Index

A

activity (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] all_group_averages() (in module opynfield.summarize_measures.summarize_groups) alpha (opynfield.config.plot_settings.PlotSettings attribute), [1] anymaze_center_convert_to_center() (opynfield.readin.track.Track method), [1] anymaze_center_convert_units() (opynfield.readin.track.Track method), [1] anymaze_center_fill_missing() (opynfield.readin.track.Track method), [1] anymaze_center_numeric() (opynfield.readin.track.Track method), [1] anymaze_center_running_line() (opynfield.readin.track.Track method), [1] anymaze_center_subsample() (opynfield.readin.track.Track method), [1] anymaze_head_convert_to_center() (opynfield.readin.track.Track method), [1]

anymaze_head_convert_units() (opynfield.readin.track.Track method), [1] anymaze_head_fill_missing() (opynfield.readin.track.Track method), [1] anymaze_head_numeric() (opynfield.readin.track.Track method), [1] anymaze_head_running_line() (opynfield.readin.track.Track method), [1] anymaze_head_subsample() (opynfield.readin.track.Track method), [1] arena_radius_cm (opynfield.config.user_input.UserInput attribute), [1] asymptote_param (opynfield.config.cov_asymptote.CoverageAsymptote attribute), [1] asymptote_sign (opynfield.config.cov_asymptote.CoverageAsymptote attribute), [1] average_points() (in module opynfield.summarize_measures.summarize_groups) axes (opynfield.config.model_settings.ModelSpecification attribute), [1]

B

bins_traversed() (in module opynfield.calculate_measures.coverage_math) bound_level (opynfield.config.user_input.UserInput attribute), [1] bounds (opynfield.config.model_settings.ExponentialModel attribute), [1] (opynfield.config.model_settings.FixedExponentialModel attribute), [1] (opynfield.config.model_settings.LinearDecreaseModel attribute), [1] (opynfield.config.model_settings.LinearIncreaseModel attribute), [1]

buri_convert_to_center() (opynfield.readin.track.Track method), [1] buri_convert_units() (opynfield.readin.track.Track method), [1] buri_fill_missing() (opynfield.readin.track.Track method), [1] buri_running_line() (opynfield.readin.track.Track method), [1] buri_subsample() (opynfield.readin.track.Track method), [1]

C

calc_center() (in module opynfield.readin.multi_tracker) calculate_coverage() (in module opynfield.calculate_measures.calculate_measures) calculate_group_coverage_asymptote() (in module opynfield.calculate_measures.calculate_measures) calculate_percent_coverage() (in module opynfield.calculate_measures.calculate_measures) calculate_pgca() (in module opynfield.calculate_measures.calculate_measures) calculate_pica() (in module opynfield.calculate_measures.calculate_measures) cartesian_to_polar() (in module opynfield.calculate_measures.calculate_measures) change_running_window_length() (opynfield.config.user_input.UserInput method) change_trim() (opynfield.config.user_input.UserInput method) change_window_step_size() (opynfield.config.user_input.UserInput method)

colormap_name (opynfield.config.plot_settings.PlotSettings attribute), [1] combine_arena_coords() (in module opynfield.readin.etho_tracker) component_model_results (opynfield.stat_test.stat_test.ManovaModels attribute), [1] convert_time_stamp() (in module opynfield.readin.anymaze_tracker) cov_measure_average() (in module opynfield.summarize_measures.summarize_groups) coverage (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] coverage_averaged_measures (opynfield.config.defaults_settings.Defaults attribute), [1] coverage_bins (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] CoverageAsymptote (class in opynfield.config.cov_asymptote) create_full_formula() (in module opynfield.stat_test.stat_test) create_pairs() (opynfield.config.defaults_settings.Defaults method)

D

Defaults (class in opynfield.config.defaults_settings) display_individual_figures (opynfield.config.plot_settings.PlotSettings attribute), [1] display_parts (opynfield.config.model_settings.ExponentialModel attribute), [1] (opynfield.config.model_settings.FixedExponentialModel attribute), [1] (opynfield.config.model_settings.LinearDecreaseModel attribute), [1] (opynfield.config.model_settings.LinearIncreaseModel attribute), [1]

display_results() (opynfield.stat_test.stat_test.ManovaModels method), [1] display_solo_group_figures (opynfield.config.plot_settings.PlotSettings attribute), [1]

