, **kwargs):
473
+ return convert_to_python(amr_r.mo_fullname(x, *args, **kwargs))
474
+ def mo_shortname(x, *args, **kwargs):
472
475
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
473
- return convert_to_python(amr_r.mo_shortname(*args, **kwargs))
474
- def mo_subspecies(*args, **kwargs):
476
+ return convert_to_python(amr_r.mo_shortname(x, *args, **kwargs))
477
+ def mo_subspecies(x, *args, **kwargs):
475
478
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
476
- return convert_to_python(amr_r.mo_subspecies(*args, **kwargs))
477
- def mo_species(*args, **kwargs):
479
+ return convert_to_python(amr_r.mo_subspecies(x, *args, **kwargs))
480
+ def mo_species(x, *args, **kwargs):
478
481
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
479
- return convert_to_python(amr_r.mo_species(*args, **kwargs))
480
- def mo_genus(*args, **kwargs):
482
+ return convert_to_python(amr_r.mo_species(x, *args, **kwargs))
483
+ def mo_genus(x, *args, **kwargs):
481
484
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
482
- return convert_to_python(amr_r.mo_genus(*args, **kwargs))
483
- def mo_family(*args, **kwargs):
485
+ return convert_to_python(amr_r.mo_genus(x, *args, **kwargs))
486
+ def mo_family(x, *args, **kwargs):
484
487
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
485
- return convert_to_python(amr_r.mo_family(*args, **kwargs))
486
- def mo_order(*args, **kwargs):
488
+ return convert_to_python(amr_r.mo_family(x, *args, **kwargs))
489
+ def mo_order(x, *args, **kwargs):
487
490
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
488
- return convert_to_python(amr_r.mo_order(*args, **kwargs))
489
- def mo_class(*args, **kwargs):
491
+ return convert_to_python(amr_r.mo_order(x, *args, **kwargs))
492
+ def mo_class(x, *args, **kwargs):
490
493
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
491
- return convert_to_python(amr_r.mo_class(*args, **kwargs))
492
- def mo_phylum(*args, **kwargs):
494
+ return convert_to_python(amr_r.mo_class(x, *args, **kwargs))
495
+ def mo_phylum(x, *args, **kwargs):
493
496
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
494
- return convert_to_python(amr_r.mo_phylum(*args, **kwargs))
495
- def mo_kingdom(*args, **kwargs):
497
+ return convert_to_python(amr_r.mo_phylum(x, *args, **kwargs))
498
+ def mo_kingdom(x, *args, **kwargs):
496
499
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
497
- return convert_to_python(amr_r.mo_kingdom(*args, **kwargs))
498
- def mo_domain(*args, **kwargs):
500
+ return convert_to_python(amr_r.mo_kingdom(x, *args, **kwargs))
501
+ def mo_domain(x, *args, **kwargs):
499
502
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
500
- return convert_to_python(amr_r.mo_domain(*args, **kwargs))
501
- def mo_type(*args, **kwargs):
503
+ return convert_to_python(amr_r.mo_domain(x, *args, **kwargs))
504
+ def mo_type(x, *args, **kwargs):
502
505
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
503
- return convert_to_python(amr_r.mo_type(*args, **kwargs))
504
- def mo_status(*args, **kwargs):
506
+ return convert_to_python(amr_r.mo_type(x, *args, **kwargs))
507
+ def mo_status(x, *args, **kwargs):
505
508
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
506
- return convert_to_python(amr_r.mo_status(*args, **kwargs))
507
- def mo_pathogenicity(*args, **kwargs):
509
+ return convert_to_python(amr_r.mo_status(x, *args, **kwargs))
510
+ def mo_pathogenicity(x, *args, **kwargs):
508
511
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
509
- return convert_to_python(amr_r.mo_pathogenicity(*args, **kwargs))
510
- def mo_gramstain(*args, **kwargs):
512
+ return convert_to_python(amr_r.mo_pathogenicity(x, *args, **kwargs))
513
