End-to-End Automated Machine Learning and Model Evaluation

Documentation for package ‘familiar’ version 1.4.6

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familiar: Fully Automated Machine Learning with Interpretable Analysis of Results

-- A --

aggregate_vimp_table	Aggregate variable importance from multiple variable importance objects.
aggregate_vimp_table-method	Aggregate variable importance from multiple variable importance objects.
as_data_object	Creates a valid data object from input data.
as_data_object-method	Creates a valid data object from input data.
as_familiar_collection	Conversion to familiarCollection object.
as_familiar_collection-method	Conversion to familiarCollection object.
as_familiar_data	Conversion to familiarData object.
as_familiar_data-method	Conversion to familiarData object.
as_familiar_ensemble	Conversion to familiarEnsemble object.
as_familiar_ensemble-method	Conversion to familiarEnsemble object.

-- C --

coef	Extract model coefficients
coef-method	Extract model coefficients

-- D --

dataObject-class

Data object

-- E --

experimentData-class	Experiment data
export_all	Extract and export all data.
export_all-method	Extract and export all data.
export_auc_data	Extract and export ROC and Precision-Recall curves.
export_auc_data-method	Extract and export ROC and Precision-Recall curves.
export_calibration_data	Extract and export calibration and goodness-of-fit tests.
export_calibration_data-method	Extract and export calibration and goodness-of-fit tests.
export_calibration_info	Extract and export calibration information.
export_calibration_info-method	Extract and export calibration information.
export_confusion_matrix_data	Extract and export confusion matrices.
export_confusion_matrix_data-method	Extract and export confusion matrices.
export_decision_curve_analysis_data	Extract and export decision curve analysis data.
export_decision_curve_analysis_data-method	Extract and export decision curve analysis data.
export_feature_expressions	Extract and export feature expressions.
export_feature_expressions-method	Extract and export feature expressions.
export_feature_similarity	Extract and export mutual correlation between features.
export_feature_similarity-method	Extract and export mutual correlation between features.
export_fs_vimp	Extract and export feature selection variable importance.
export_fs_vimp-method	Extract and export feature selection variable importance.
export_hyperparameters	Extract and export model hyperparameters.
export_hyperparameters-method	Extract and export model hyperparameters.
export_ice_data	Extract and export individual conditional expectation data.
export_ice_data-method	Extract and export individual conditional expectation data.
export_model_performance	Extract and export metrics for model performance.
export_model_performance-method	Extract and export metrics for model performance.
export_model_vimp	Extract and export model-based variable importance.
export_model_vimp-method	Extract and export model-based variable importance.
export_partial_dependence_data	Extract and export partial dependence data.
export_partial_dependence_data-method	Extract and export partial dependence data.
export_permutation_vimp	Extract and export permutation variable importance.
export_permutation_vimp-method	Extract and export permutation variable importance.
export_prediction_data	Extract and export predicted values.
export_prediction_data-method	Extract and export predicted values.
export_risk_stratification_data	Extract and export sample risk group stratification and associated tests.
export_risk_stratification_data-method	Extract and export sample risk group stratification and associated tests.
export_risk_stratification_info	Extract and export cut-off values for risk group stratification.
export_risk_stratification_info-method	Extract and export cut-off values for risk group stratification.
export_sample_similarity	Extract and export mutual correlation between features.
export_sample_similarity-method	Extract and export mutual correlation between features.
export_univariate_analysis_data	Extract and export univariate analysis data of features.
export_univariate_analysis_data-method	Extract and export univariate analysis data of features.

-- F --

familiar	familiar: Fully Automated Machine Learning with Interpretable Analysis of Results
familiarCollection-class	Collection of familiar data.
familiarData-class	Dataset obtained after evaluating models on a dataset.
familiarDataElement-class	Data container for evaluation data.
familiarEnsemble-class	Ensemble of familiar models.
familiarHyperparameterLearner-class	Hyperparameter learner.
familiarMetric-class	Model performance metric.
familiarModel-class	Familiar model.
familiarNoveltyDetector-class	Novelty detector.
familiarVimpMethod-class	Variable importance method object.
featureInfo-class	Feature information object.
featureInfoParameters-class	Feature information parameters object.

