Index

Symbols

{{ obj.name }}{% if obj.args %}({{ obj.args|join(',') }}){% endif %}() (class)

_

__author__ (in module easypheno)

__credits__ (in module easypheno) __version__ (in module easypheno)

A

append_index_file() (in module easypheno.preprocess.raw_data_functions)

apply_final_model() (in module easypheno.postprocess.model_reuse)

B

BaseModel (class in easypheno.model._base_model) Bayes (class in easypheno.model._bayesian_linreg) Bayes_R (class in easypheno.model._bayesfromR) BayesA (class in easypheno.model.bayesAfromR)

BayesB (class in easypheno.model.bayesBfromR) BayesC (class in easypheno.model.bayesCfromR) BayesRidge (class in easypheno.model.bayes_ridge) Blup (class in easypheno.model.blup)

C

calc_runtime_stats() (easypheno.optimization.optuna_optim.OptunaOptim method) check_all_specified_arguments() (in module easypheno.utils.check_functions) check_and_load_phenotype_matrix() (in module easypheno.preprocess.raw_data_functions) check_and_save_filtered_snp_ids() (easypheno.preprocess.base_dataset.Dataset method) check_datasplit() (easypheno.preprocess.base_dataset.Dataset method) check_datasplit_user_input() (in module easypheno.preprocess.raw_data_functions) check_duplicate_samples() (in module easypheno.preprocess.raw_data_functions) check_encoding_of_genotype() (in module easypheno.preprocess.encoding_functions) check_exist_directories() (in module easypheno.utils.check_functions) check_exist_files() (in module easypheno.utils.check_functions) check_genotype_binary_plink_file() (in module easypheno.preprocess.raw_data_functions) check_genotype_csv_file() (in module easypheno.preprocess.raw_data_functions) check_genotype_h5_file() (in module easypheno.preprocess.raw_data_functions) check_genotype_plink_file() (in module easypheno.preprocess.raw_data_functions)

check_genotype_shape() (in module easypheno.preprocess.raw_data_functions) check_index_file() (in module easypheno.preprocess.raw_data_functions) check_params_for_duplicate() (easypheno.optimization.optuna_optim.OptunaOptim method) check_sim_id() (in module easypheno.simulate.synthetic_phenotypes) check_train_test_splits() (in module easypheno.preprocess.raw_data_functions) check_transform_format_genotype_matrix() (in module easypheno.preprocess.raw_data_functions) clean_up_after_exception() (easypheno.optimization.optuna_optim.OptunaOptim method) Cnn (class in easypheno.model.cnn) common_hyperparams() (easypheno.model._tensorflow_model.TensorflowModel static method) (easypheno.model._torch_model.TorchModel static method) compare_snp_id_vectors() (in module easypheno.utils.check_functions) create_genotype_h5_file() (in module easypheno.preprocess.raw_data_functions) create_index_file() (in module easypheno.preprocess.raw_data_functions) create_maf_filter() (in module easypheno.preprocess.raw_data_functions) create_new_study() (easypheno.optimization.optuna_optim.OptunaOptim method)

D

Dataset (class in easypheno.preprocess.base_dataset) define_hyperparams_to_tune() (easypheno.model._base_model.BaseModel method) (easypheno.model._template_sklearn_model.TemplateSklearnModel method) (easypheno.model._template_tensorflow_model.TemplateTensorflowModel method) (easypheno.model._template_torch_model.TemplateTorchModel method) (easypheno.model.cnn.Cnn method) (easypheno.model.elasticnet.ElasticNet method) (easypheno.model.linearregression.LinearRegression method) (easypheno.model.localcnn.LocalCnn method) (easypheno.model.mlp.Mlp method) (easypheno.model.randomforest.RandomForest method) (easypheno.model.svm.SupportVectorMachine method) (easypheno.model.xgboost.XgBoost method)

define_model() (easypheno.model._base_model.BaseModel method) (easypheno.model._template_sklearn_model.TemplateSklearnModel method) (easypheno.model._template_tensorflow_model.TemplateTensorflowModel method) (easypheno.model._template_torch_model.TemplateTorchModel method) (easypheno.model.cnn.Cnn method) (easypheno.model.elasticnet.ElasticNet method) (easypheno.model.linearregression.LinearRegression method) (easypheno.model.localcnn.LocalCnn method) (easypheno.model.mlp.Mlp method) (easypheno.model.randomforest.RandomForest method) (easypheno.model.svm.SupportVectorMachine method) (easypheno.model.xgboost.XgBoost method)