+ def mo_gramstain(x, *args, **kwargs):
511
514
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
512
- return convert_to_python(amr_r.mo_gramstain(*args, **kwargs))
513
- def mo_is_gram_negative(*args, **kwargs):
515
+ return convert_to_python(amr_r.mo_gramstain(x, *args, **kwargs))
516
+ def mo_is_gram_negative(x, *args, **kwargs):
514
517
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
515
- return convert_to_python(amr_r.mo_is_gram_negative(*args, **kwargs))
516
- def mo_is_gram_positive(*args, **kwargs):
518
+ return convert_to_python(amr_r.mo_is_gram_negative(x, *args, **kwargs))
519
+ def mo_is_gram_positive(x, *args, **kwargs):
517
520
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
518
- return convert_to_python(amr_r.mo_is_gram_positive(*args, **kwargs))
519
- def mo_is_yeast(*args, **kwargs):
521
+ return convert_to_python(amr_r.mo_is_gram_positive(x, *args, **kwargs))
522
+ def mo_is_yeast(x, *args, **kwargs):
520
523
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
521
- return convert_to_python(amr_r.mo_is_yeast(*args, **kwargs))
522
- def mo_is_intrinsic_resistant(*args, **kwargs):
524
+ return convert_to_python(amr_r.mo_is_yeast(x, *args, **kwargs))
525
+ def mo_is_intrinsic_resistant(x, *args, **kwargs):
523
526
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
524
- return convert_to_python(amr_r.mo_is_intrinsic_resistant(*args, **kwargs))
525
- def mo_oxygen_tolerance(*args, **kwargs):
527
+ return convert_to_python(amr_r.mo_is_intrinsic_resistant(x, *args, **kwargs))
528
+ def mo_oxygen_tolerance(x, *args, **kwargs):
526
529
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
527
- return convert_to_python(amr_r.mo_oxygen_tolerance(*args, **kwargs))
528
- def mo_is_anaerobic(*args, **kwargs):
530
+ return convert_to_python(amr_r.mo_oxygen_tolerance(x, *args, **kwargs))
531
+ def mo_is_anaerobic(x, *args, **kwargs):
529
532
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
530
- return convert_to_python(amr_r.mo_is_anaerobic(*args, **kwargs))
531
- def mo_snomed(*args, **kwargs):
533
+ return convert_to_python(amr_r.mo_is_anaerobic(x, *args, **kwargs))
534
+ def mo_snomed(x, *args, **kwargs):
532
535
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
533
- return convert_to_python(amr_r.mo_snomed(*args, **kwargs))
534
- def mo_ref(*args, **kwargs):
536
+ return convert_to_python(amr_r.mo_snomed(x, *args, **kwargs))
537
+ def mo_ref(x, *args, **kwargs):
535
538
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
536
- return convert_to_python(amr_r.mo_ref(*args, **kwargs))
537
- def mo_authors(*args, **kwargs):
539
+ return convert_to_python(amr_r.mo_ref(x, *args, **kwargs))
540
+ def mo_authors(x, *args, **kwargs):
538
541
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
539
- return convert_to_python(amr_r.mo_authors(*args, **kwargs))
540
- def mo_year(*args, **kwargs):
542
+ return convert_to_python(amr_r.mo_authors(x, *args, **kwargs))
543
+ def mo_year(x, *args, **kwargs):
541
544
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
542
- return convert_to_python(amr_r.mo_year(*args, **kwargs))
543
- def mo_lpsn(*args, **kwargs):
545
+ return convert_to_python(amr_r.mo_year(x, *args, **kwargs))
546
+ def mo_lpsn(x, *args, **kwargs):
544
547
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
545
- return convert_to_python(amr_r.mo_lpsn(*args, **kwargs))
546
- def mo_mycobank(*args, **kwargs):
548
+ return convert_to_python(amr_r.mo_lpsn(x, *args, **kwargs))
549
+ def mo_mycobank(x, *args, **kwargs):
547
550
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
548
- return convert_to_python(amr_r.mo_mycobank(*args, **kwargs))
549
- def mo_gbif(*args, **kwargs):
551
