logLik.gam: AIC and Log likelihood for a fitted GAM

In mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

AIC and Log likelihood for a fitted GAM

Description

Function to extract the log-likelihood for a fitted gam model (note that the models are usually fitted by penalized likelihood maximization). Used by AIC. See details for more information on AIC computation.

Usage

## S3 method for class 'gam'
logLik(object,...)

Arguments

object	fitted model objects of class gam as produced by gam().
...	un-used in this case

Details

Modification of logLik.glm which corrects the degrees of freedom for use with gam objects.

The function is provided so that AIC functions correctly with gam objects, and uses the appropriate degrees of freedom (accounting for penalization). See e.g. Wood, Pya and Saefken (2016) for a derivation of an appropriate AIC.

For gaussian family models the MLE of the scale parameter is used. For other families with a scale parameter the estimated scale parameter is used. This is usually not exactly the MLE, and is not the simple deviance based estimator used with glm models. This is because the simple deviance based estimator can be badly biased in some cases, for example when a Tweedie distribution is employed with low count data.

There are two possibile AIC's that might be considered for use with GAMs. Marginal AIC is based on the marginal likelihood of the GAM, that is the likelihood based on treating penalized (e.g. spline) coefficients as random and integrating them out. The degrees of freedom is then the number of smoothing/variance parameters + the number of fixed effects. The problem with Marginal AIC is that marginal likelihood underestimates variance components/oversmooths, so that the approach favours simpler models excessively (substituting REML does not work, because REML is not comparable between models with different unpenalized/fixed components). Conditional AIC uses the likelihood of all the model coefficients, evaluated at the penalized MLE. The degrees of freedom to use then is the effective degrees of freedom for the model. However, Greven and Kneib (2010) show that the neglect of smoothing parameter uncertainty can lead to this conditional AIC being excessively likely to select larger models. Wood, Pya and Saefken (2016) propose a simple correction to the effective degrees of freedom to fix this problem. mgcv applies this correction whenever possible: that is when using ML or REML smoothing parameter selection with gam or bam. The correction is not computable when using the Extended Fellner Schall or BFGS optimizer (since the correction requires an estimate of the covariance matrix of the log smoothing parameters).

Value

Standard logLik object: see logLik.

Author(s)

Simon N. Wood [e-mail] based directly on logLik.glm

References

Greven, S., and Kneib, T. (2010), On the Behaviour of Marginal and Conditional AIC in Linear Mixed Models, Biometrika, 97, 773-789.

Wood, S.N., N. Pya and B. Saefken (2016), Smoothing parameter and model selection for general smooth models (with discussion). Journal of the American Statistical Association 111, 1548-1575 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/01621459.2016.1180986")}

Wood S.N. (2017) Generalized Additive Models: An Introduction with R (2nd edition). Chapman and Hall/CRC Press. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1201/9781315370279")}

See Also

AIC

mgcv documentation built on May 29, 2024, 4:34 a.m.