Index

_

_batch_init() (geogenie.geogenie.GeoGenIE method) _compute_S_matrix() (geogenie.utils.transformers.MCA method) _create_metrics_dictionary() (geogenie.geogenie.GeoGenIE method) _define_model() (geogenie.models.models.MLPRegressor method) _ensure_is_gdf() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) _ensure_is_numpy() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) _ensure_is_pandas() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) _fill_kde_with_gradient() (geogenie.plotting.plotting.PlotGenIE method) _highlight_counties() (geogenie.plotting.plotting.PlotGenIE method) _make_colorbar() (geogenie.plotting.plotting.PlotGenIE method)

_normalize_data() (geogenie.utils.transformers.MCA method) _plot_scatter_map() (geogenie.plotting.plotting.PlotGenIE method) _plot_smote_scatter() (geogenie.plotting.plotting.PlotGenIE method) _remove_spines() (geogenie.plotting.plotting.PlotGenIE method) _run_kriging() (geogenie.plotting.plotting.PlotGenIE method) _set_cbar_fontsize() (geogenie.plotting.plotting.PlotGenIE method) _sklearn_auto_wrap_output_keys (geogenie.utils.scorers.LocallyLinearEmbeddingWrapper attribute) (geogenie.utils.transformers.MCA attribute) (geogenie.utils.transformers.MinMaxScalerGeo attribute) _store_results() (geogenie.utils.transformers.MCA method) _validate_dists() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method)

A

analysis() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) args (geogenie.geogenie.GeoGenIE attribute) (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute)

assign_to_bins() (in module geogenie.utils.utils)

B

basemap_fips (geogenie.plotting.plotting.PlotGenIE attribute) (geogenie.utils.spatial_data_processors.SpatialDataProcessor attribute) basemap_highlights (geogenie.plotting.plotting.PlotGenIE attribute) batch_size (geogenie.models.models.MLPRegressor attribute)

best_score (geogenie.utils.callbacks.EarlyStopping attribute) boot (geogenie.geogenie.GeoGenIE attribute) (geogenie.utils.callbacks.EarlyStopping attribute) buffer (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute)

C

calculate_bounding_box() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) calculate_convex_hull() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) calculate_dgeo() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) calculate_prediction_metrics() (geogenie.geogenie.GeoGenIE method) calculate_r2_knn() (in module geogenie.utils.scorers) calculate_rmse() (in module geogenie.utils.scorers) calculate_statistic() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) calculate_statistics() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) call_create_dataloaders() (geogenie.utils.data_structure.DataStructure method) callback_init() (in module geogenie.utils.callbacks)

categories (geogenie.utils.transformers.MCA attribute) check_column_dtype() (in module geogenie.utils.utils) check_input (geogenie.utils.transformers.MCA attribute) composite_outlier_detection() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) compute_rolling_statistics() (geogenie.geogenie.GeoGenIE method) count_alleles() (geogenie.utils.data_structure.DataStructure method) counter (geogenie.utils.callbacks.EarlyStopping attribute) create_dataloaders() (geogenie.utils.data_structure.DataStructure method) crs (geogenie.utils.spatial_data_processors.SpatialDataProcessor attribute) CustomDataset (class in geogenie.utils.data)

D

DataStructure (class in geogenie.utils.data_structure) DataStructureError debug (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) define_params() (geogenie.utils.data_structure.DataStructure method) delta (geogenie.utils.callbacks.EarlyStopping attribute) (geogenie.utils.loss.WeightedHuberLoss attribute) detect_clusters() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) detect_outliers() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) (geogenie.utils.spatial_data_processors.SpatialDataProcessor method)

detect_separator() (in module geogenie.utils.utils) device (geogenie.geogenie.GeoGenIE attribute) (geogenie.models.models.MLPRegressor attribute) (geogenie.plotting.plotting.PlotGenIE attribute) dropout_prop (geogenie.models.models.MLPRegressor attribute) dtype (geogenie.geogenie.GeoGenIE attribute) (geogenie.models.models.MLPRegressor attribute)

E

early_stop (geogenie.utils.callbacks.EarlyStopping attribute) EarlyStopping (class in geogenie.utils.callbacks) embed() (geogenie.utils.data_structure.DataStructure method) EmbeddingError epsilon (geogenie.utils.transformers.MCA attribute)

evaluate_and_save_results() (geogenie.geogenie.GeoGenIE method) EvaluateAction (class in geogenie.utils.argument_parser) extract_basemap_path_url() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) extract_best_params() (geogenie.geogenie.GeoGenIE method) extract_datasets() (geogenie.utils.data_structure.DataStructure method)