+ return convert_to_python(amr_r.mo_mycobank(x, *args, **kwargs))
552
+ def mo_gbif(x, *args, **kwargs):
550
553
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
551
- return convert_to_python(amr_r.mo_gbif(*args, **kwargs))
552
- def mo_rank(*args, **kwargs):
554
+ return convert_to_python(amr_r.mo_gbif(x, *args, **kwargs))
555
+ def mo_rank(x, *args, **kwargs):
553
556
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
554
- return convert_to_python(amr_r.mo_rank(*args, **kwargs))
555
- def mo_taxonomy(*args, **kwargs):
557
+ return convert_to_python(amr_r.mo_rank(x, *args, **kwargs))
558
+ def mo_taxonomy(x, *args, **kwargs):
556
559
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
557
- return convert_to_python(amr_r.mo_taxonomy(*args, **kwargs))
558
- def mo_synonyms(*args, **kwargs):
560
+ return convert_to_python(amr_r.mo_taxonomy(x, *args, **kwargs))
561
+ def mo_synonyms(x, *args, **kwargs):
559
562
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
560
- return convert_to_python(amr_r.mo_synonyms(*args, **kwargs))
563
+ return convert_to_python(amr_r.mo_synonyms(x, *args, **kwargs))
561
564
  def mo_current(x, *args, **kwargs):
562
565
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
563
566
  return convert_to_python(amr_r.mo_current(x, *args, **kwargs))
564
- def mo_group_members(*args, **kwargs):
567
+ def mo_group_members(x, *args, **kwargs):
565
568
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
566
- return convert_to_python(amr_r.mo_group_members(*args, **kwargs))
567
- def mo_info(*args, **kwargs):
569
+ return convert_to_python(amr_r.mo_group_members(x, *args, **kwargs))
570
+ def mo_info(x, *args, **kwargs):
568
571
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
569
- return convert_to_python(amr_r.mo_info(*args, **kwargs))
570
- def mo_url(*args, **kwargs):
572
+ return convert_to_python(amr_r.mo_info(x, *args, **kwargs))
573
+ def mo_url(x, *args, **kwargs):
571
574
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
572
- return convert_to_python(amr_r.mo_url(*args, **kwargs))
573
- def mo_property(*args, **kwargs):
575
+ return convert_to_python(amr_r.mo_url(x, *args, **kwargs))
576
+ def mo_property(x, *args, **kwargs):
574
577
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
575
- return convert_to_python(amr_r.mo_property(*args, **kwargs))
576
- def pca(*args, **kwargs):
578
+ return convert_to_python(amr_r.mo_property(x, *args, **kwargs))
579
+ def pca(x, *args, **kwargs):
577
580
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
578
- return convert_to_python(amr_r.pca(*args, **kwargs))
581
+ return convert_to_python(amr_r.pca(x, *args, **kwargs))
579
582
  def theme_sir(*args, **kwargs):
580
583
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
581
584
  return convert_to_python(amr_r.theme_sir(*args, **kwargs))
582
- def labels_sir_count(*args, **kwargs):
585
+ def labels_sir_count(position = None, *args, **kwargs):
583
586
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
584
- return convert_to_python(amr_r.labels_sir_count(*args, **kwargs))
587
+ return convert_to_python(amr_r.labels_sir_count(position = None, *args, **kwargs))
585
588
  def resistance(*args, **kwargs):
586
589
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
587
590
  return convert_to_python(amr_r.resistance(*args, **kwargs))
@@ -606,12 +609,12 @@ def proportion_SI(*args, **kwargs):
606
609
  def proportion_S(*args, **kwargs):
607
610
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
608
611
  return convert_to_python(amr_r.proportion_S(*args, **kwargs))
609
- def proportion_df(*args, **kwargs):
612
+ def proportion_df(data, *args, **kwargs):
610
613
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
