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SNP_NLMM: A SAS Macro to Implement a Flexible Random Effects Density for Generalized Linear and Nonlinear Mixed Models

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  • Vock, David
  • Davidian, Marie
  • Tsiatis, Anastasios

Abstract

Generalized linear and nonlinear mixed models (GLMMs and NLMMs) are commonly used to represent non-Gaussian or nonlinear longitudinal or clustered data. A common assumption is that the random effects are Gaussian. However, this assumption may be unrealistic in some applications, and misspecification of the random effects density may lead to maximum likelihood parameter estimators that are inconsistent, biased, and inefficient. Because testing if the random effects are Gaussian is difficult, previous research has recommended using a flexible random effects density. However, computational limitations have precluded widespread use of flexible random effects densities for GLMMs and NLMMs. We develop a SAS macro, SNP_NLMM, that overcomes the computational challenges to fit GLMMs and NLMMs where the random effects are assumed to follow a smooth density that can be represented by the seminonparametric formulation proposed by Gallant and Nychka (1987). The macro is flexible enough to allow for any density of the response conditional on the random effects and any nonlinear mean trajectory. We demonstrate the SNP_NLMM macro on a GLMM of the disease progression of toenail infection and on a NLMM of intravenous drug concentration over time.

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  • Vock, David & Davidian, Marie & Tsiatis, Anastasios, 2014. "SNP_NLMM: A SAS Macro to Implement a Flexible Random Effects Density for Generalized Linear and Nonlinear Mixed Models," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 56(c02).
    • Handle: RePEc:jss:jstsof:v:056:c02
    DOI: http://hdl.handle.net/10.18637/jss.v056.c02
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    1. Murray Aitkin, 1999. "A General Maximum Likelihood Analysis of Variance Components in Generalized Linear Models," Biometrics, The International Biometric Society, vol. 55(1), pages 117-128, March.
    2. Huageng Tao & Mari Palta & Brian S. Yandell & Michael A. Newton, 1999. "An Estimation Method for the Semiparametric Mixed Effects Model," Biometrics, The International Biometric Society, vol. 55(1), pages 102-110, March.
    3. Verbeke, Geert & Lesaffre, Emmanuel, 1997. "The effect of misspecifying the random-effects distribution in linear mixed models for longitudinal data," Computational Statistics & Data Analysis, Elsevier, vol. 23(4), pages 541-556, February.
    4. R. Bock & Murray Aitkin, 1981. "Marginal maximum likelihood estimation of item parameters: Application of an EM algorithm," Psychometrika, Springer;The Psychometric Society, vol. 46(4), pages 443-459, December.
    5. Irina Irincheeva & Eva Cantoni & Marc G. Genton, 2012. "Generalized Linear Latent Variable Models with Flexible Distribution of Latent Variables," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 39(4), pages 663-680, December.
    6. Rabe-Hesketh, Sophia & Skrondal, Anders & Pickles, Andrew, 2005. "Maximum likelihood estimation of limited and discrete dependent variable models with nested random effects," Journal of Econometrics, Elsevier, vol. 128(2), pages 301-323, October.
    7. Victor H. Lachos & Dipankar Bandyopadhyay & Dipak K. Dey, 2011. "Linear and Nonlinear Mixed-Effects Models for Censored HIV Viral Loads Using Normal/Independent Distributions," Biometrics, The International Biometric Society, vol. 67(4), pages 1594-1604, December.
    8. Xiao Song & Marie Davidian & Anastasios A. Tsiatis, 2002. "A Semiparametric Likelihood Approach to Joint Modeling of Longitudinal and Time-to-Event Data," Biometrics, The International Biometric Society, vol. 58(4), pages 742-753, December.
    9. Agresti, Alan & Caffo, Brian & Ohman-Strickland, Pamela, 2004. "Examples in which misspecification of a random effects distribution reduces efficiency, and possible remedies," Computational Statistics & Data Analysis, Elsevier, vol. 47(3), pages 639-653, October.
    10. Hartford, Alan & Davidian, Marie, 2000. "Consequences of misspecifying assumptions in nonlinear mixed effects models," Computational Statistics & Data Analysis, Elsevier, vol. 34(2), pages 139-164, August.
    11. Yanyuan Ma & Marc G. Genton, 2010. "Explicit estimating equations for semiparametric generalized linear latent variable models," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(4), pages 475-495, September.
    12. Daowen Zhang & Marie Davidian, 2001. "Linear Mixed Models with Flexible Distributions of Random Effects for Longitudinal Data," Biometrics, The International Biometric Society, vol. 57(3), pages 795-802, September.
    13. Min Zhang & Marie Davidian, 2008. "“Smooth” Semiparametric Regression Analysis for Arbitrarily Censored Time-to-Event Data," Biometrics, The International Biometric Society, vol. 64(2), pages 567-576, June.
    14. Stephen Schilling & R. Bock, 2005. "High-dimensional maximum marginal likelihood item factor analysis by adaptive quadrature," Psychometrika, Springer;The Psychometric Society, vol. 70(3), pages 533-555, September.
    15. Rizopoulos, Dimitris, 2012. "Fast fitting of joint models for longitudinal and event time data using a pseudo-adaptive Gaussian quadrature rule," Computational Statistics & Data Analysis, Elsevier, vol. 56(3), pages 491-501.
    16. Emmanuel Lesaffre & Bart Spiessens, 2001. "On the effect of the number of quadrature points in a logistic random effects model: an example," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 50(3), pages 325-335.
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