E

easypheno module easypheno.evaluation module easypheno.evaluation.eval_metrics module easypheno.model module easypheno.model._base_model module easypheno.model._bayesfromR module easypheno.model._bayesian_linreg module easypheno.model._model_functions module easypheno.model._param_free_base_model module easypheno.model._sklearn_model module easypheno.model._template_sklearn_model module easypheno.model._template_tensorflow_model module easypheno.model._template_torch_model module easypheno.model._tensorflow_model module easypheno.model._torch_model module easypheno.model.bayes_ridge module easypheno.model.bayesAfromR module easypheno.model.bayesBfromR module easypheno.model.bayesCfromR module easypheno.model.blup module easypheno.model.cnn module easypheno.model.elasticnet module easypheno.model.linearregression module easypheno.model.localcnn module

easypheno.model.mlp module easypheno.model.randomforest module easypheno.model.svm module easypheno.model.xgboost module easypheno.optim_pipeline module easypheno.optimization module easypheno.optimization.optuna_optim module easypheno.optimization.paramfree_fitting module easypheno.postprocess module easypheno.postprocess.feat_importance module easypheno.postprocess.model_reuse module easypheno.postprocess.results_analysis module easypheno.preprocess module easypheno.preprocess.base_dataset module easypheno.preprocess.encoding_functions module easypheno.preprocess.raw_data_functions module easypheno.simulate module easypheno.simulate.results_analysis_synthetic_data module easypheno.simulate.synthetic_phenotypes module easypheno.utils module easypheno.utils.check_functions module easypheno.utils.helper_functions module easypheno.utils.print_functions module ElasticNet (class in easypheno.model.elasticnet) encode_genotype() (in module easypheno.preprocess.encoding_functions)

F

featimps_vs_simulation() (in module easypheno.simulate.results_analysis_synthetic_data) filter_duplicate_snps() (easypheno.preprocess.base_dataset.Dataset method) filter_duplicates() (in module easypheno.simulate.synthetic_phenotypes) filter_non_informative_snps() (in module easypheno.preprocess.raw_data_functions)

fit() (easypheno.model._bayesfromR.Bayes_R method) (easypheno.model._bayesian_linreg.Bayes method) (easypheno.model._param_free_base_model.ParamFreeBaseModel method) (easypheno.model.blup.Blup method)

G

gather_feature_importances() (in module easypheno.simulate.results_analysis_synthetic_data) gather_sim_configs() (in module easypheno.simulate.results_analysis_synthetic_data) generate_results_on_test() (easypheno.optimization.optuna_optim.OptunaOptim method) generate_scatterplots_featimps_vs_simulation() (in module easypheno.simulate.results_analysis_synthetic_data) genotype_phenotype_matching() (in module easypheno.preprocess.raw_data_functions) get_additive_encoding() (in module easypheno.preprocess.encoding_functions) get_all_files() (in module easypheno.utils.helper_functions) get_all_files_with_suffix() (in module easypheno.utils.helper_functions) get_all_subdirectories_non_recursive() (in module easypheno.utils.helper_functions) get_base_encoding() (in module easypheno.preprocess.encoding_functions) get_dataloader() (easypheno.model._tensorflow_model.TensorflowModel method) (easypheno.model._torch_model.TorchModel method) get_datasplit_config_info_for_resultfolder() (in module easypheno.utils.helper_functions) get_encoding() (in module easypheno.preprocess.encoding_functions)

get_evaluation_report() (in module easypheno.evaluation.eval_metrics) get_feature_importance() (easypheno.optimization.optuna_optim.OptunaOptim method) (easypheno.optimization.paramfree_fitting.ParamFreeFitting method) get_index_file_name() (easypheno.preprocess.base_dataset.Dataset static method) get_list_of_encodings() (in module easypheno.preprocess.encoding_functions) get_list_of_implemented_models() (in module easypheno.utils.helper_functions) get_loss() (easypheno.model._torch_model.TorchModel method) get_mapping_name_to_class() (in module easypheno.utils.helper_functions) get_matched_data() (in module easypheno.preprocess.raw_data_functions) get_minor_allele_freq() (in module easypheno.preprocess.raw_data_functions) get_onehot_encoding() (in module easypheno.preprocess.encoding_functions) get_simulation() (in module easypheno.simulate.synthetic_phenotypes) get_statistics_featimps_vs_simulation() (in module easypheno.simulate.results_analysis_synthetic_data) get_subpath_for_datasplit() (in module easypheno.utils.helper_functions) get_torch_object_for_string() (easypheno.model._torch_model.TorchModel static method)