F

features (geogenie.utils.data.CustomDataset property) filetype (geogenie.plotting.plotting.PlotGenIE attribute) filter_and_detect() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) filter_gt() (geogenie.utils.data_structure.DataStructure method) find_gen_knn() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) find_geo_knn() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) find_optimal_k() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method)

find_optimal_nmf_components() (geogenie.utils.data_structure.DataStructure method) fit() (geogenie.utils.transformers.MCA method) (geogenie.utils.transformers.MinMaxScalerGeo method) fit_gamma_mle() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) fontsize (geogenie.plotting.plotting.PlotGenIE attribute) forward() (geogenie.models.models.MLPRegressor method) (geogenie.utils.loss.WeightedDRMSLoss method) (geogenie.utils.loss.WeightedHuberLoss method)

G

gamma_neg_log_likelihood() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) generate_unknowns() (geogenie.utils.data_structure.DataStructure method) genetic_data (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) genotypes (geogenie.geogenie.GeoGenIE attribute) geo_coords_is_valid() (in module geogenie.utils.utils) geodesic_distance() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) GeoGeneticOutlierDetector (class in geogenie.outliers.detect_outliers) geogenie module GeoGenIE (class in geogenie.geogenie) geogenie.cli module geogenie.geogenie module geogenie.models module geogenie.models.models module geogenie.outliers module geogenie.outliers.detect_outliers module geogenie.plotting module geogenie.plotting.plotting module geogenie.utils module

geogenie.utils.argument_parser module geogenie.utils.callbacks module geogenie.utils.data module geogenie.utils.data_structure module geogenie.utils.exceptions module geogenie.utils.logger module geogenie.utils.loss module geogenie.utils.scorers module geogenie.utils.spatial_data_processors module geogenie.utils.transformers module geogenie.utils.utils module geographic_data (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) get_all_stats() (geogenie.geogenie.GeoGenIE method) get_correlation_coef() (geogenie.geogenie.GeoGenIE method) get_iupac_dict() (in module geogenie.utils.utils) get_num_pca_comp() (geogenie.utils.data_structure.DataStructure method) get_sample_weights() (geogenie.utils.data_structure.DataStructure method) GPUUnavailableError

H

haversine_distance() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) (in module geogenie.utils.scorers)

haversine_error() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method)

I

impute_missing() (geogenie.utils.data_structure.DataStructure method) input_size (geogenie.models.models.MLPRegressor attribute) InvalidInputShapeError

InvalidSampleDataError inverse_transform() (geogenie.utils.transformers.MinMaxScalerGeo method) is_biallelic() (geogenie.utils.data_structure.DataStructure method)

K

kstest() (in module geogenie.utils.scorers)

L

labels (geogenie.utils.data.CustomDataset property) lat_range (geogenie.utils.transformers.MinMaxScalerGeo attribute) lle_reconstruction_scorer() (geogenie.utils.scorers.LocallyLinearEmbeddingWrapper static method) load_and_preprocess_data() (geogenie.utils.data_structure.DataStructure method) load_best_model() (geogenie.utils.callbacks.EarlyStopping method) load_best_params() (geogenie.geogenie.GeoGenIE method) load_config() (in module geogenie.utils.argument_parser) load_data() (geogenie.geogenie.GeoGenIE method)

LocallyLinearEmbeddingWrapper (class in geogenie.utils.scorers) locs (geogenie.geogenie.GeoGenIE attribute) logger (geogenie.geogenie.GeoGenIE attribute) (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) (geogenie.utils.callbacks.EarlyStopping attribute) (geogenie.utils.spatial_data_processors.SpatialDataProcessor attribute) (geogenie.utils.transformers.MCA attribute) (geogenie.utils.transformers.MinMaxScalerGeo attribute) lon_range (geogenie.utils.transformers.MinMaxScalerGeo attribute)