E

edge_color (opynfield.config.plot_settings.PlotSettings attribute), [1] edge_dist_cm (opynfield.config.user_input.UserInput attribute), [1] equation (opynfield.config.plot_settings.PlotSettings attribute), [1] error_color (opynfield.config.plot_settings.PlotSettings attribute), [1] error_width (opynfield.config.plot_settings.PlotSettings attribute), [1] etho_ml_convert_to_center() (opynfield.readin.track.Track method), [1] etho_ml_fill_missing() (opynfield.readin.track.Track method), [1] etho_ml_numeric() (opynfield.readin.track.Track method), [1] etho_ml_subsample() (opynfield.readin.track.Track method), [1] etho_txt_convert_to_center() (opynfield.readin.track.Track method), [1] etho_txt_fill_missing() (opynfield.readin.track.Track method), [1] etho_txt_numeric() (opynfield.readin.track.Track method), [1]

etho_txt_subsample() (opynfield.readin.track.Track method), [1] etho_v1_convert_to_center() (opynfield.readin.track.Track method), [1] etho_v1_fill_missing() (opynfield.readin.track.Track method), [1] etho_v1_numeric() (opynfield.readin.track.Track method), [1] etho_v1_subsample() (opynfield.readin.track.Track method), [1] etho_v2_convert_to_center() (opynfield.readin.track.Track method), [1] etho_v2_fill_missing() (opynfield.readin.track.Track method), [1] etho_v2_numeric() (opynfield.readin.track.Track method), [1] etho_v2_subsample() (opynfield.readin.track.Track method), [1] exponential() (in module opynfield.config.cov_asymptote) ExponentialModel (class in opynfield.config.model_settings) extract_arena_center_point() (in module opynfield.readin.etho_tracker)

F

f_name (opynfield.config.cov_asymptote.CoverageAsymptote attribute) f_name() (opynfield.config.cov_asymptote.CoverageAsymptote method) fig_extension (opynfield.config.plot_settings.PlotSettings attribute), [1] fill_missing_data() (in module opynfield.readin.multi_tracker) find_fit_bounds() (in module opynfield.fit_models.fit_individual_models) fit_all() (in module opynfield.fit_models.fit_individual_models) fit_by_cov_measure() (in module opynfield.fit_models.fit_individual_models) fit_by_time() (in module opynfield.fit_models.fit_individual_models)

fit_color (opynfield.config.plot_settings.PlotSettings attribute), [1] fit_measure_by_cov() (in module opynfield.fit_models.fit_individual_models) fit_measure_by_time() (in module opynfield.fit_models.fit_individual_models) fixed_exponential() (in module opynfield.config.cov_asymptote) FixedExponentialModel (class in opynfield.config.model_settings) fly_coverage() (in module opynfield.calculate_measures.coverage_math) format_group_params() (in module opynfield.stat_test.stat_test) format_params() (in module opynfield.stat_test.stat_test) full_model (opynfield.stat_test.stat_test.ManovaModels attribute), [1]

G

generate_fig_title() (in module opynfield.plotting.plot_group_comparisons) (in module opynfield.plotting.plot_individuals) (in module opynfield.plotting.plot_solo_groups) generate_group_equation_str() (in module opynfield.plotting.plot_solo_groups) generate_individual_equation_str() (in module opynfield.plotting.plot_individuals) generate_models() (in module opynfield.stat_test.stat_test) generate_view_title() (in module opynfield.plotting.plot_solo_groups_with_individuals) get_col_names_from_prefix() (in module opynfield.stat_test.stat_test) get_meta_info() (in module opynfield.readin.buridian_tracker) get_x() (opynfield.config.model_settings.ModelSpecification method), [1] get_y() (opynfield.config.model_settings.ModelSpecification method), [1] group (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] (opynfield.readin.track.Track attribute), [1]

group_colors (opynfield.config.plot_settings.PlotSettings attribute), [1] group_error_bars (opynfield.config.plot_settings.PlotSettings attribute), [1] group_fit_all() (in module opynfield.fit_models.fit_group_models) group_fit_by_cov_measure() (in module opynfield.fit_models.fit_group_models) group_fit_by_time() (in module opynfield.fit_models.fit_group_models) group_fit_measure_by_cov_measure() (in module opynfield.fit_models.fit_group_models) group_fit_measure_by_time() (in module opynfield.fit_models.fit_group_models) group_model_fit (opynfield.config.plot_settings.PlotSettings attribute), [1] groups_and_types (opynfield.config.user_input.UserInput attribute), [1] groups_to_paths (opynfield.config.user_input.UserInput attribute), [1] groups_to_types() (in module opynfield.readin.run_all)

