SIMPLICITY

• setup module
• simplicity package
  • Subpackages
    • simplicity.evolution package
      • Submodules
      • simplicity.evolution.decoder module
      • simplicity.evolution.mutations module
      • simplicity.evolution.reference module
      • Module contents
    • simplicity.phenotype package
      • Submodules
      • simplicity.phenotype.consensus module
      • simplicity.phenotype.distance module
      • simplicity.phenotype.update module
      • simplicity.phenotype.weight module
      • Module contents
    • simplicity.runners package
      • Submodules
      • simplicity.runners.multiprocessing module
      • simplicity.runners.serial module
      • simplicity.runners.slurm module
      • simplicity.runners.unit_run module
      • Module contents
    • simplicity.tree package
      • Submodules
      • simplicity.tree.filtered_infection_tree module
      • simplicity.tree.json_tree module
      • simplicity.tree.newick module
      • simplicity.tree.nexus module
      • simplicity.tree.tree_builder module
      • Module contents
    • simplicity.tuning package
      • Submodules
      • simplicity.tuning.diagnosis_rate module
      • simplicity.tuning.evolutionary_rate module
      • Module contents
  • Submodules
  • simplicity.dir_manager module
    • create_directories()
    • get_data_dir()
    • get_experiment_cluster_dir()
    • get_experiment_dir()
    • get_experiment_fit_result_dir()
    • get_experiment_foldername_from_SSOD()
    • get_experiment_output_dir()
    • get_experiment_plots_dir()
    • get_experiment_settings_dir()
    • get_experiment_simulations_plots_dir()
    • get_experiment_tree_dir()
    • get_experiment_tree_simulation_dir()
    • get_experiment_tree_simulation_files_dir()
    • get_experiment_tree_simulation_plots_dir()
    • get_nextstrain_dir()
    • get_reference_parameters_dir()
    • get_seed_from_SSOD()
    • get_seeded_simulation_output_dirs()
    • get_seeded_simulation_parameters_dir()
    • get_simulation_output_dirs()
    • get_simulation_output_foldername_from_SSOD()
    • get_simulation_parameters_dir()
    • get_slurm_id_map_dir()
    • get_slurm_logs_dir()
    • get_ssod()
    • set_data_dir()
  • simplicity.extrande module
    • ProgressReporter
      • ProgressReporter.__init__()
      • ProgressReporter.close()
      • ProgressReporter.update()
    • extrande_core_loop()
    • extrande_factory()
    • get_helpers()
  • simplicity.intra_host_model module
    • Host
      • Host.__init__()
      • Host.compute_all_probabilities()
      • Host.data_plot_ih_solution()
      • Host.factory_get_A_t()
      • Host.get_jump_rate()
      • Host.get_p_t()
      • Host.get_update_mode()
      • Host.simulate_trajectory()
      • Host.update_state()
    • compute_phase_durations()
    • compute_state_durations()
    • load_results()
    • main()
    • plot_duration_summary_scatter()
    • plot_infectious_duration_vs_step()
    • plot_state_duration_stats_grid()
    • plot_state_timeline_summary()
    • run_parallel_simulations()
    • save_results()
  • simplicity.output_manager module
    • archive_experiment()
    • create_combined_sequencing_df()
    • detect_sod_outliers()
    • export_tree()
    • filter_lineage_frequency_df()
    • filter_sequencing_files_by_simulation_lenght()
    • get_IH_lineages_data_experiment()
    • get_IH_lineages_data_simulation()
    • get_OSR_vs_parameter_csv_file_path()
    • get_all_individuals_data_for_simulation_output_dir()
    • get_clustering_table_filepath()
    • get_combined_OSR_vs_parameter_csv_file_path()
    • get_fit_results_filepath()
    • get_mean_std_OSR()
    • get_nextstrain_dataset_paths()
    • get_procomputed_matrix_table_filepath()
    • get_r_effective_lineages_csv_filepath()
    • get_r_effective_lineages_traj()
    • get_r_effective_population_csv_filepath()
    • get_r_effective_population_traj()
    • get_tree_file_filepath()
    • get_tree_filename()
    • get_tree_plot_filepath()
    • read_OSR_vs_parameter_csv()
    • read_R_effective_trajectory()
