pyamr package

Subpackages

• pyamr.core package
  • Subpackages
    • pyamr.core.regression package
      • Submodules
      • pyamr.core.regression.arima module
      • pyamr.core.regression.pyarima module
      • pyamr.core.regression.pyarima2 module
      • pyamr.core.regression.sarimax module
      • pyamr.core.regression.theilsens module
      • pyamr.core.regression.wbase module
      • pyamr.core.regression.wls module
      • pyamr.core.regression.wlsarma module
      • pyamr.core.regression.wreg module
      • pyamr.core.regression.wregression module
      • Module contents
    • pyamr.core.stats package
      • Submodules
      • pyamr.core.stats.adfuller module
      • pyamr.core.stats.correlation module
      • pyamr.core.stats.kendall module
      • pyamr.core.stats.kpss module
      • pyamr.core.stats.stationarity module
      • pyamr.core.stats.wbase module
      • Module contents
    • pyamr.core.table package
      • Submodules
      • pyamr.core.table.acronym module
      • pyamr.core.table.antibiotic module
      • pyamr.core.table.organism module
      • pyamr.core.table.utils module
      • Module contents
  • Submodules
  • pyamr.core.acsi module
    • ACSI
      • ACSI.c_abx
      • ACSI.c_dat
      • ACSI.c_lab
      • ACSI.c_org
      • ACSI.c_sns
      • ACSI.c_spe
      • ACSI.combinations()
      • ACSI.compute()
      • ACSI.compute_from_combinations()
      • ACSI.compute_from_contingency()
    • CRI()
    • collateral_resistance_index()
    • create_combinations_v1()
    • mutual_info_matrix_v3()
  • pyamr.core.asai module
    • ASAI
      • ASAI.c_fre
      • ASAI.c_gen
      • ASAI.c_res
      • ASAI.c_spe
      • ASAI.c_thr
      • ASAI.c_wgen
      • ASAI.c_wspe
      • ASAI.compute()
    • ASAI_old
      • ASAI_old.c_abx
      • ASAI_old.c_fre
      • ASAI_old.c_gen
      • ASAI_old.c_res
      • ASAI_old.c_spe
      • ASAI_old.c_thr
      • ASAI_old.c_wgen
      • ASAI_old.c_wspe
      • ASAI_old.compute()
    • antimicrobial_spectrum_activity_index()
    • asai()
  • pyamr.core.dri module
    • DRI
      • DRI.c_res
      • DRI.c_use
      • DRI.compute()
    • dri()
    • drug_resistance_index()
    • drug_resistance_index_v2()
  • pyamr.core.freq module
    • Frequency
      • Frequency.c_abx
      • Frequency.c_dat
      • Frequency.c_org
      • Frequency.c_out
      • Frequency.compute()
      • Frequency.fit()
  • pyamr.core.mari module
    • MARI
      • MARI.c_dat
      • MARI.c_lab
      • MARI.c_org
      • MARI.c_out
      • MARI.c_spe
      • MARI.compute()
      • MARI.compute_v1()
      • MARI.compute_v2()
      • MARI.compute_v3()
      • MARI.compute_v4()
      • MARI.grouping()
      • MARI.rolling()
  • pyamr.core.sari module
    • SARI
      • SARI.c_abx
      • SARI.c_dat
      • SARI.c_org
      • SARI.c_out
      • SARI.c_spe
      • SARI.compute()
      • SARI.grouping()
      • SARI.rolling()
    • sari()
  • pyamr.core.sart module
    • SART
      • SART.c_abx
      • SART.c_dat
      • SART.c_org
      • SART.c_out
      • SART.c_res
      • SART.c_spe
      • SART.compute()
  • Module contents
• pyamr.datasets package
  • Subpackages
    • pyamr.datasets.microbiology package
      • Submodules
      • pyamr.datasets.microbiology.create_quickimport module
      • pyamr.datasets.microbiology.create_susceptibility module
      • pyamr.datasets.microbiology.quickimport_create module
      • pyamr.datasets.microbiology.quickimport_run module
      • pyamr.datasets.microbiology.test module
      • Module contents
  • Submodules
  • pyamr.datasets.clean module
    • clean_basic()
    • clean_clwsql008()
    • clean_clwsql008_old()
    • clean_common()
    • clean_format()
    • clean_legacy()
    • clean_legacy_old()
    • clean_microorganism()
    • clean_mimic()
    • hyphen_before()
    • invert()
    • string_replace()
    • word_to_start()
  • pyamr.datasets.load module
    • fixture()
    • load_data_mimic()
    • load_data_nhs()
    • load_microbiology_folder()
    • load_registry_antimicrobials()