I

inactivity_threshold (opynfield.config.user_input.UserInput attribute), [1] independent_var (opynfield.stat_test.stat_test.ManovaModels attribute), [1] individual_measures_to_dfs() (in module opynfield.summarize_measures.summarize_individuals) individual_model_fit (opynfield.config.plot_settings.PlotSettings attribute), [1]

initial_parameters (opynfield.config.cov_asymptote.CoverageAsymptote attribute), [1] initial_params (opynfield.config.model_settings.ExponentialModel attribute), [1] (opynfield.config.model_settings.FixedExponentialModel attribute), [1] (opynfield.config.model_settings.LinearDecreaseModel attribute), [1] (opynfield.config.model_settings.LinearIncreaseModel attribute), [1]

L

linear() (in module opynfield.config.cov_asymptote) LinearDecreaseModel (class in opynfield.config.model_settings)

LinearIncreaseModel (class in opynfield.config.model_settings) locate_bin() (in module opynfield.calculate_measures.calculate_measures)

M

make_formula_from_list() (in module opynfield.stat_test.stat_test) make_measures_by_cov_measure() (in module opynfield.summarize_measures.summarize_groups) make_measures_by_pcov() (in module opynfield.summarize_measures.summarize_groups) ManovaModels (class in opynfield.stat_test.stat_test) mapper() (in module opynfield.config.model_settings) marker_color (opynfield.config.plot_settings.PlotSettings attribute), [1] marker_size (opynfield.config.plot_settings.PlotSettings attribute), [1] max_eval (opynfield.config.model_settings.ExponentialModel attribute), [1] (opynfield.config.model_settings.FixedExponentialModel attribute), [1] (opynfield.config.model_settings.LinearDecreaseModel attribute), [1] (opynfield.config.model_settings.LinearIncreaseModel attribute), [1] max_f_eval (opynfield.config.cov_asymptote.CoverageAsymptote attribute), [1] model (opynfield.config.model_settings.ModelSpecification attribute), [1] model_function() (opynfield.config.model_settings.ExponentialModel method) (opynfield.config.model_settings.ExponentialModel static method) (opynfield.config.model_settings.FixedExponentialModel method) (opynfield.config.model_settings.FixedExponentialModel static method) (opynfield.config.model_settings.LinearDecreaseModel method) (opynfield.config.model_settings.LinearDecreaseModel static method) (opynfield.config.model_settings.LinearIncreaseModel method) (opynfield.config.model_settings.LinearIncreaseModel static method) ModelSpecification (class in opynfield.config.model_settings) module opynfield opynfield.calculate_measures opynfield.calculate_measures.calculate_measures opynfield.calculate_measures.coverage_math opynfield.calculate_measures.standard_track opynfield.config opynfield.config.cov_asymptote opynfield.config.defaults_settings opynfield.config.model_settings opynfield.config.plot_settings opynfield.config.user_input opynfield.fit_models opynfield.fit_models.fit_group_models opynfield.fit_models.fit_individual_models opynfield.plotting opynfield.plotting.plot_group_comparisons opynfield.plotting.plot_individuals opynfield.plotting.plot_solo_groups opynfield.plotting.plot_solo_groups_with_individuals opynfield.readin opynfield.readin.anymaze_tracker opynfield.readin.buridian_tracker opynfield.readin.etho_tracker opynfield.readin.multi_tracker opynfield.readin.read_in opynfield.readin.run_all opynfield.readin.summary_file opynfield.readin.track opynfield.run opynfield.stat_test opynfield.stat_test.stat_test opynfield.summarize_measures opynfield.summarize_measures.summarize_groups opynfield.summarize_measures.summarize_individuals

motion_probabilities() (in module opynfield.calculate_measures.calculate_measures) motion_probabilities_given_previous() (in module opynfield.calculate_measures.calculate_measures)

