Index

_

__init__() (simplicity.extrande.ProgressReporter method) (simplicity.intra_host_model.Host method) (simplicity.population.Population method) (simplicity.simulation.Simplicity method)

A

add_lineage() (in module simplicity.population_model) apply_plos_rcparams() (in module simplicity.plots_manager)

apply_standard_axis_style() (in module simplicity.plots_manager) archive_experiment() (in module simplicity.output_manager) assign_sub() (in module simplicity.evolution.mutations)

B

build_ete_from_anytree() (in module simplicity.tree.tree_builder)

build_weighted_consensus_matrix() (in module simplicity.phenotype.consensus)

C

check_parameters_names() (in module simplicity.settings_manager) close() (simplicity.extrande.ProgressReporter method) completed (simplicity.runners.slurm.SimulationsStatus attribute) compute_all_probabilities() (simplicity.intra_host_model.Host method) compute_calibrated_parameter() (in module simplicity.tuning.evolutionary_rate)

compute_phase_durations() (in module simplicity.intra_host_model) compute_state_durations() (in module simplicity.intra_host_model) create_combined_sequencing_df() (in module simplicity.output_manager) create_directories() (in module simplicity.dir_manager) create_infection_node() (in module simplicity.tree.tree_builder) create_population() (in module simplicity.population)

D

data_plot_ih_solution() (simplicity.intra_host_model.Host method) decode_genome() (in module simplicity.evolution.decoder) deserialize() (in module simplicity.tree.json_tree)

detect_sod_outliers() (in module simplicity.output_manager) diagnosis() (in module simplicity.population_model) diagnosis_rate_table() (in module simplicity.tuning.diagnosis_rate)

E

evaluate_model() (in module simplicity.tuning.evolutionary_rate) export_newick() (in module simplicity.tree.newick) export_tree() (in module simplicity.output_manager)

extend_parent_node() (in module simplicity.tree.tree_builder) extrande_core_loop() (in module simplicity.extrande) extrande_factory() (in module simplicity.extrande)

F

factory_get_A_t() (simplicity.intra_host_model.Host method) factory_model_func() (in module simplicity.tuning.evolutionary_rate) factory_model_lmfit() (in module simplicity.tuning.evolutionary_rate) failed (simplicity.runners.slurm.SimulationsStatus attribute) fetch_bases() (in module simplicity.evolution.mutations)

filter_lineage_frequency_df() (in module simplicity.output_manager) filter_sequencing_files_by_simulation_lenght() (in module simplicity.output_manager) fit_observed_substitution_rate_regressor() (in module simplicity.tuning.evolutionary_rate) fit_weight() (in module simplicity.tuning.evolutionary_rate) fit_weight_time() (in module simplicity.tuning.evolutionary_rate) fitness_trajectory_to_df() (simplicity.population.Population method)

G

generate_experiment_settings() (in module simplicity.settings_manager) generate_filename_from_params() (in module simplicity.settings_manager) get_all_individuals_data_for_simulation_output_dir() (in module simplicity.output_manager) get_B() (in module simplicity.tuning.diagnosis_rate) get_clustering_table_filepath() (in module simplicity.output_manager) get_combined_OSR_vs_parameter_csv_file_path() (in module simplicity.output_manager) get_consensus() (in module simplicity.phenotype.consensus) get_data_dir() (in module simplicity.dir_manager) get_diagnosis_rate_in_percent() (in module simplicity.tuning.diagnosis_rate) get_diagnosis_rates() (in module simplicity.tuning.diagnosis_rate) get_effective_diagnosis_rate() (in module simplicity.tuning.diagnosis_rate) get_experiment_cluster_dir() (in module simplicity.dir_manager) get_experiment_dir() (in module simplicity.dir_manager) get_experiment_fit_result_dir() (in module simplicity.dir_manager) get_experiment_foldername_from_SSOD() (in module simplicity.dir_manager) get_experiment_output_dir() (in module simplicity.dir_manager) get_experiment_plots_dir() (in module simplicity.dir_manager) get_experiment_settings_dir() (in module simplicity.dir_manager) get_experiment_settings_file_path() (in module simplicity.settings_manager) get_experiment_simulations_plots_dir() (in module simplicity.dir_manager) get_experiment_tree_dir() (in module simplicity.dir_manager) get_experiment_tree_simulation_dir() (in module simplicity.dir_manager) get_experiment_tree_simulation_files_dir() (in module simplicity.dir_manager) get_experiment_tree_simulation_plots_dir() (in module simplicity.dir_manager) get_fit_results_filepath() (in module simplicity.output_manager) get_fitness_color() (in module simplicity.plots_manager) get_helpers() (in module simplicity.extrande) get_IH_lineages_data_experiment() (in module simplicity.output_manager) get_IH_lineages_data_simulation() (in module simplicity.output_manager) get_individuals_to_update() (in module simplicity.evolution.mutations) get_jump_rate() (simplicity.intra_host_model.Host method) get_k_d_from_diagnosis_rate() (in module simplicity.tuning.diagnosis_rate) get_lineage_color() (in module simplicity.plots_manager) get_lineage_genome() (simplicity.population.Population method) get_lineage_name() (in module simplicity.evolution.mutations) get_mean_std_OSR() (in module simplicity.output_manager) get_n_seeds_file_path() (in module simplicity.settings_manager)

