Description

This set of functions implements an nlme library pdMat class to allow tensor product smooths to be estimated by lme as called by gamm. Tensor product smooths have a penalty matrix made up of a weighted sum of penalty matrices, where the weights are the smoothing parameters. In the mixed model formulation the penalty matrix is the inverse of the covariance matrix for the random effects of a term, and the smoothing parameters (times a half) are variance parameters to be estimated. It's not possible to transform the problem to make the required random effects covariance matrix look like one of the standard pdMat classes: hence the need for the pdTens class. A notLog2 parameterization ensures that the parameters are positive.

These functions (pdTens, pdConstruct.pdTens, pdFactor.pdTens, pdMatrix.pdTens, coef.pdTens and summary.pdTens) would not normally be called directly.

Usage

Arguments

Details

If using this class directly note that it is worthwhile scaling the S matrices to be of ‘moderate size’, for example by dividing each matrix by its largest singular value: this avoids problems with lme defaults (smooth.construct.tensor.smooth.spec does this automatically).

This appears to be the minimum set of functions required to implement a new pdMat class.

Note that while the pdFactor and pdMatrix functions return the inverse of the scaled random effect covariance matrix or its factor, the pdConstruct function is sometimes initialised with estimates of the scaled covariance matrix, and sometimes intialized with its inverse.

Value

A class pdTens object, or its coefficients or the matrix it represents or the factor of that matrix. pdFactor returns the factor as a vector (packed column-wise) (pdMatrix always returns a matrix).

Author(s)

Simon N. Wood simon.wood@r-project.org

References

Pinheiro J.C. and Bates, D.M. (2000) Mixed effects Models in S and S-PLUS. Springer

The nlme source code.

https://www.maths.ed.ac.uk/~swood34/

See Also

te gamm

Examples