L

LinearRegression (class in easypheno.model.linearregression) load_datasplit_indices() (easypheno.preprocess.base_dataset.Dataset method) load_match_raw_data() (easypheno.preprocess.base_dataset.Dataset method)

load_model() (in module easypheno.model._model_functions) load_retrain_model() (in module easypheno.model._model_functions) LocalCnn (class in easypheno.model.localcnn)

M

maf_filter_raw_data() (easypheno.preprocess.base_dataset.Dataset method) make_bins() (in module easypheno.preprocess.raw_data_functions) make_nested_cv() (in module easypheno.preprocess.raw_data_functions) make_stratified_cv() (in module easypheno.preprocess.raw_data_functions) make_train_test_split() (in module easypheno.preprocess.raw_data_functions) Mlp (class in easypheno.model.mlp) module easypheno easypheno.evaluation easypheno.evaluation.eval_metrics easypheno.model easypheno.model._base_model easypheno.model._bayesfromR easypheno.model._bayesian_linreg easypheno.model._model_functions easypheno.model._param_free_base_model easypheno.model._sklearn_model easypheno.model._template_sklearn_model easypheno.model._template_tensorflow_model easypheno.model._template_torch_model easypheno.model._tensorflow_model easypheno.model._torch_model easypheno.model.bayes_ridge easypheno.model.bayesAfromR easypheno.model.bayesBfromR easypheno.model.bayesCfromR easypheno.model.blup easypheno.model.cnn easypheno.model.elasticnet easypheno.model.linearregression easypheno.model.localcnn easypheno.model.mlp easypheno.model.randomforest easypheno.model.svm easypheno.model.xgboost easypheno.optim_pipeline easypheno.optimization easypheno.optimization.optuna_optim easypheno.optimization.paramfree_fitting easypheno.postprocess easypheno.postprocess.feat_importance easypheno.postprocess.model_reuse easypheno.postprocess.results_analysis easypheno.preprocess easypheno.preprocess.base_dataset easypheno.preprocess.encoding_functions easypheno.preprocess.raw_data_functions easypheno.simulate easypheno.simulate.results_analysis_synthetic_data easypheno.simulate.synthetic_phenotypes easypheno.utils easypheno.utils.check_functions easypheno.utils.helper_functions easypheno.utils.print_functions

O

objective() (easypheno.optimization.optuna_optim.OptunaOptim method)

OptunaOptim (class in easypheno.optimization.optuna_optim)

P

ParamFreeBaseModel (class in easypheno.model._param_free_base_model) ParamFreeFitting (class in easypheno.optimization.paramfree_fitting) plot_heatmap_results() (in module easypheno.postprocess.results_analysis) possible_encodings (easypheno.model._base_model.BaseModel property) (easypheno.model._bayesfromR.Bayes_R attribute) (easypheno.model._bayesian_linreg.Bayes attribute) (easypheno.model._param_free_base_model.ParamFreeBaseModel property) (easypheno.model._template_sklearn_model.TemplateSklearnModel attribute) (easypheno.model._template_tensorflow_model.TemplateTensorflowModel attribute) (easypheno.model._template_torch_model.TemplateTorchModel attribute) (easypheno.model.blup.Blup attribute) (easypheno.model.cnn.Cnn attribute) (easypheno.model.elasticnet.ElasticNet attribute) (easypheno.model.linearregression.LinearRegression attribute) (easypheno.model.localcnn.LocalCnn attribute) (easypheno.model.mlp.Mlp attribute) (easypheno.model.randomforest.RandomForest attribute) (easypheno.model.svm.SupportVectorMachine attribute) (easypheno.model.xgboost.XgBoost attribute)

post_generate_feature_importances() (in module easypheno.postprocess.feat_importance) predict() (easypheno.model._base_model.BaseModel method) (easypheno.model._bayesfromR.Bayes_R method) (easypheno.model._bayesian_linreg.Bayes method) (easypheno.model._param_free_base_model.ParamFreeBaseModel method) (easypheno.model._sklearn_model.SklearnModel method) (easypheno.model._tensorflow_model.TensorflowModel method) (easypheno.model._torch_model.TorchModel method) (easypheno.model.blup.Blup method) prepare_data_files() (in module easypheno.preprocess.raw_data_functions) print_config_info() (in module easypheno.utils.print_functions) probability_model() (easypheno.model._bayesian_linreg.Bayes method) (easypheno.model.bayes_ridge.BayesRidge method)