get_n_seeds_from_experiment_settings() (in module simplicity.settings_manager) get_newick_str_from_root() (in module simplicity.tree.newick) get_nextstrain_dataset_paths() (in module simplicity.output_manager) get_nextstrain_dir() (in module simplicity.dir_manager) get_node_attributes() (in module simplicity.tree.json_tree) get_node_color() (in module simplicity.plots_manager) get_OSR_vs_parameter_csv_file_path() (in module simplicity.output_manager) get_p_t() (simplicity.intra_host_model.Host method) get_parameter_specs_file_path() (in module simplicity.settings_manager) get_parameter_value_from_simulation_output_dir() (in module simplicity.settings_manager) get_platform_executable_extension() (in module simplicity.runners.slurm) get_procomputed_matrix_table_filepath() (in module simplicity.output_manager) get_r_effective_lineages_csv_filepath() (in module simplicity.output_manager) get_r_effective_lineages_traj() (in module simplicity.output_manager) get_r_effective_population_csv_filepath() (in module simplicity.output_manager) get_r_effective_population_traj() (in module simplicity.output_manager) get_reference() (in module simplicity.evolution.reference) get_reference_parameters_dir() (in module simplicity.dir_manager) get_seed_from_SSOD() (in module simplicity.dir_manager) get_seeded_simulation_output_dirs() (in module simplicity.dir_manager) get_seeded_simulation_parameters_dir() (in module simplicity.dir_manager) get_seeded_simulation_parameters_paths() (in module simplicity.settings_manager) get_seq_weights() (in module simplicity.phenotype.consensus) get_simulation_output_dirs() (in module simplicity.dir_manager) get_simulation_output_foldername_from_SSOD() (in module simplicity.dir_manager) get_simulation_parameters_dir() (in module simplicity.dir_manager) get_simulation_parameters_filepath_of_simulation_output_dir() (in module simplicity.settings_manager) get_slurm_id_map_dir() (in module simplicity.dir_manager) get_slurm_logs_dir() (in module simplicity.dir_manager) get_ssod() (in module simplicity.dir_manager) get_standard_parameters_values_file_path() (in module simplicity.settings_manager) get_state_color() (in module simplicity.plots_manager) get_subst_numbers() (in module simplicity.evolution.mutations) get_tree() (in module simplicity.tree.tree_builder) get_tree_file_filepath() (in module simplicity.output_manager) get_tree_filename() (in module simplicity.output_manager) get_tree_plot_filepath() (in module simplicity.output_manager) get_update_mode() (simplicity.intra_host_model.Host method)

H

hamming() (in module simplicity.phenotype.distance)

hamming_iw() (in module simplicity.phenotype.distance) Host (class in simplicity.intra_host_model)

I

ideal_subplot_grid() (in module simplicity.plots_manager) immune_waning_fitness_score() (in module simplicity.phenotype.update) import_tree() (in module simplicity.tree.json_tree) individuals_data_to_df() (simplicity.population.Population method) infect_long_shedder() (in module simplicity.population_model)

infection() (in module simplicity.population_model) infection_tree() (in module simplicity.tree.tree_builder) inverse_exp_regressor() (in module simplicity.tuning.evolutionary_rate) inverse_linear_regressor() (in module simplicity.tuning.evolutionary_rate) inverse_log_regressor() (in module simplicity.tuning.evolutionary_rate) inverse_tan_regressor() (in module simplicity.tuning.evolutionary_rate)

J

job() (in module simplicity.runners.slurm)

L

left (simplicity.runners.slurm.SimulationsStatus attribute)

lineage_frequency_to_df() (simplicity.population.Population method) load_results() (in module simplicity.intra_host_model)

