familiarCollection-class {familiar} | R Documentation |
Collection of familiar data.
Description
A familiarCollection object aggregates data from one or more familiarData objects.
Slots
name
Name of the collection.
data_sets
Name of the individual underlying datasets.
outcome_type
Outcome type for which the collection was created.
outcome_info
Outcome information object, which contains information concerning the outcome, such as class levels.
fs_vimp
Variable importance data collected by feature selection methods.
model_vimp
Variable importance data collected from model-specific algorithms implemented by models created by familiar.
permutation_vimp
Data collected for permutation variable importance.
hyperparameters
Hyperparameters collected from created models.
hyperparameter_data
Additional data concerning hyperparameters. This is currently not used yet.
required_features
The set of features required for complete reproduction, i.e. with imputation.
model_features
The set of features that are required for using the model, but without imputation.
learner
Learning algorithm(s) used for data in the collection.
fs_method
Feature selection method(s) used for data in the collection.
prediction_data
Model predictions for the data in the collection.
confusion_matrix
Confusion matrix information for the data in the collection.
decision_curve_data
Decision curve analysis data for the data in the collection.
calibration_info
Calibration information, e.g. baseline survival in the development cohort.
calibration_data
Model calibration data collected from data in the collection.
model_performance
Collection of model performance data for data in the collection.
km_info
Information concerning risk-stratification cut-off values for data in the collection.
km_data
Kaplan-Meier survival data for data in the collection.
auc_data
AUC-ROC and AUC-PR data for data in the collection.
ice_data
Individual conditional expectation data for data in the collection. Partial dependence data are computed on the fly from these data.
univariate_analysis
Univariate analysis results of data in the collection.
feature_expressions
Feature expression values for data in the collection.
feature_similarity
Feature similarity information for data in the collection.
sample_similarity
Sample similarity information for data in the collection.
data_set_labels
Labels for the different datasets in the collection. See
get_data_set_names
andset_data_set_names
.learner_labels
Labels for the different learning algorithms used to create the collection. See
get_learner_names
andset_learner_names
.fs_method_labels
Labels for the different feature selection methods used to create the collection. See
get_fs_method_names
andset_fs_method_names
.feature_labels
Labels for the features in this collection. See
get_feature_names
andset_feature_names
.km_group_labels
Labels for the risk strata in this collection. See
get_risk_group_names
andset_risk_group_names
.class_labels
Labels of the response variable. See
get_class_names
andset_class_names
.project_id
Identifier of the project that generated this collection.
familiar_version
Version of the familiar package.
familiarCollection objects collect data from one or more familiarData objects. This objects are important, as all plotting and export functions use it. The fact that one can supply familiarModel, familiarEnsemble and familiarData objects as arguments for these methods, is because familiar internally converts these into familiarCollection objects prior to executing the method.