M

main() (in module geogenie.cli) make_optuna_plots() (geogenie.plotting.plotting.PlotGenIE method) make_unseen_predictions() (geogenie.geogenie.GeoGenIE method) map_alleles_to_iupac() (geogenie.utils.data_structure.DataStructure method) map_outliers_through_filters() (geogenie.utils.data_structure.DataStructure method) MCA (class in geogenie.utils.transformers) MinMaxScalerGeo (class in geogenie.utils.transformers) MLPRegressor (class in geogenie.models.models) module geogenie geogenie.cli geogenie.geogenie geogenie.models geogenie.models.models geogenie.outliers geogenie.outliers.detect_outliers geogenie.plotting geogenie.plotting.plotting geogenie.utils geogenie.utils.argument_parser geogenie.utils.callbacks geogenie.utils.data geogenie.utils.data_structure geogenie.utils.exceptions geogenie.utils.logger geogenie.utils.loss geogenie.utils.scorers geogenie.utils.spatial_data_processors geogenie.utils.transformers geogenie.utils.utils

multi_stage_outlier_knn() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method)

N

n_components (geogenie.utils.transformers.MCA attribute) n_features (geogenie.utils.data.CustomDataset property) n_iter (geogenie.utils.transformers.MCA attribute) n_jobs (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute)

n_labels (geogenie.utils.data.CustomDataset property) nearest_neighbor() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) nlayers (geogenie.models.models.MLPRegressor attribute) normalize_target() (geogenie.utils.data_structure.DataStructure method)

O

obp (geogenie.plotting.plotting.PlotGenIE property) one_hot (geogenie.utils.transformers.MCA attribute) optimize_parameters() (geogenie.geogenie.GeoGenIE method) outdir (geogenie.plotting.plotting.PlotGenIE property)

OutlierDetectionError output_dir (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) (geogenie.plotting.plotting.PlotGenIE attribute) (geogenie.utils.callbacks.EarlyStopping attribute) (geogenie.utils.spatial_data_processors.SpatialDataProcessor attribute)

P

params (geogenie.utils.data_structure.DataStructure property) patience (geogenie.utils.callbacks.EarlyStopping attribute) perform_bootstrap_training() (geogenie.geogenie.GeoGenIE method) perform_mca_and_select_components() (geogenie.utils.data_structure.DataStructure method) perform_standard_training() (geogenie.geogenie.GeoGenIE method) pfx (geogenie.plotting.plotting.PlotGenIE property) plot_bootstrap_aggregates() (geogenie.geogenie.GeoGenIE method) (geogenie.plotting.plotting.PlotGenIE method) plot_cumulative_error_distribution() (geogenie.plotting.plotting.PlotGenIE method) plot_data_distributions() (geogenie.plotting.plotting.PlotGenIE method) plot_error_distribution() (geogenie.plotting.plotting.PlotGenIE method) plot_gamma_dist() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) plot_gamma_distribution() (geogenie.plotting.plotting.PlotGenIE method) plot_geographic_error_distribution() (geogenie.plotting.plotting.PlotGenIE method) plot_history() (geogenie.plotting.plotting.PlotGenIE method) plot_mca_curve() (geogenie.plotting.plotting.PlotGenIE method) plot_nmf_error() (geogenie.plotting.plotting.PlotGenIE method)

plot_outliers() (geogenie.plotting.plotting.PlotGenIE method) plot_pca_curve() (geogenie.plotting.plotting.PlotGenIE method) plot_sample_with_density() (geogenie.plotting.plotting.PlotGenIE method) plot_scatter_samples_map() (geogenie.plotting.plotting.PlotGenIE method) plot_smote_bins() (geogenie.plotting.plotting.PlotGenIE method) plot_times() (geogenie.plotting.plotting.PlotGenIE method) plot_zscores() (geogenie.plotting.plotting.PlotGenIE method) PlotGenIE (class in geogenie.plotting.plotting) plotting (geogenie.geogenie.GeoGenIE attribute) (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) polynomial_regression_plot() (geogenie.plotting.plotting.PlotGenIE method) predict() (geogenie.utils.scorers.LocallyLinearEmbeddingWrapper method) predict_coords_knn() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) predict_locations() (geogenie.geogenie.GeoGenIE method) prefix (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) (geogenie.plotting.plotting.PlotGenIE attribute) (geogenie.utils.callbacks.EarlyStopping attribute) print_stats_to_logger() (geogenie.geogenie.GeoGenIE method)

R

radius (geogenie.utils.loss.WeightedDRMSLoss attribute) random_state (geogenie.utils.transformers.MCA attribute) read_csv_with_dynamic_sep() (in module geogenie.utils.utils)

rescale_statistic() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) ResourceAllocationError run_multistage() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) run_outlier_detection() (geogenie.utils.data_structure.DataStructure method)

