mimic package

Subpackages

• mimic.data_imputation package
  • Submodules
  • mimic.data_imputation.base_imputator module
  • mimic.data_imputation.impute_GP module
  • Module contents
• mimic.model_infer package
  • Submodules
  • mimic.model_infer.cLV module
    • CompositionalLotkaVolterra
      • CompositionalLotkaVolterra.get_params()
      • CompositionalLotkaVolterra.get_regularizers()
      • CompositionalLotkaVolterra.predict()
      • CompositionalLotkaVolterra.set_regularizers()
      • CompositionalLotkaVolterra.train()
    • choose_denom()
    • compute_prediction_error()
    • compute_rel_abun()
    • construct_alr()
    • elastic_net_clv()
    • estimate_elastic_net_regularizers_cv()
    • estimate_relative_abundances()
    • estimate_ridge_regularizers_cv()
    • predict()
    • ridge_regression_clv()
  • mimic.model_infer.infer_VAR_bayes module
    • infer_VAR
      • infer_VAR.make_plot_stacked()
      • infer_VAR.plot_heatmap()
      • infer_VAR.posterior_analysis()
      • infer_VAR.run_inference()
      • infer_VAR.set_parameters()
  • mimic.model_infer.infer_gMLV_lm module
    • Ridge1
      • Ridge1.fit()
      • Ridge1.get_params()
      • Ridge1.predict()
      • Ridge1.set_score_request()
    • Ridge2
      • Ridge2.fit()
      • Ridge2.get_params()
      • Ridge2.predict()
      • Ridge2.set_score_request()
    • do_bootstrapping()
    • do_final_fit_Ridge1()
    • do_final_fit_Ridge2()
    • fit_alpha_Ridge1()
    • fit_alpha_Ridge2()
    • fit_alpha_lasso()
    • linearise_time_course_metabolites()
    • linearize_time_course()
    • linearize_time_course_16S()
    • linearize_time_course_16S_u()
    • plot_alpha_lasso()
    • plot_coeffs()
    • ridge_fit()
    • ridge_fit_pert()
    • ridge_fit_test()
  • mimic.model_infer.multi_penalty_lasso module
    • MultiPenaltyLasso
      • MultiPenaltyLasso.fit()
      • MultiPenaltyLasso.get_params()
      • MultiPenaltyLasso.non_zero_penalties()
      • MultiPenaltyLasso.penalised_lasso()
      • MultiPenaltyLasso.predict()
      • MultiPenaltyLasso.set_score_request()
    • fit_alpha_MPLasso()
  • Module contents
• mimic.model_simulate package
  • Submodules
  • mimic.model_simulate.base_model module
    • BaseModel
      • BaseModel.check_params()
      • BaseModel.debug
      • BaseModel.load_data()
      • BaseModel.print_parameters()
      • BaseModel.read_parameters()
      • BaseModel.save_data()
      • BaseModel.save_parameters()
      • BaseModel.set_parameters()
      • BaseModel.simulate()
      • BaseModel.update_attributes()
  • mimic.model_simulate.sim_VAR module
    • sim_VAR
      • sim_VAR.generate_mvar1_data()
      • sim_VAR.generate_var1_data()
      • sim_VAR.make_plot()
      • sim_VAR.make_plot_overlay()
      • sim_VAR.make_plot_stacked()
      • sim_VAR.set_parameters()
      • sim_VAR.simulate()
  • mimic.model_simulate.sim_gMLV module
    • gMLV()
    • sim_gMLV
      • sim_gMLV.set_parameters()
      • sim_gMLV.simulate()
  • Module contents
• mimic.utilities package
  • Submodules
  • mimic.utilities.utilities module
    • compare_params()
    • plot_CRM()
    • plot_CRM_with_intervals()
    • plot_fit_gLV()
    • plot_fit_gMLV()
    • plot_gLV()
    • plot_gMLV()
    • read_parameters()
    • set_all_seeds()
  • Module contents

Module contents