Index

_

__init__() (stag.analysis.label_analysis.LabelAnalyser method) (stag.clustering.meta_analysis.ClusterMetaAnalysis method) (stag.clustering.meta_analysis.ClusterPlotter method) (stag.clustering.plotting.CentroidDashboard method) (stag.database.handler.DeerDatabaseHandler method) (stag.sync.data_sync.BetterDataSync method) (stag.utils.csv_formatter.CsvFormatter method)

A

abs_speed_mPs (stag.database.orm.TrajectoryData attribute) accelerometer_data (stag.database.orm.ClusterLabels attribute) (stag.database.orm.DeerInfo attribute) (stag.database.orm.VideoAvailability attribute) accelerometer_data_id (stag.database.orm.VideoAvailability attribute)

ACCELEROMETER_RANGE_G (in module stag.constants) AccelerometerData (class in stag.database.orm) aggregate_all_data() (in module stag.database.make_cluster_data) aggregate_durations_across_animals() (in module stag.analysis.super_prototypes) analyze() (stag.clustering.meta_analysis.ClusterMetaAnalysis method) apply_figure_defaults() (in module stag.constants)

B

BetterDataSync (class in stag.sync.data_sync) bout_duration_stats() (in module stag.analysis.super_prototypes)

bout_stream() (in module stag.analysis.super_prototypes) BoutStream (class in stag.analysis.super_prototypes) build_transition_matrix() (in module stag.analysis.markov)

C

calculate_and_assign_instability() (stag.clustering.meta_analysis.ClusterMetaAnalysis method) calculate_instability() (stag.clustering.meta_analysis.ClusterMetaAnalysis static method) calculate_statistics_for_cluster() (stag.database.handler.DeerDatabaseHandler method) calculate_time_axis() (in module stag.gps.plotting) calculate_tortuosity_and_speed() (in module stag.gps.analysis) (in module stag.gps.tortuosity) CANONICAL_K8_LABELS (in module stag.constants) CentroidDashboard (class in stag.clustering.plotting) centroids_to_c_header() (in module stag.embedded.export_centroids) classify_day_night() (in module stag.analysis.circadian)

CLUSTER_RESULTS_DIR (in module stag.constants) ClusterLabels (class in stag.database.orm) ClusterMetaAnalysis (class in stag.clustering.meta_analysis) ClusterPlotter (class in stag.clustering.meta_analysis) comment (stag.database.orm.VideoObservationReference attribute) compute_inertia() (in module stag.clustering.internal_metrics) compute_silhouette_stratified() (in module stag.clustering.internal_metrics) conditional_transition_matrix() (in module stag.analysis.markov) correct_calibration() (in module stag.sync.utils) create_database() (stag.database.handler.DeerDatabaseHandler method) CsvFormatter (class in stag.utils.csv_formatter)

D

data_id (stag.database.orm.AccelerometerData attribute) (stag.database.orm.ClusterLabels attribute) (stag.database.orm.TrajectoryData attribute) decode_q_format() (in module stag.embedded.export_centroids) deer (stag.database.orm.VideoObservationReference attribute) DEER_DB (in module stag.constants) deer_id (stag.database.orm.AccelerometerData attribute) (stag.database.orm.DeerInfo attribute) (stag.database.orm.TrajectoryData attribute)

deer_info (stag.database.orm.AccelerometerData attribute) (stag.database.orm.TrajectoryData attribute) deer_number (stag.database.orm.DeerInfo attribute) DeerDatabaseHandler (class in stag.database.handler) DeerInfo (class in stag.database.orm) detect_drops() (stag.sync.data_sync.BetterDataSync method) double_banner() (in module stag.utils.banners)

E

ear_flick_day_night_test() (in module stag.analysis.circadian) encode_q_format() (in module stag.embedded.export_centroids) expected_bout_duration() (in module stag.analysis.markov)

extract_n_grams() (in module stag.analysis.super_prototypes) extract_tort_and_speed() (in module stag.gps.tortuosity) extract_triplets() (in module stag.analysis.super_prototypes)

F

FEATURE_LABELS (in module stag.constants) FIGURE_DPI (in module stag.constants) FIGURE_SIZE_DOUBLE (in module stag.constants) FIGURE_SIZE_SINGLE (in module stag.constants) fill_linearly_df() (in module stag.gps.analysis) filterIDX() (stag.analysis.label_analysis.LabelAnalyser method) find_most_stable_centroids() (stag.clustering.meta_analysis.ClusterMetaAnalysis method) find_nan_sequences() (in module stag.analysis.nan_handler)

flag_above_below_baseline() (in module stag.analysis.markov) flag_significant_ngrams() (in module stag.analysis.null_models) FONT_FAMILY (in module stag.constants) format() (stag.utils.csv_formatter.CsvFormatter method) FPS (in module stag.constants) frac_bits (stag.embedded.export_centroids.QFormat attribute) frame (stag.database.orm.VideoAvailability attribute) frame_count (stag.database.orm.VideoObservationReference attribute)