S

sample_data (geogenie.geogenie.GeoGenIE attribute) sample_ids (geogenie.utils.data.CustomDataset property) sample_weights (geogenie.utils.data.CustomDataset property) SampleOrderingError samples (geogenie.geogenie.GeoGenIE attribute) save_checkpoint() (geogenie.utils.callbacks.EarlyStopping method) save_execution_times() (in module geogenie.geogenie) save_model() (geogenie.geogenie.GeoGenIE method) scale_max (geogenie.utils.transformers.MinMaxScalerGeo attribute) scale_min (geogenie.utils.transformers.MinMaxScalerGeo attribute) search_nn_optk() (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector method) seed (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) select_optimal_components() (geogenie.utils.data_structure.DataStructure method)

seqmodel (geogenie.models.models.MLPRegressor attribute) set_inverse_transform_request() (geogenie.utils.transformers.MinMaxScalerGeo method) setup_index_masks() (geogenie.utils.data_structure.DataStructure method) setup_logger() (in module geogenie.utils.logger) setup_parser() (in module geogenie.utils.argument_parser) show_plots (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) (geogenie.plotting.plotting.PlotGenIE attribute) smoothing_factor (geogenie.utils.loss.WeightedHuberLoss attribute) snps_to_012() (geogenie.utils.data_structure.DataStructure method) sort_samples() (geogenie.utils.data_structure.DataStructure method) SpatialDataProcessor (class in geogenie.utils.spatial_data_processors) spherical_mean() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) split_train_test() (geogenie.utils.data_structure.DataStructure method)

T

tensors (geogenie.utils.data.CustomDataset attribute) test_step() (geogenie.geogenie.GeoGenIE method) time_limit() (in module geogenie.utils.utils) TimeoutException timer() (in module geogenie.geogenie) tmpdir (geogenie.utils.spatial_data_processors.SpatialDataProcessor attribute) to_geopandas() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) to_numpy() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method)

to_pandas() (geogenie.utils.spatial_data_processors.SpatialDataProcessor method) total_execution_time_decorator() (geogenie.geogenie.GeoGenIE method) train_model() (geogenie.geogenie.GeoGenIE method) train_rf() (geogenie.geogenie.GeoGenIE method) train_step() (geogenie.geogenie.GeoGenIE method) train_test_predict() (geogenie.geogenie.GeoGenIE method) transform() (geogenie.utils.transformers.MCA method) (geogenie.utils.transformers.MinMaxScalerGeo method) trial (geogenie.utils.callbacks.EarlyStopping attribute)

U

update_config_labels() (geogenie.plotting.plotting.PlotGenIE method)

update_metric_labels() (geogenie.plotting.plotting.PlotGenIE method) url (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute)

V

val_loss_min (geogenie.utils.callbacks.EarlyStopping attribute) validate_colorscale() (in module geogenie.utils.argument_parser) validate_dtype() (in module geogenie.utils.argument_parser) validate_embeddings() (in module geogenie.utils.argument_parser) validate_feature_target_len() (geogenie.utils.data_structure.DataStructure method) validate_gb_params() (in module geogenie.utils.argument_parser) validate_gpu_number() (in module geogenie.utils.argument_parser) validate_inputs() (in module geogenie.utils.argument_parser) validate_is_numpy() (in module geogenie.utils.utils) validate_lower_str() (in module geogenie.utils.argument_parser) validate_max_neighbors() (in module geogenie.utils.argument_parser) validate_n_jobs() (in module geogenie.utils.argument_parser)

validate_positive_float() (in module geogenie.utils.argument_parser) validate_positive_int() (in module geogenie.utils.argument_parser) validate_seed() (in module geogenie.utils.argument_parser) validate_significance_levels() (in module geogenie.utils.argument_parser) validate_smote() (in module geogenie.utils.argument_parser) validate_split() (in module geogenie.utils.argument_parser) validate_str2list() (in module geogenie.utils.argument_parser) validate_verbosity() (in module geogenie.utils.argument_parser) validate_weighted_opts() (in module geogenie.utils.argument_parser) verbose (geogenie.outliers.detect_outliers.GeoGeneticOutlierDetector attribute) (geogenie.utils.callbacks.EarlyStopping attribute) visualize_oversample_clusters() (geogenie.plotting.plotting.PlotGenIE method) visualize_oversampling() (geogenie.geogenie.GeoGenIE method)

W

weighted_rmse_loss() (in module geogenie.utils.loss) WeightedDRMSLoss (class in geogenie.utils.loss)

WeightedHuberLoss (class in geogenie.utils.loss) width (geogenie.models.models.MLPRegressor attribute) write_pred_locations() (geogenie.geogenie.GeoGenIE method)