# End-to-End Automated Machine Learning and Model Evaluation

## Documentation for package ‘familiar’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G O P S T U V W

familiar-package | 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.
as_prediction_table | Convert to prediction table object

## -- C --

coef | Extract model coefficients
coef-method | Extract model coefficients

## -- D --

dataObject-class | Data object
delayedDataObject-class | Data object with delayed loading

## -- 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_shap | Extract and export individual conditional expectation data.
export_shap-method | Extract and export individual conditional expectation data.
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_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_method_names | Get current variable importance method name labels
get_vimp_method_names-method | Get current variable importance method name 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_shap_dependence | Create SHAP dependence plot.
plot_shap_dependence-method | Create SHAP dependence plot.
plot_shap_force | Create SHAP force plot
plot_shap_force-method | Create SHAP force plot
plot_shap_summary | Plot SHAP summary.
plot_shap_summary-method | Plot SHAP summary.
plot_shap_waterfall | Create SHAP waterfall plot
plot_shap_waterfall-method | Create SHAP waterfall plot
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_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
set_vimp_method_names | Rename variable importance methods for plotting and export
set_vimp_method_names-method | Rename variable importance methods 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