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Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R.
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“Unconstrained parametrizations for variance-covariance matrices.”
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“Small sample inference for fixed effects from restricted maximum likelihood.”
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Mixed-Effects Models in S and S-Plus
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“Patterns of performance degradation and restoration during sleep restriction and subsequent recovery: a sleep dose-response study.”
Belenky G, Wesensten NJ, Thorne DR, Thomas ML, Sing HC, Redmond DP, Russo MB, Balkin TJ (2003) · 2003
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“Linear mixed models and penalized least squares.”
Bates DM, DebRoy S (2004) · 2004
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Gelman A (2005) · 2005
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Direct Methods for Sparse Linear Systems
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“Influence.ME: Tools for Detecting Influential Data in Mixed Effects Models.”
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boot: Bootstrap R (S-Plus) Functions
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blme: Bayesian Linear Mixed-Effects Models
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Bayesian data analysis
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“Nelder-Mead Simplex Optimization Routine for Large-Scale Problems: A Distributed Memory Implementation.”
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gamm4: Generalized additive mixed models using mgcv and lme4
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Data Analysis Using Regression and Multilevel/Hierarchical Models
Gelman A, Hill J (2006) · 2006
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“Estimating the multilevel Rasch model: With the lme4 package.”
Doran H, Bates D, Bliese P, Dowling M (2007) · 2007
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“Algorithm 887: CHOLMOD, Supernodal Sparse Cholesky Factorization and Update/Downdate.”
Chen Y, Davis TA, Hager WW, Rajamanickam S (2008) · 2008
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“The BOBYQA algorithm for bound constrained optimization without derivatives.”
Powell MJD (2009) · 2009
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“An R implementation of bootstrap procedures for mixed models.”
Sánchez-Espigares JA, Ocaña J (2009) · 2009
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“Unifying Optimization Algorithms to Aid Software System Users: optimx for R.”
Nash JC, Varadhan R (2011) · 2011
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Matrix: Sparse and Dense Matrix Classes and Methods
Bates D, Maechler M (2014) · 2014
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minqa: Derivative-free optimization algorithms by quadratic approximation
Bates D, Mullen KM, Nash JC, Varadhan R (2014) · 2014
Closest in time.
“The \code
Johnson SG (2014) · 2014
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“HLMdiag: A Suite of Diagnostics for Hierarchical Linear Models in R.”
Loy A, Hofmann H (2014) · 2014
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nlme: Linear and Nonlinear Mixed Effects Models
Pinheiro J, Bates D, DebRoy S, Sarkar D, R Core Team (2014) · 2014
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“Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS.”
Bolker BM, Gardner B, Maunder M, Berg CW, Brooks M, Comita L, Crone E, Cubaynes S, Davies T, de Valpine P, Ford J, Gimenez O, Kéry M, Kim EJ, Lennert-Cody C, Magnusson A, Martell S, Nash J, Nielsen A, Regetz J, Skaug H, Zipkin E (2013) · 2041
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