G

gaussian_filter_column() (in module stag.gps.analysis) generate_filename() (in module stag.clustering.kmeans) (in module stag.utils.filename_generator) generate_video_availability_csv() (stag.database.handler.DeerDatabaseHandler method) get_calibrated_absolute_accelleration() (in module stag.sync.utils) get_consecutive_differences() (in module stag.sync.utils) get_data_for_deer() (in module stag.database.make_cluster_data) get_deer_id_from_filename() (stag.database.handler.DeerDatabaseHandler method)

get_deer_ids() (in module stag.database.make_cluster_data) get_mean_durations() (stag.analysis.label_analysis.LabelAnalyser method) get_path() (in module stag.local_paths) get_path_obj() (in module stag.local_paths) get_percentage() (stag.analysis.label_analysis.LabelAnalyser method) get_quality() (in module stag.clustering.kmeans) get_transitions() (stag.analysis.label_analysis.LabelAnalyser method) GPS_FPS (in module stag.constants)

H

HCS_SOURCE_DIR (in module stag.constants)

highlight_area() (in module stag.gps.plotting) hourly_proportions() (in module stag.analysis.circadian)

I

id (stag.database.orm.VideoAvailability attribute) (stag.database.orm.VideoObservationReference attribute) identify_super_prototypes() (in module stag.analysis.super_prototypes) import_video_availability_from_csv() (stag.database.handler.DeerDatabaseHandler method) insert_cluster_labels_from_npy() (stag.database.handler.DeerDatabaseHandler method)

insert_data_from_directory() (stag.database.handler.DeerDatabaseHandler method) insert_trajectory_data_from_h5() (stag.database.handler.DeerDatabaseHandler method) insert_video_observation_data() (stag.database.handler.DeerDatabaseHandler method) int_bits (stag.embedded.export_centroids.QFormat attribute) interpolate_nan_sequences() (in module stag.analysis.nan_handler)

L

label (stag.database.orm.ClusterLabels attribute) LABEL_TIMELINE_DEER_IDS (in module stag.constants) LABEL_TIMELINE_TIMESTAMPS (in module stag.constants) LabelAnalyser (class in stag.analysis.label_analysis) labels (stag.analysis.super_prototypes.BoutStream attribute) lat_lon_vec_to_meter_vec() (in module stag.gps.tortuosity) lengths (stag.analysis.super_prototypes.BoutStream attribute)

load_centroids_for_analysis() (stag.clustering.meta_analysis.ClusterMetaAnalysis method) load_data() (in module stag.analysis.nan_handler) (stag.clustering.meta_analysis.ClusterMetaAnalysis method) load_df() (stag.clustering.meta_analysis.ClusterMetaAnalysis method) load_trajectory_data() (in module stag.gps.plotting) LOCAL_DATA_DIR (in module stag.constants) LocalPathNotConfiguredError locate_elbow_kneedle() (in module stag.clustering.internal_metrics)

M

main() (in module stag.clustering.kmeans) (in module stag.embedded.export_centroids) (in module stag.gps.analysis) (stag.analysis.label_analysis.LabelAnalyser method) main_plot_with_closeup() (in module stag.gps.plotting) make_absolute() (in module stag.sync.utils) make_session() (stag.database.handler.DeerDatabaseHandler method) marginal_rates() (in module stag.analysis.markov) max_signed (stag.embedded.export_centroids.QFormat property) MAXABS_CLUSTERING_INPUT (in module stag.constants) MAXABS_SCALER_CSV (in module stag.constants) min_signed (stag.embedded.export_centroids.QFormat property) module stag.analysis.circadian stag.analysis.label_analysis stag.analysis.markov stag.analysis.nan_handler stag.analysis.null_models stag.analysis.super_prototypes stag.clustering.internal_metrics stag.clustering.kmeans stag.clustering.meta_analysis stag.clustering.plotting stag.constants stag.database.handler stag.database.make_cluster_data stag.database.orm stag.embedded.export_centroids stag.gps.analysis stag.gps.plotting stag.gps.tortuosity stag.local_paths stag.sync.data_sync stag.sync.utils stag.utils.banners stag.utils.csv_formatter stag.utils.filename_generator

N

n_bouts (stag.analysis.super_prototypes.BoutStream property) ngram_frequencies() (in module stag.analysis.null_models)

normalize_centroids() (stag.clustering.meta_analysis.ClusterMetaAnalysis static method) null_distribution() (in module stag.analysis.null_models) NZ_DateTime (stag.database.orm.AccelerometerData attribute)

O

open_session() (in module stag.database.make_cluster_data)

original_file_path (stag.database.orm.VideoObservationReference attribute)

