Newton’s algorithm requires initial values for the variance parameter q. Supply these values in the Linear Mixed Effects object’s General Options tab, by clicking the Generate button under Initial Variance Parameters. More often, LinMix will determine initial values. For variance structures that are linear in q (Variance Components, Unstructured, Compound Symmetry, and Toeplitz), the initial values are determined by the method of moments. If the variance structure is nonlinear, then LinMix will calculate a “sample” variance by solving for random effects and taking their sums of squares and cross-products. The sample variance will then be equated with the parametric variance, and the system of equations will be solved to obtain initial parameter estimates. If either method fails, LinMix will use values that should yield a reasonable variance matrix, e.g., 1.0 for variance components and standard deviations, 0.01 for correlations.
Sometimes the method of moments will yield estimates of q that are REML estimates. In this case the program will not need to iterate.
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