TY - JOUR
T1 - ICARE
T2 - An R package to build, validate and apply absolute risk models
AU - Choudhury, Parichoy Pal
AU - Maas, Paige
AU - Wilcox, Amber
AU - Wheeler, William
AU - Brook, Mark
AU - Check, David
AU - Garcia-Closas, Montserrat
AU - Chatterjee, Nilanjan
N1 - Publisher Copyright:
Copyright: © This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
PY - 2020/2/1
Y1 - 2020/2/1
N2 - 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.
AB - 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.
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U2 - 10.1371/journal.pone.0228198
DO - 10.1371/journal.pone.0228198
M3 - Article
C2 - 32023287
AN - SCOPUS:85079046076
SN - 1932-6203
VL - 15
JO - PloS one
JF - PloS one
IS - 2
M1 - e0228198
ER -