P

parse_args() (in module stag.embedded.export_centroids) per_animal_bout_streams() (in module stag.analysis.super_prototypes) per_animal_pm_duration_stats() (in module stag.analysis.super_prototypes) per_animal_time_budget() (in module stag.analysis.circadian) plot_internal_metrics_panel() (in module stag.clustering.plotting) plot_metric() (stag.clustering.meta_analysis.ClusterPlotter method) plot_radar_and_metrics() (stag.clustering.plotting.CentroidDashboard method) plot_radar_charts() (stag.clustering.meta_analysis.ClusterPlotter static method) plot_speed_and_tortuosity_with_highlight() (in module stag.gps.plotting) plot_trajectory() (in module stag.gps.plotting) PM_CATEGORY (in module stag.constants) PM_CATEGORY_COLOURS (in module stag.constants)

PM_COLOURS (in module stag.constants) PM_DISPLAY_NAMES (in module stag.constants) PM_DISPLAY_NAMES_SHORT (in module stag.constants) PM_NAMES (in module stag.constants) pos_NZMG_x_meter (stag.database.orm.TrajectoryData attribute) pos_NZMG_y_meter (stag.database.orm.TrajectoryData attribute) pos_WGS84_lat (stag.database.orm.TrajectoryData attribute) pos_WGS84_lon (stag.database.orm.TrajectoryData attribute) pos_x_meter_filt (stag.database.orm.TrajectoryData attribute) pos_y_meter_filt (stag.database.orm.TrajectoryData attribute) prepare_line_collection() (in module stag.gps.plotting) project_to_NZ_map_grid() (in module stag.gps.analysis)

Q

QFormat (class in stag.embedded.export_centroids)

R

range_float (stag.embedded.export_centroids.QFormat property) RAW_CLUSTERING_INPUT (in module stag.constants) read_h5_file() (stag.database.handler.DeerDatabaseHandler static method) recompute_inertia_for_meta_dir() (in module stag.clustering.internal_metrics)

repetition (stag.database.orm.VideoObservationReference attribute) repetition_number (stag.database.orm.DeerInfo attribute) reset_cache() (in module stag.local_paths) RESULTS_DIR_DEFAULT (in module stag.constants) run_synchronization() (stag.sync.data_sync.BetterDataSync method)

S

save_data_to_npy() (in module stag.database.make_cluster_data) save_df() (stag.clustering.meta_analysis.ClusterMetaAnalysis method) save_figure() (in module stag.constants) save_output() (in module stag.clustering.kmeans) save_results_to_json() (stag.analysis.label_analysis.LabelAnalyser method) scale (stag.embedded.export_centroids.QFormat property) section_banner() (in module stag.utils.banners) selection_summary() (in module stag.clustering.internal_metrics) shrink_data() (in module stag.clustering.kmeans) shuffle_first_order() (in module stag.analysis.null_models) shuffle_marginal() (in module stag.analysis.null_models) split_by_day() (in module stag.analysis.circadian) stag.analysis.circadian module stag.analysis.label_analysis module stag.analysis.markov module stag.analysis.nan_handler module stag.analysis.null_models module stag.analysis.super_prototypes module stag.clustering.internal_metrics module stag.clustering.kmeans module stag.clustering.meta_analysis module stag.clustering.plotting module

stag.constants module stag.database.handler module stag.database.make_cluster_data module stag.database.orm module stag.embedded.export_centroids module stag.gps.analysis module stag.gps.plotting module stag.gps.tortuosity module stag.local_paths module stag.sync.data_sync module stag.sync.utils module stag.utils.banners module stag.utils.csv_formatter module stag.utils.filename_generator module start_index (stag.analysis.super_prototypes.BoutStream attribute) start_time (stag.database.orm.VideoObservationReference attribute) stop_time (stag.database.orm.VideoObservationReference attribute) sum_columns() (in module stag.sync.utils)

T

thin_rule() (in module stag.utils.banners) top_n_super_prototypes() (in module stag.analysis.null_models) tortuosity (stag.database.orm.TrajectoryData attribute)

total_bits (stag.embedded.export_centroids.QFormat property) trajectory_data (stag.database.orm.DeerInfo attribute) TrajectoryData (class in stag.database.orm) triplet_frequencies() (in module stag.analysis.null_models)

U

update_df_to_cartesian_positions() (in module stag.gps.analysis)

update_json_with_statistics() (stag.database.handler.DeerDatabaseHandler method)

V

verify_round_trip() (in module stag.embedded.export_centroids) VIDEO_FPS (in module stag.constants) video_observation_reference (stag.database.orm.VideoAvailability attribute)

video_observation_reference_id (stag.database.orm.VideoAvailability attribute) VideoAvailability (class in stag.database.orm) VideoObservationReference (class in stag.database.orm)

W

WONG (in module stag.constants)

write_trajectory_data_for_deer() (stag.database.handler.DeerDatabaseHandler method)

X

X_ear (stag.database.orm.AccelerometerData attribute)

X_head (stag.database.orm.AccelerometerData attribute)

Y

Y_ear (stag.database.orm.AccelerometerData attribute)

Y_head (stag.database.orm.AccelerometerData attribute)

Z

Z_ear (stag.database.orm.AccelerometerData attribute)

Z_head (stag.database.orm.AccelerometerData attribute)