ICARE: An R package to build, validate and apply absolute risk models

Parichoy Pal Choudhury, Paige Maas, Amber Wilcox, William Wheeler, Mark Brook, David Check, Montserrat Garcia-Closas, Nilanjan Chatterjee

Research output: Contribution to journalArticle

Abstract

This report describes an R package, called the Individualized Coherent Absolute Risk Estimator (iCARE) tool, that allows researchers to build and evaluate models for absolute risk and apply them to estimate an individual's risk of developing disease during a specified time interval based on a set of user defined input parameters. An attractive feature of the software is that it gives users flexibility to update models rapidly based on new knowledge on risk factors and tailor models to different populations by specifying three input arguments: a model for relative risk, an age-specific disease incidence rate and the distribution of risk factors for the population of interest. The tool can handle missing information on risk factors for individuals for whom risks are to be predicted using a coherent approach where all estimates are derived from a single model after appropriate model averaging. The software allows single nucleotide polymorphisms (SNPs) to be incorporated into the model using published odds ratios and allele frequencies. The validation component of the software implements the methods for evaluation of model calibration, discrimination and risk-stratification based on independent validation datasets. We provide an illustration of the utility of iCARE for building, validating and applying absolute risk models using breast cancer as an example.

Original languageEnglish (US)
Article numbere0228198
JournalPloS one
Volume15
Issue number2
DOIs
StatePublished - Jan 1 2020

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Choudhury, P. P., Maas, P., Wilcox, A., Wheeler, W., Brook, M., Check, D., Garcia-Closas, M., & Chatterjee, N. (2020). ICARE: An R package to build, validate and apply absolute risk models. PloS one, 15(2), [e0228198]. https://doi.org/10.1371/journal.pone.0228198