N

n_between_error (opynfield.config.plot_settings.PlotSettings attribute), [1] n_bins (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] n_bins_average_pcov() (in module opynfield.summarize_measures.summarize_groups) n_bins_percent_coverage (opynfield.config.defaults_settings.Defaults attribute), [1]

n_points_average_cov_measure() (in module opynfield.summarize_measures.summarize_groups) n_points_coverage (opynfield.config.defaults_settings.Defaults attribute), [1] n_points_pgca (opynfield.config.defaults_settings.Defaults attribute), [1] n_points_pica (opynfield.config.defaults_settings.Defaults attribute), [1] node_size (opynfield.config.defaults_settings.Defaults attribute), [1]

O

options (opynfield.readin.track.Track attribute), [1] opynfield module opynfield.calculate_measures module opynfield.calculate_measures.calculate_measures module opynfield.calculate_measures.coverage_math module opynfield.calculate_measures.standard_track module opynfield.config module opynfield.config.cov_asymptote module opynfield.config.defaults_settings module opynfield.config.model_settings module opynfield.config.plot_settings module opynfield.config.user_input module opynfield.fit_models module opynfield.fit_models.fit_group_models module opynfield.fit_models.fit_individual_models module opynfield.plotting module opynfield.plotting.plot_group_comparisons module opynfield.plotting.plot_individuals module

opynfield.plotting.plot_solo_groups module opynfield.plotting.plot_solo_groups_with_individuals module opynfield.readin module opynfield.readin.anymaze_tracker module opynfield.readin.buridian_tracker module opynfield.readin.etho_tracker module opynfield.readin.multi_tracker module opynfield.readin.read_in module opynfield.readin.run_all module opynfield.readin.summary_file module opynfield.readin.track module opynfield.run module opynfield.stat_test module opynfield.stat_test.stat_test module opynfield.summarize_measures module opynfield.summarize_measures.summarize_groups module opynfield.summarize_measures.summarize_individuals module

P

p_plus_minus (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_minus_given_any (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_minus_given_plus (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_plus (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_plus_given_any (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_plus_given_plus (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_zero (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_zero_given_any (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_plus_zero_given_plus (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_zero_plus (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_zero_plus_given_any (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_zero_plus_given_zero (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_zero_zero (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_zero_zero_given_any (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] p_zero_zero_given_zero (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] pair_to_cov_measure() (in module opynfield.summarize_measures.summarize_groups) parameter_bounds (opynfield.config.cov_asymptote.CoverageAsymptote attribute), [1] parameter_names() (opynfield.stat_test.stat_test.ManovaModels method), [1] path_coverage() (in module opynfield.calculate_measures.coverage_math) percent_coverage (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] percent_coverage_average() (in module opynfield.summarize_measures.summarize_groups) pgca (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1]

pgca_asymptote (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] pica (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] pica_asymptote (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] plot_all_group_comparisons() (in module opynfield.plotting.plot_group_comparisons) plot_all_individuals() (in module opynfield.plotting.plot_individuals) plot_all_individuals_by_cmeasure() (in module opynfield.plotting.plot_individuals) plot_all_individuals_by_time() (in module opynfield.plotting.plot_individuals) plot_all_solo_groups() (in module opynfield.plotting.plot_solo_groups) plot_cmeasure_comparison() (in module opynfield.plotting.plot_group_comparisons) plot_cmeasure_measure() (in module opynfield.plotting.plot_individuals) plot_components_of_solo_groups() (in module opynfield.plotting.plot_solo_groups_with_individuals) plot_group_individual_comparison_cmeasure() (in module opynfield.plotting.plot_solo_groups_with_individuals) plot_group_individual_comparison_time() (in module opynfield.plotting.plot_solo_groups_with_individuals) plot_individual_trace() (in module opynfield.plotting.plot_individuals) plot_solo_group_by_cmeasure() (in module opynfield.plotting.plot_solo_groups) plot_solo_group_by_time() (in module opynfield.plotting.plot_solo_groups) plot_solo_group_measure_by_time() (in module opynfield.plotting.plot_solo_groups) plot_time_comparison() (in module opynfield.plotting.plot_group_comparisons) plot_time_measure() (in module opynfield.plotting.plot_individuals) plot_traces() (in module opynfield.plotting.plot_individuals) PlotSettings (class in opynfield.config.plot_settings) prep_directory() (opynfield.config.user_input.UserInput method)