-- G --

get_class_names	Get outcome class labels
get_class_names-method	Get outcome class labels
get_data_set_names	Get current name of datasets
get_data_set_names-method	Get current name of datasets
get_feature_names	Get current feature labels
get_feature_names-method	Get current feature labels
get_fs_method_names	Get current feature selection method name labels
get_fs_method_names-method	Get current feature selection method name labels
get_learner_names	Get current learner name labels
get_learner_names-method	Get current learner name labels
get_risk_group_names	Get current risk group labels
get_risk_group_names-method	Get current risk group labels
get_vimp_table	Extract variable importance table.
get_vimp_table-method	Extract variable importance table.
get_xml_config	Create an empty xml configuration file

-- O --

outcomeInfo-class

Outcome information object.

-- P --

plot_auc_precision_recall_curve	Plot the precision-recall curve.
plot_auc_precision_recall_curve-method	Plot the precision-recall curve.
plot_auc_roc_curve	Plot the receiver operating characteristic curve.
plot_auc_roc_curve-method	Plot the receiver operating characteristic curve.
plot_calibration_data	Plot calibration figures.
plot_calibration_data-method	Plot calibration figures.
plot_confusion_matrix	Plot confusion matrix.
plot_confusion_matrix-method	Plot confusion matrix.
plot_decision_curve	Plot decision curves.
plot_decision_curve-method	Plot decision curves.
plot_feature_selection_occurrence	Plot variable importance scores of features during feature selection or after training a model.
plot_feature_selection_variable_importance	Plot variable importance scores of features during feature selection or after training a model.
plot_feature_similarity	Plot heatmaps for pairwise similarity between features.
plot_feature_similarity-method	Plot heatmaps for pairwise similarity between features.
plot_ice	Plot individual conditional expectation plots.
plot_ice-method	Plot individual conditional expectation plots.
plot_kaplan_meier	Plot Kaplan-Meier survival curves.
plot_kaplan_meier-method	Plot Kaplan-Meier survival curves.
plot_model_performance	Plot model performance.
plot_model_performance-method	Plot model performance.
plot_model_signature_occurrence	Plot variable importance scores of features during feature selection or after training a model.
plot_model_signature_variable_importance	Plot variable importance scores of features during feature selection or after training a model.
plot_pd	Plot partial dependence.
plot_pd-method	Plot partial dependence.
plot_permutation_variable_importance	Plot permutation variable importance.
plot_permutation_variable_importance-method	Plot permutation variable importance.
plot_sample_clustering	Plot heatmaps for pairwise similarity between features.
plot_sample_clustering-method	Plot heatmaps for pairwise similarity between features.
plot_univariate_importance	Plot univariate importance.
plot_univariate_importance-method	Plot univariate importance.
plot_variable_importance	Plot variable importance scores of features during feature selection or after training a model.
plot_variable_importance-method	Plot variable importance scores of features during feature selection or after training a model.
precompute_data_assignment	Pre-compute data assignment
precompute_feature_info	Pre-compute feature information
precompute_vimp	Pre-compute variable importance
predict	Model predictions for familiar models and model ensembles
predict-method	Model predictions for familiar models and model ensembles

-- S --

set_class_names	Rename outcome classes for plotting and export
set_class_names-method	Rename outcome classes for plotting and export
set_data_set_names	Name datasets for plotting and export
set_data_set_names-method	Name datasets for plotting and export
set_feature_names	Rename features for plotting and export
set_feature_names-method	Rename features for plotting and export
set_fs_method_names	Rename feature selection methods for plotting and export
set_fs_method_names-method	Rename feature selection methods for plotting and export
set_learner_names	Rename learners for plotting and export
set_learner_names-method	Rename learners for plotting and export
set_risk_group_names	Rename risk groups for plotting and export
set_risk_group_names-method	Rename risk groups for plotting and export
summary	Model summaries
summary-method	Model summaries
summon_familiar	Perform end-to-end machine learning and data analysis

-- T --

theme_familiar	Familiar ggplot2 theme
train_familiar	Create models using end-to-end machine learning

-- U --

update_model_dir_path	Updates model directory path for ensemble objects.
update_model_dir_path-method	Updates model directory path for ensemble objects.
update_object	Update familiar S4 objects to the most recent version.
update_object-method	Update familiar S4 objects to the most recent version.

-- V --

vcov	Calculate variance-covariance matrix for a model
vcov-method	Calculate variance-covariance matrix for a model
vimpTable-class	Variable importance table

-- W --

waiver

Create a waiver object