M

main() (in module simplicity.intra_host_model) make_lineages_colormap() (in module simplicity.plots_manager) map_to_dic() (in module simplicity.evolution.mutations) map_to_lin() (in module simplicity.evolution.mutations) module simplicity simplicity.dir_manager simplicity.evolution simplicity.evolution.decoder simplicity.evolution.mutations simplicity.evolution.reference simplicity.extrande simplicity.intra_host_model simplicity.output_manager simplicity.phenotype simplicity.phenotype.consensus simplicity.phenotype.distance simplicity.phenotype.update simplicity.phenotype.weight simplicity.plots_manager simplicity.population simplicity.population_model simplicity.random_gen simplicity.runme simplicity.runners simplicity.runners.multiprocessing simplicity.runners.serial simplicity.runners.slurm simplicity.runners.unit_run simplicity.settings_manager simplicity.simulation simplicity.tree simplicity.tree.json_tree simplicity.tree.newick simplicity.tree.nexus simplicity.tree.tree_builder simplicity.tuning simplicity.tuning.diagnosis_rate simplicity.tuning.evolutionary_rate

mutate() (in module simplicity.evolution.mutations)

P

pending (simplicity.runners.slurm.SimulationsStatus attribute) phylogenetic_data_to_df() (simplicity.population.Population method) phylogenetic_tree() (in module simplicity.tree.tree_builder) plot() (simplicity.simulation.Simplicity method) plot_circular_tree() (in module simplicity.plots_manager) plot_combined_OSR_fit() (in module simplicity.plots_manager) plot_combined_OSR_vs_parameter() (in module simplicity.plots_manager) plot_combined_tempest_regressions() (in module simplicity.plots_manager) plot_comparison_intra_host_models() (in module simplicity.plots_manager) plot_duration_summary_scatter() (in module simplicity.intra_host_model) plot_effective_theoretical_diagnosis_rate() (in module simplicity.plots_manager) plot_extrande_pop_runtime() (in module simplicity.plots_manager) plot_fitness() (in module simplicity.plots_manager) plot_heatmap_R_diagnosis_rate() (in module simplicity.plots_manager) plot_histograms() (in module simplicity.plots_manager) plot_IH_lineage_distribution() (in module simplicity.plots_manager) plot_IH_lineage_distribution_grouped_by_simulation() (in module simplicity.plots_manager) plot_IH_lineage_distribution_simulation() (in module simplicity.plots_manager)

plot_infection_tree() (in module simplicity.plots_manager) plot_infections_hist() (in module simplicity.plots_manager) plot_infectious_duration_vs_step() (in module simplicity.intra_host_model) plot_intra_host() (in module simplicity.plots_manager) plot_lineages_colors_tab() (in module simplicity.plots_manager) plot_OSR_and_IH_lineages_by_parameter() (in module simplicity.plots_manager) plot_OSR_fit() (in module simplicity.plots_manager) plot_OSR_fit_figure() (in module simplicity.plots_manager) plot_phylogenetic_tree() (in module simplicity.plots_manager) plot_R_effective() (in module simplicity.plots_manager) plot_simulation() (in module simplicity.plots_manager) plot_state_duration_stats_grid() (in module simplicity.intra_host_model) plot_state_timeline_summary() (in module simplicity.intra_host_model) plot_tempest_regression() (in module simplicity.plots_manager) plot_trajectory() (in module simplicity.plots_manager) plot_w_t() (in module simplicity.plots_manager) poll_simulations_status() (in module simplicity.runners.slurm) Population (class in simplicity.population) ProgressReporter (class in simplicity.extrande)

R

randomgen() (in module simplicity.random_gen) read_clustering_table() (in module simplicity.output_manager) read_combined_OSR_vs_parameter_csv() (in module simplicity.output_manager) read_experiment_settings() (in module simplicity.settings_manager) read_final_time() (in module simplicity.output_manager) read_fit_results_csv() (in module simplicity.output_manager) read_individuals_data() (in module simplicity.output_manager) read_lineage_frequency() (in module simplicity.output_manager) read_n_seeds_file() (in module simplicity.settings_manager) read_OSR_NSR_regressor_parameters() (in module simplicity.settings_manager) read_OSR_vs_parameter_csv() (in module simplicity.output_manager) read_parameter_specs() (in module simplicity.settings_manager) read_phylogenetic_data() (in module simplicity.output_manager) read_R_effective_trajectory() (in module simplicity.output_manager) read_r_effective_trajs_csv() (in module simplicity.output_manager) read_seeded_simulation_parameters() (in module simplicity.settings_manager)

read_sequencing_data_regression() (in module simplicity.output_manager) read_settings_and_write_simulation_parameters() (in module simplicity.settings_manager) read_simulation_trajectory() (in module simplicity.output_manager) read_standard_parameters_values() (in module simplicity.settings_manager) read_user_set_parameters_file() (in module simplicity.settings_manager) release_simulations() (in module simplicity.runners.slurm) released (simplicity.runners.slurm.SimulationsStatus attribute) run() (simplicity.simulation.Simplicity method) run_experiment() (in module simplicity.runme) run_parallel_simulations() (in module simplicity.intra_host_model) run_seeded_simulation() (in module simplicity.runners) (in module simplicity.runners.unit_run) run_seeded_simulations() (in module simplicity.runners) (in module simplicity.runners.multiprocessing) (in module simplicity.runners.serial) (in module simplicity.runners.slurm) running (simplicity.runners.slurm.SimulationsStatus attribute)

