CARRoT: R-package for predictive modelling by means of regression, adjusted for multiple regularisation methods

Abstract

We present an R-package for predictive modelling, CARRoT (Cross-validation, Accuracy, Regression, Rule of Ten). CARRoT is a tool for initial exploratory analysis of the data, which performs exhaustive search for a regression model yielding the best predictive power with heuristic ‘rules of thumb’ and expert knowledge as regularization parameters. It uses multiple hold-outs in order to internally validate the model. The package allows to take into account multiple factors such as collinearity of the predictors, event per variable rules (EPVs) and R-squared statistics during the model selection. In addition, other constraints, such as forcing specific terms and restricting complexity of the predictive models can be used. The package allows taking pairwise and three-way interactions between variables into account as well. These candidate models are then ranked by predictive power, which is assessed via multiple hold-out procedures and can be parallelised in order to reduce the computational time. Models which exhibited the highest average predictive power over all hold-outs are returned. This is quantified as absolute and relative error in case of continuous outcomes, accuracy and AUROC values in case of categorical outcomes. In this paper we briefly present statistical framework of the package and discuss the complexity of the underlying algorithm. Moreover, using CARRoT and a number of datasets available in R we provide comparison of different model selection techniques: based on EPVs alone, on EPVs and R-squared statistics, on lasso regression, on including only statistically significant predictors and on stepwise forward selection technique.