611
- return convert_to_python(amr_r.proportion_df(*args, **kwargs))
612
- def sir_df(*args, **kwargs):
614
+ return convert_to_python(amr_r.proportion_df(data, *args, **kwargs))
615
+ def sir_df(data, *args, **kwargs):
613
616
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
614
- return convert_to_python(amr_r.sir_df(*args, **kwargs))
617
+ return convert_to_python(amr_r.sir_df(data, *args, **kwargs))
615
618
  def random_mic(size = None, *args, **kwargs):
616
619
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
617
620
  return convert_to_python(amr_r.random_mic(size = None, *args, **kwargs))
@@ -621,18 +624,21 @@ def random_disk(size = None, *args, **kwargs):
621
624
  def random_sir(size = None, *args, **kwargs):
622
625
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
623
626
  return convert_to_python(amr_r.random_sir(size = None, *args, **kwargs))
624
- def resistance_predict(*args, **kwargs):
627
+ def resistance_predict(x, *args, **kwargs):
625
628
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
626
- return convert_to_python(amr_r.resistance_predict(*args, **kwargs))
627
- def sir_predict(*args, **kwargs):
629
+ return convert_to_python(amr_r.resistance_predict(x, *args, **kwargs))
630
+ def sir_predict(x, *args, **kwargs):
628
631
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
629
- return convert_to_python(amr_r.sir_predict(*args, **kwargs))
630
- def ggplot_sir_predict(*args, **kwargs):
632
+ return convert_to_python(amr_r.sir_predict(x, *args, **kwargs))
633
+ def ggplot_sir_predict(x, *args, **kwargs):
631
634
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
632
- return convert_to_python(amr_r.ggplot_sir_predict(*args, **kwargs))
635
+ return convert_to_python(amr_r.ggplot_sir_predict(x, *args, **kwargs))
633
636
  def skewness(x, *args, **kwargs):
634
637
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
635
638
  return convert_to_python(amr_r.skewness(x, *args, **kwargs))
639
+ def top_n_microorganisms(x, *args, **kwargs):
640
+ """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
641
+ return convert_to_python(amr_r.top_n_microorganisms(x, *args, **kwargs))
636
642
  def reset_AMR_locale(*args, **kwargs):
637
643
  """See our website of the R package for the manual: https://msberends.github.io/AMR/index.html"""
638
644
  return convert_to_python(amr_r.reset_AMR_locale(*args, **kwargs))
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
2
2
  Name: AMR
3
- Version: 2.1.1.9125
3
+ Version: 2.1.1.9126
4
4
  Summary: A Python wrapper for the AMR R package
5
5
  Home-page: https://github.com/msberends/AMR
6
6
  Author: Matthijs Berends
@@ -0,0 +1,7 @@
1
+ AMR/__init__.py,sha256=-3zoWVuhybnYkXePzljDrtcxxaAQscPpCPP75EiqLfQ,7540
2
+ AMR/datasets.py,sha256=DtzZAmuaFK3H4LZIycEfCDS7BIY5iyNxDzfTj2bGsdU,2574
3
+ AMR/functions.py,sha256=JSh-0_mfrAj7ajpazlv2KFyEtRAglj7oQV9Iiaux7eo,45557
4
+ AMR-2.1.1.9126.dist-info/METADATA,sha256=3PIASuWvjNhLvT6r17T7tuTO_10GnMzk_EDNTgIUxUk,9625
5
+ AMR-2.1.1.9126.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
6
+ AMR-2.1.1.9126.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
7
+ AMR-2.1.1.9126.dist-info/RECORD,,
@@ -1,7 +0,0 @@
1
- AMR/__init__.py,sha256=cSUa6bz_aXEUR5o0D3dh8opo6XdlgS10hoIgYH1r_mY,7467
2
- AMR/datasets.py,sha256=IDeqfVGjzvhMhKZRlS6Pc3xIO4HBlRDvPdQjDQ8qVTc,2426
3
- AMR/functions.py,sha256=FmEKlH-hCyJBaJIU6dCX6WAKjYhhpGAo4qSwHP_XkzE,44231
4
- AMR-2.1.1.9125.dist-info/METADATA,sha256=-djWW_YblmGp77vLBC2SNMUBvzH9h2kciSISdA1s8cE,9625
5
- AMR-2.1.1.9125.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
6
- AMR-2.1.1.9125.dist-info/top_level.txt,sha256=7K6Mq_X_OHdXOzQM5y06VUadXjYkze6yzufL1d7_6xc,4
7
- AMR-2.1.1.9125.dist-info/RECORD,,