R

RandomForest (class in easypheno.model.randomforest) reml() (easypheno.model.blup.Blup static method) result_string_to_dictionary() (in module easypheno.postprocess.results_analysis) retrain() (easypheno.model._base_model.BaseModel method) (easypheno.model._sklearn_model.SklearnModel method) (easypheno.model._tensorflow_model.TensorflowModel method) (easypheno.model._torch_model.TorchModel method)

retrain_model_with_results_file() (in module easypheno.model._model_functions) retrain_on_new_data() (in module easypheno.postprocess.model_reuse) run() (in module easypheno.optim_pipeline) run_fitting() (easypheno.optimization.paramfree_fitting.ParamFreeFitting method) run_optuna_optimization() (easypheno.optimization.optuna_optim.OptunaOptim method)

S

save_all_data_files() (in module easypheno.preprocess.raw_data_functions) save_model() (easypheno.model._base_model.BaseModel method) (easypheno.model._param_free_base_model.ParamFreeBaseModel method) (easypheno.model._tensorflow_model.TensorflowModel method) save_model_overview_dict() (in module easypheno.utils.helper_functions) save_sim_overview() (in module easypheno.simulate.synthetic_phenotypes) save_simulation() (in module easypheno.simulate.synthetic_phenotypes) set_all_seeds() (in module easypheno.utils.helper_functions) SklearnModel (class in easypheno.model._sklearn_model) sort_models_by_encoding() (in module easypheno.utils.helper_functions) standard_encoding (easypheno.model._base_model.BaseModel property) (easypheno.model._bayesfromR.Bayes_R attribute) (easypheno.model._bayesian_linreg.Bayes attribute) (easypheno.model._param_free_base_model.ParamFreeBaseModel property) (easypheno.model._template_sklearn_model.TemplateSklearnModel attribute) (easypheno.model._template_tensorflow_model.TemplateTensorflowModel attribute) (easypheno.model._template_torch_model.TemplateTorchModel attribute) (easypheno.model.blup.Blup attribute) (easypheno.model.cnn.Cnn attribute) (easypheno.model.elasticnet.ElasticNet attribute) (easypheno.model.linearregression.LinearRegression attribute) (easypheno.model.localcnn.LocalCnn attribute) (easypheno.model.mlp.Mlp attribute) (easypheno.model.randomforest.RandomForest attribute) (easypheno.model.svm.SupportVectorMachine attribute) (easypheno.model.xgboost.XgBoost attribute)

suggest_all_hyperparams_to_optuna() (easypheno.model._base_model.BaseModel method) suggest_hyperparam_to_optuna() (easypheno.model._base_model.BaseModel method) summarize_results_per_phenotype_and_datasplit() (in module easypheno.postprocess.results_analysis) SupportVectorMachine (class in easypheno.model.svm)

T

TemplateSklearnModel (class in easypheno.model._template_sklearn_model) TemplateTensorflowModel (class in easypheno.model._template_tensorflow_model) TemplateTorchModel (class in easypheno.model._template_torch_model) TensorflowModel (class in easypheno.model._tensorflow_model) test_likely_categorical() (in module easypheno.utils.helper_functions)

TorchModel (class in easypheno.model._torch_model) train_one_epoch() (easypheno.model._torch_model.TorchModel method) train_val_loop() (easypheno.model._base_model.BaseModel method) (easypheno.model._sklearn_model.SklearnModel method) (easypheno.model._tensorflow_model.TensorflowModel method) (easypheno.model._torch_model.TorchModel method)

V

validate_one_epoch() (easypheno.model._torch_model.TorchModel method)

W

write_runtime_csv() (easypheno.optimization.optuna_optim.OptunaOptim method) (easypheno.optimization.paramfree_fitting.ParamFreeFitting method)

X

XgBoost (class in easypheno.model.xgboost)