R

r (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] re_fit_all() (in module opynfield.fit_models.fit_individual_models) re_fit_by_cov_measure() (in module opynfield.fit_models.fit_individual_models) re_fit_by_time() (in module opynfield.fit_models.fit_individual_models) re_fit_measure_by_cov_measure() (in module opynfield.fit_models.fit_individual_models) re_fit_measure_by_time() (in module opynfield.fit_models.fit_individual_models) read_anymaze_center() (in module opynfield.readin.anymaze_tracker) read_anymaze_head() (in module opynfield.readin.anymaze_tracker) read_buridian() (in module opynfield.readin.buridian_tracker) read_etho_ml() (in module opynfield.readin.etho_tracker) read_etho_txt() (in module opynfield.readin.etho_tracker)

read_etho_v1() (in module opynfield.readin.etho_tracker) read_etho_v2() (in module opynfield.readin.etho_tracker) read_track_types() (in module opynfield.readin.read_in) result_path (opynfield.config.user_input.UserInput attribute), [1] run() (in module opynfield.run) run_all_track_types() (in module opynfield.readin.run_all) run_component_tests() (in module opynfield.stat_test.stat_test) run_full_test() (in module opynfield.stat_test.stat_test) run_tests() (in module opynfield.stat_test.stat_test) running_line() (in module opynfield.readin.multi_tracker) running_window_length (opynfield.config.user_input.UserInput attribute), [1]

S

sample_freq (opynfield.config.user_input.UserInput attribute), [1] save_all_group_csvs (opynfield.config.defaults_settings.Defaults attribute), [1] save_all_group_model_csvs (opynfield.config.defaults_settings.Defaults attribute), [1] save_combined_view_figures (opynfield.config.plot_settings.PlotSettings attribute), [1] save_group__comparison_figures (opynfield.config.plot_settings.PlotSettings attribute), [1] save_group_csvs (opynfield.config.defaults_settings.Defaults attribute), [1] save_group_model_csvs (opynfield.config.defaults_settings.Defaults attribute), [1] save_individual_figures (opynfield.config.plot_settings.PlotSettings attribute), [1] save_solo_group_figures (opynfield.config.plot_settings.PlotSettings attribute), [1] set_edge_radius() (opynfield.config.user_input.UserInput method)

set_pgca() (opynfield.calculate_measures.standard_track.StandardTrack method) set_up_fits() (in module opynfield.config.model_settings) sign_to_step() (in module opynfield.calculate_measures.coverage_math) sort_by_cov_measure() (in module opynfield.summarize_measures.summarize_groups) sort_tracks_by_arena() (in module opynfield.readin.etho_tracker) standardized (opynfield.readin.track.Track attribute), [1] StandardTrack (class in opynfield.calculate_measures.standard_track) step_distance() (in module opynfield.calculate_measures.calculate_measures) subsample() (in module opynfield.readin.multi_tracker) summarize() (in module opynfield.readin.summary_file) summary_file() (in module opynfield.readin.summary_file)

T

t (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] (opynfield.readin.track.Track attribute), [1] theta (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] time_average() (in module opynfield.summarize_measures.summarize_groups) time_averaged_measures (opynfield.config.defaults_settings.Defaults attribute), [1] time_bin_size (opynfield.config.user_input.UserInput attribute), [1] to_dataframes() (opynfield.calculate_measures.standard_track.StandardTrack class method) Track (class in opynfield.readin.track)

track_type (opynfield.readin.track.Track attribute), [1] tracks_to_measures() (in module opynfield.calculate_measures.calculate_measures) trim (opynfield.config.user_input.UserInput attribute), [1] truncate() (in module opynfield.plotting.plot_individuals) (in module opynfield.plotting.plot_solo_groups) turn (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] turning_angle() (in module opynfield.calculate_measures.calculate_measures) types_to_groups() (in module opynfield.readin.run_all)

U

update_first_visit() (in module opynfield.calculate_measures.coverage_math) update_visits() (in module opynfield.calculate_measures.coverage_math)

update_visits_for_steps_between_bins() (in module opynfield.calculate_measures.coverage_math) UserInput (class in opynfield.config.user_input)

V

verbose (opynfield.config.user_input.UserInput attribute), [1]

W

window_step_size (opynfield.config.user_input.UserInput attribute), [1]

X

x (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] (opynfield.readin.track.Track attribute), [1]

Y

y (opynfield.calculate_measures.standard_track.StandardTrack attribute), [1] (opynfield.readin.track.Track attribute), [1]