FamEvent: An R Package for Generating and Modeling Time-to-Event Data in Family Designs

J Stat Softw. 2021 Mar;97(7):10.18637/jss.v097.i07. doi: 10.18637/jss.v097.i07. Epub 2021 Mar 19.

Abstract

FamEvent is a comprehensive R package for simulating and modelling age-at-disease onset in families carrying a rare gene mutation. The package can simulate complex family data for variable time-to-event outcomes under three common family study designs (population, high-risk clinic and multi-stage) with various levels of missing genetic information among family members. Residual familial correlation can be induced through the inclusion of a frailty term or a second gene. Disease-gene carrier probabilities are evaluated assuming Mendelian transmission or empirically from the data. When genetic information on the disease gene is missing, an Expectation-Maximization algorithm is employed to calculate the carrier probabilities. Penetrance model functions with ascertainment correction adapted to the sampling design provide age-specific cumulative disease risks by sex, mutation status, and other covariates for simulated data as well as real data analysis. Robust standard errors and 95% confidence intervals are available for these estimates. Plots of pedigrees and penetrance functions based on the fitted model provide graphical displays to evaluate and summarize the models.

Keywords: EM algorithm; ascertainment correction; correlated time-to-event data; family study designs; mutation carrier probability; penetrance function estimation.