S

save_consensus() (simplicity.simulation.Simplicity method) save_final_time() (in module simplicity.output_manager) save_fitness_trajectory() (in module simplicity.output_manager) save_individuals_data() (in module simplicity.output_manager) save_lineage_frequency() (in module simplicity.output_manager) save_phylogenetic_data() (in module simplicity.output_manager) save_plos_figure() (in module simplicity.plots_manager) save_R_effective_trajectory() (in module simplicity.output_manager) save_results() (in module simplicity.intra_host_model) save_sequencing_dataset() (in module simplicity.output_manager) save_simulation_trajectory() (in module simplicity.output_manager) select_positions() (in module simplicity.evolution.mutations) serialize() (in module simplicity.tree.json_tree) set_data_dir() (in module simplicity.dir_manager) setup_output_directory() (in module simplicity.output_manager) SIDR_propensities() (in module simplicity.population_model) simplicity module Simplicity (class in simplicity.simulation) simplicity.dir_manager module simplicity.evolution module simplicity.evolution.decoder module simplicity.evolution.mutations module simplicity.evolution.reference module simplicity.extrande module simplicity.intra_host_model module simplicity.output_manager module simplicity.phenotype module simplicity.phenotype.consensus module simplicity.phenotype.distance module simplicity.phenotype.update module simplicity.phenotype.weight module simplicity.plots_manager module

simplicity.population module simplicity.population_model module simplicity.random_gen module simplicity.runme module simplicity.runners module simplicity.runners.multiprocessing module simplicity.runners.serial module simplicity.runners.slurm module simplicity.runners.unit_run module simplicity.settings_manager module simplicity.simulation module simplicity.tree module simplicity.tree.json_tree module simplicity.tree.newick module simplicity.tree.nexus module simplicity.tree.tree_builder module simplicity.tuning module simplicity.tuning.diagnosis_rate module simplicity.tuning.evolutionary_rate module simulate_trajectory() (simplicity.intra_host_model.Host method) SimulationsStatus (class in simplicity.runners.slurm) started (simplicity.runners.slurm.SimulationsStatus attribute) sub_events() (in module simplicity.evolution.mutations) sub_matrix() (in module simplicity.evolution.mutations) submit_simulations() (in module simplicity.runners.slurm) submitted (simplicity.runners.slurm.SimulationsStatus attribute) substitution() (in module simplicity.evolution.mutations)

T

tempest_regression() (in module simplicity.tuning.evolutionary_rate)

total (simplicity.runners.slurm.SimulationsStatus attribute) tree_fitness_legend() (in module simplicity.plots_manager)

U

update() (simplicity.extrande.ProgressReporter method) update_fitness_factory() (in module simplicity.phenotype.update) update_fitness_trajectory() (simplicity.population.Population method) update_ih_lineages_trajectories() (simplicity.population.Population method) update_lineage_frequency_t() (simplicity.population.Population method)

update_lineages() (in module simplicity.evolution.mutations) update_state() (simplicity.intra_host_model.Host static method) update_states() (simplicity.population.Population method) update_time() (simplicity.population.Population method) update_trajectory() (simplicity.population.Population method) user_set_experiment_settings() (in module simplicity.runme)

W

w_t_params() (in module simplicity.phenotype.weight) weighted_consensus() (in module simplicity.phenotype.consensus) weights() (in module simplicity.phenotype.weight) write_clustering_table() (in module simplicity.output_manager) write_combined_OSR_vs_parameter_csv() (in module simplicity.output_manager) write_experiment_settings() (in module simplicity.settings_manager) write_fit_results_csv() (in module simplicity.output_manager) write_json_tree_file() (in module simplicity.tree.json_tree)

write_newick_file() (in module simplicity.tree.newick) write_nexus_file() (in module simplicity.tree.nexus) write_OSR_vs_parameter_csv() (in module simplicity.output_manager) write_parameter_specs() (in module simplicity.settings_manager) write_r_effective_trajs_csv() (in module simplicity.output_manager) write_seeded_simulation_parameters() (in module simplicity.settings_manager) write_simulation_parameters() (in module simplicity.settings_manager) write_standard_parameters_values() (in module simplicity.settings_manager) write_user_set_parameters_file() (in module simplicity.settings_manager)