Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Yun-Hee Choi, Laurent Briollais, Wenqing He, Karen Kopciuk
Title: FamEvent: An R Package for Generating and Modeling Time-to-Event Data in Family Designs
Abstract: FamEvent is a comprehensive R package for simulating and modeling 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.

Page views:: 852. Submitted: 2017-01-21. Published: 2021-03-19.
Paper: FamEvent: An R Package for Generating and Modeling Time-to-Event Data in Family Designs     Download PDF (Downloads: 259)
FamEvent_2.1.tar.gz: R source package Download (Downloads: 21; 57KB)
v97i07.R: R replication code Download (Downloads: 28; 10KB)

DOI: 10.18637/jss.v097.i07

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Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.