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September 2013 Local adaptation and genetic effects on fitness: Calculations for exponential family models with random effects
Charles J. Geyer, Caroline E. Ridley, Robert G. Latta, Julie R. Etterson, Ruth G. Shaw
Ann. Appl. Stat. 7(3): 1778-1795 (September 2013). DOI: 10.1214/13-AOAS653

Abstract

Random effects are implemented for aster models using two approximations taken from Breslow and Clayton [J. Amer. Statist. Assoc. 88 (1993) 9–25]. Random effects are analytically integrated out of the Laplace approximation to the complete data log likelihood, giving a closed-form expression for an approximate missing data log likelihood. Third and higher derivatives of the complete data log likelihood with respect to the random effects are ignored, giving a closed-form expression for second derivatives of the approximate missing data log likelihood, hence approximate observed Fisher information. This method is applicable to any exponential family random effects model. It is implemented in the CRAN package aster (R Core Team [R: A Language and Environment for Statistical Computing (2012) R Foundation for Statistical Computing], Geyer [R package aster (2012) http://cran.r-project.org/package=aster]). Applications are analyses of local adaptation in the invasive California wild radish (Raphanus sativus) and the slender wild oat (Avena barbata) and of additive genetic variance for fitness in the partridge pea (Chamaecrista fasciculata).

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Charles J. Geyer. Caroline E. Ridley. Robert G. Latta. Julie R. Etterson. Ruth G. Shaw. "Local adaptation and genetic effects on fitness: Calculations for exponential family models with random effects." Ann. Appl. Stat. 7 (3) 1778 - 1795, September 2013. https://doi.org/10.1214/13-AOAS653

Information

Published: September 2013
First available in Project Euclid: 3 October 2013

zbMATH: 06237197
MathSciNet: MR3127968
Digital Object Identifier: 10.1214/13-AOAS653

Rights: Copyright © 2013 Institute of Mathematical Statistics

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Vol.7 • No. 3 • September 2013
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