gam.selection              package:mgcv              R Documentation

_G_e_n_e_r_a_l_i_z_e_d _A_d_d_i_t_i_v_e _M_o_d_e_l _S_e_l_e_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     This page is intended to provide some more information on how to
     select GAMs. Given a model structure specified by a gam model
     formula, 'gam()' attempts to find the appropriate smoothness for
     each applicable model  term using Generalized Cross Validation
     (GCV) or an Un-Biased Risk Estimator (UBRE). The latter is used in
     cases in which the scale parameter is assumed known, in which case
     it is very similar to AIC or Mallows' Cp. GCV and UBRE are covered
     in Craven and Wahba (1979) and Wahba (1990), see 'gam.method' for
     more detail about the numerical optimization approaches available. 

     Automatic smoothness selection is unlikely to be successful with
     few data, particularly with multiple terms to be selected. In
     addition GCV and UBRE/AIC score can occasionally display local
     minima that can trap the minimisation algorithms. GCV/UBRE/AIC
     scores become constant with changing smoothing parameters at very
     low or very high smoothng parameters, and on occasion these `flat'
     regions can be separated from regions of lower score by a small
     `lip'. This seems to be the most common form of local minimum, but
     is usually avoidable by avoiding extreme smoothing parameters as
     starting values in optimization, and by avoiding big jumps in
     smoothing parameters while optimizing. Never the less, if you are
     suspicious of smoothing parameter estimates, try changing fit
     method (see 'gam.method') and see if the estimates change, or try
     changing some or all of the smoothing parameters `manually'
     (argument 'sp' of 'gam', or 'sp' arguments to 's' or 'te'). 

     In general the most logically consistent method to use for
     deciding which terms to include in the model is to compare
     GCV/UBRE scores for models with  and without the term. When UBRE
     is the smoothness selection method this will give the same result
     as comparing by 'AIC' (the AIC in this case uses the model EDF in
     place of the usual model DF). Similarly, comparison via GCV score
     and via AIC seldom yields different answers. Note that the
     negative binomial with estimated 'theta' parameter is a special
     case: the GCV score is not informative, because of the 'theta'
     estimation scheme used.

     More generally the score for the model with a smooth  term can be
     compared to the score for the model with  the smooth term replaced
     by appropriate parametric terms. Candidates for removal can be
     identified by reference to the approximate p-values provided  by
     'summary.gam'. Candidates for replacement by parametric terms are 
     smooth terms with estimated degrees of freedom close to their 
     minimum possible.

     One appealing approach to model selection is via shrinkage. Smooth
     classes 'cs.smooth' and 'tprs.smooth' (specified by '"cs"' and
     '"ts"' respectively) have smoothness penalties which include a
     small shrinkage component, so that for large enough smoothing
     parameters the smooth  becomes identically zero. This allows
     automatic smoothing parameter selection methods to effectively
     remove the term from the model altogether. The shrinkage component
     of the penalty is set at a level that usually makes negligable
     contribution to the penalization of the model, only becoming
     effective when the term is effectively `completely smooth'
     according to the conventional penalty.

     Note that GCV and UBRE are not appropriate for comparing models
     using different families:  in that case AIC should be used.

_A_u_t_h_o_r(_s):

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

_R_e_f_e_r_e_n_c_e_s:

     Craven and Wahba (1979) Smoothing Noisy Data with Spline
     Functions. Numer. Math. 31:377-403

     Venables and Ripley (1999) Modern Applied Statistics with S-PLUS

     Wahba (1990) Spline Models of Observational Data. SIAM.

     Wood, S.N. (2003) Thin plate regression splines. J.R.Statist.Soc.B
     65(1):95-114

     Wood, S.N. (2008) Fast stable direct fitting and smoothness
     selection for generalized additive models. J.R.Statist. Soc. B
     70(3):495-518

     <URL: http://www.maths.bath.ac.uk/~sw283/>

_E_x_a_m_p_l_e_s:

     ## an example of GCV based model selection
     library(mgcv)
     set.seed(0);n<-400
     dat <- gamSim(1,n=n,scale=2) ## simulate data
     dat$x4 <- runif(n, 0, 1);dat$x5 <- runif(n, 0, 1) ## spurious
     ## Note the increased gamma parameter below to favour
     ## slightly smoother models (See Kim & Gu, 2004, JRSSB)...
     b<-gam(y~s(x0,bs="ts")+s(x1,bs="ts")+s(x2,bs="ts")+
        s(x3,bs="ts")+s(x4,bs="ts")+s(x5,bs="ts"),gamma=1.4,data=dat)
     summary(b)
     plot(b,pages=1)