    • read_clustering_table()
    • read_combined_OSR_vs_parameter_csv()
    • read_final_time()
    • read_fit_results_csv()
    • read_individuals_data()
    • read_lineage_frequency()
    • read_phylogenetic_data()
    • read_r_effective_trajs_csv()
    • read_sequencing_data_regression()
    • read_simulation_trajectory()
    • save_R_effective_trajectory()
    • save_final_time()
    • save_fitness_trajectory()
    • save_individuals_data()
    • save_lineage_frequency()
    • save_phylogenetic_data()
    • save_sequencing_dataset()
    • save_simulation_trajectory()
    • setup_output_directory()
    • write_OSR_vs_parameter_csv()
    • write_clustering_table()
    • write_combined_OSR_vs_parameter_csv()
    • write_fit_results_csv()
    • write_r_effective_trajs_csv()
  • simplicity.plots_manager module
    • apply_plos_rcparams()
    • apply_standard_axis_style()
    • get_fitness_color()
    • get_lineage_color()
    • get_node_color()
    • get_state_color()
    • ideal_subplot_grid()
    • make_lineages_colormap()
    • plot_IH_lineage_distribution()
    • plot_IH_lineage_distribution_grouped_by_simulation()
    • plot_IH_lineage_distribution_simulation()
    • plot_OSR_and_IH_lineages_by_parameter()
    • plot_OSR_fit()
    • plot_OSR_fit_figure()
    • plot_R_effective()
    • plot_circular_tree()
    • plot_combined_OSR_fit()
    • plot_combined_OSR_vs_parameter()
    • plot_combined_tempest_regressions()
    • plot_comparison_intra_host_models()
    • plot_effective_theoretical_diagnosis_rate()
    • plot_extrande_pop_runtime()
    • plot_fitness()
    • plot_heatmap_R_diagnosis_rate()
    • plot_histograms()
    • plot_infection_tree()
    • plot_infections_hist()
    • plot_intra_host()
    • plot_lineages_colors_tab()
    • plot_phylogenetic_tree()
    • plot_simulation()
    • plot_tempest_regression()
    • plot_trajectory()
    • plot_w_t()
    • save_plos_figure()
    • tree_fitness_legend()
  • simplicity.population module
    • Population
      • Population.__init__()
      • Population.fitness_trajectory_to_df()
      • Population.get_lineage_genome()
      • Population.individuals_data_to_df()
      • Population.lineage_frequency_to_df()
      • Population.phylogenetic_data_to_df()
      • Population.update_fitness_trajectory()
      • Population.update_ih_lineages_trajectories()
      • Population.update_lineage_frequency_t()
      • Population.update_states()
      • Population.update_time()
      • Population.update_trajectory()
    • create_population()
  • simplicity.population_model module
    • SIDR_propensities()
    • add_lineage()
    • diagnosis()
    • infect_long_shedder()
    • infection()
  • simplicity.random_gen module
    • randomgen()
  • simplicity.runme module
    • run_experiment()
    • user_set_experiment_settings()
  • simplicity.settings_manager module
    • check_parameters_names()
    • generate_experiment_settings()
    • generate_filename_from_params()
    • get_experiment_settings_file_path()
    • get_n_seeds_file_path()
    • get_n_seeds_from_experiment_settings()
    • get_parameter_specs_file_path()
    • get_parameter_value_from_simulation_output_dir()
    • get_seeded_simulation_parameters_paths()
    • get_simulation_parameters_filepath_of_simulation_output_dir()
    • get_standard_parameters_values_file_path()
    • read_OSR_NSR_regressor_parameters()
    • read_experiment_settings()
    • read_n_seeds_file()
    • read_parameter_specs()
    • read_seeded_simulation_parameters()
    • read_settings_and_write_simulation_parameters()
    • read_standard_parameters_values()
    • read_user_set_parameters_file()
    • write_experiment_settings()
    • write_parameter_specs()
    • write_seeded_simulation_parameters()
    • write_simulation_parameters()
    • write_standard_parameters_values()
    • write_user_set_parameters_file()
  • simplicity.simulation module
    • Simplicity
      • Simplicity.__init__()
      • Simplicity.plot()
      • Simplicity.run()
      • Simplicity.save_consensus()
  • Module contents