    • load_registry_microorganisms()
    • make_susceptibility()
    • make_timeseries()
  • pyamr.datasets.registries module
    • AntimicrobialRegistry
      • AntimicrobialRegistry.combine()
      • AntimicrobialRegistry.reg
    • MicroorganismRegistry
      • MicroorganismRegistry.binomial_name()
      • MicroorganismRegistry.combine()
      • MicroorganismRegistry.reg
      • MicroorganismRegistry.taxonomy
      • MicroorganismRegistry.uuid()
    • Registry
      • Registry.FCLEAN
      • Registry.ORDER
      • Registry.REG
      • Registry.RENAME_COLUMNS
      • Registry.SUBSET
      • Registry.clean()
      • Registry.combine()
      • Registry.fit()
      • Registry.fit_transform()
      • Registry.getr()
      • Registry.replace()
      • Registry.transform()
    • acronym_series()
    • acronym_series_unique()
    • clean_specimen()
    • create_registry()
    • invert()
    • length_exceptions()
  • Module contents
• pyamr.examples package
  • Submodules
  • pyamr.examples.plot_function module
    • Plot function
    • main()
  • Module contents
• pyamr.graphics package
  • Submodules
  • pyamr.graphics.antibiogram module
    • Antibiogram
      • Antibiogram.c_abx
      • Antibiogram.c_cat
      • Antibiogram.c_gen
      • Antibiogram.c_idx
      • Antibiogram.c_org
      • Antibiogram.fit()
      • Antibiogram.plot()
  • pyamr.graphics.table_graph module
    • TableGraph
      • TableGraph.fontsize
      • TableGraph.get_map_config()
      • TableGraph.plot()
      • TableGraph.plot_array()
      • TableGraph.plot_dataframe()
      • TableGraph.plot_matrix()
      • TableGraph.plot_vertical_line()
    • TableGraph2
      • TableGraph2.add_vline()
      • TableGraph2.check_vmin_vmax()
      • TableGraph2.display_column()
      • TableGraph2.plot()
  • pyamr.graphics.utils_to_delete module
    • MidpointNormalize
    • hlinebgplot()
    • scalar_colormap()
    • vlinebgplot()
  • Module contents
• pyamr.metrics package
  • Submodules
  • pyamr.metrics.scores module
  • pyamr.metrics.weights module
    • SigmoidA
      • SigmoidA.approximated_sigmoid()
      • SigmoidA.threshold()
      • SigmoidA.weights()
      • SigmoidA.weights_percentile()
      • SigmoidA.weights_standard()
  • Module contents
• pyamr.tests package
  • Submodules
  • pyamr.tests.test_manual module
    • fixture()
    • fixture1()
    • fixture3()
    • fixture4()
    • fixture5()
    • fixture_acsi_lancet_test()
    • fixture_dri_cddep_test()
    • fixture_index_mari()
    • func()
    • test_acsi_lancet()
    • test_answer()
    • test_asai_class()
    • test_asai_error_missing_column()
    • test_asai_error_weights_not_valid()
    • test_asai_error_weights_wcolumn_not_valid()
    • test_asai_warn_threshold_double_defined()
    • test_asai_warn_threshold_not_defined()
    • test_asai_weights_frequency()
    • test_asai_weights_from_column()
    • test_asai_weights_uniform()
    • test_dri_cddep()
    • test_mari_class()
    • test_mari_class_temporal_iti_period_is_integer_fails()
    • test_mari_class_temporal_oti()
    • test_sari_class_overall()
    • test_sari_class_timeseries()
    • test_sari_empty_dataframe()
    • test_sari_method_empty()
    • test_sari_strategy()
    • timeseries()
  • pyamr.tests.test_scripts module
    • pyamr
    • test_script_run_pyamr_core()
    • test_script_run_pyamr_core_regression()
    • test_script_run_pyamr_core_stats()
    • test_script_run_pyamr_core_table()
    • test_script_run_pyamr_graphics()
    • test_script_run_pyamr_metrics()
  • Module contents
• pyamr.utils package
  • Subpackages
    • pyamr.utils.io package
      • Submodules
      • pyamr.utils.io.read module
      • Module contents
  • Submodules
  • pyamr.utils.plot module
    • MidpointNormalize
    • create_mapper()
    • get_category_colors()
    • hlinebgplot()
    • plot_sns_clustermap()
    • plot_sns_heatmap()
    • plot_sns_relmap()
    • plot_spectrum()
    • plot_timeseries()
    • scalar_colormap()
    • vlinebgplot()
  • Module contents

Module contents