anova.gam {mgcv}  R Documentation 
Approximate hypothesis tests related to GAM fits
Description
Performs hypothesis tests relating to one or more fitted
gam
objects. For a single fitted gam
object, Wald tests of
the significance of each parametric and smooth term are performed, so interpretation
is analogous to drop1
rather than anova.lm
(i.e. it's like type III ANOVA,
rather than a sequential type I ANOVA). Otherwise the fitted models are compared using an analysis of deviance table or GLRT test: this latter approach should not be use to test the significance of terms which can be penalized
to zero. Models to be compared should be fitted to the same data using the same smoothing parameter selection method.
Usage
## S3 method for class 'gam'
anova(object, ..., dispersion = NULL, test = NULL,
freq = FALSE)
## S3 method for class 'anova.gam'
print(x, digits = max(3, getOption("digits")  3),...)
Arguments
object , ... 
fitted model objects of class 
x 
an 
dispersion 
a value for the dispersion parameter: not normally used. 
test 
what sort of test to perform for a multimodel call. One of

freq 
whether to use frequentist or Bayesian approximations for parametric term
pvalues. See 
digits 
number of digits to use when printing output. 
Details
If more than one fitted model is provided than anova.glm
is
used, with the difference in model degrees of freedom being taken as the difference
in effective degress of freedom (when possible this is a smoothing parameter uncertainty corrected version).
For extended and general families this is set so that a GLRT test is used. The pvalues resulting from the multimodel case are only approximate,
and must be used with care. The approximation is most accurate when the comparison
relates to unpenalized terms, or smoothers with a null space of dimension greater than zero.
(Basically we require that the difference terms could be well approximated by unpenalized
terms with degrees of freedom approximately the effective degrees of freedom). In simulations the
pvalues are usually slightly too low. For terms with a zerodimensional null space
(i.e. those which can be penalized to zero) the approximation is often very poor, and significance
can be greatly overstated: i.e. pvalues are often substantially too low. This case applies to random effect terms.
Note also that in the multimodel call to anova.gam
, it is quite possible for a model with more terms to end up with lower effective degrees of freedom, but better fit, than the notionally null model with fewer terms. In such cases it is very rare that it makes sense to perform any sort of test, since there is then no basis on which to accept the notional null model.
If only one model is provided then the significance of each model term
is assessed using Wald like tests, conditional on the smoothing parameter estimates: see summary.gam
and Wood (2013a,b) for details. The pvalues provided here are better justified than in the multi model case, and have close to the
correct distribution under the null, unless smoothing parameters are poorly identified. ML or REML smoothing parameter selection leads to
the best results in simulations as they tend to avoid occasional severe undersmoothing. In replication of the full simulation study of Scheipl et al. (2008) the tests give almost indistinguishable power to the method recommended there, but slightly too low pvalues under the null in their section 3.1.8 test for a smooth interaction (the Scheipl et al. recommendation is not used directly, because it only applies in the Gaussian case, and requires model refits, but it is available in package RLRsim
).
In the single model case print.anova.gam
is used as the printing method.
By default the pvalues for parametric model terms are also based on Wald tests using the Bayesian
covariance matrix for the coefficients. This is appropriate when there are "re" terms present, and is
otherwise rather similar to the results using the frequentist covariance matrix (freq=TRUE
), since
the parametric terms themselves are usually unpenalized. Default Pvalues for parameteric terms that are
penalized using the paraPen
argument will not be good.
Value
In the multimodel case anova.gam
produces output identical to
anova.glm
, which it in fact uses.
In the single model case an object of class anova.gam
is produced,
which is in fact an object returned from summary.gam
.
print.anova.gam
simply produces tabulated output.
WARNING
If models 'a' and 'b' differ only in terms with no unpenalized components (such as random effects) then p values from anova(a,b) are unreliable, and usually much too low.
Default Pvalues will usually be wrong for parametric terms penalized using ‘paraPen’: use freq=TRUE to obtain better pvalues when the penalties are full rank and represent conventional random effects.
For a single model, interpretation is similar to drop1, not anova.lm.
Author(s)
Simon N. Wood simon.wood@rproject.org with substantial improvements by Henric Nilsson.
References
Scheipl, F., Greven, S. and Kuchenhoff, H. (2008) Size and power of tests for a zero random effect variance or polynomial regression in additive and linear mixed models. Comp. Statist. Data Anal. 52, 32833299
Wood, S.N. (2013a) On pvalues for smooth components of an extended generalized additive model. Biometrika 100:221228 doi:10.1093/biomet/ass048
Wood, S.N. (2013b) A simple test for random effects in regression models. Biometrika 100:10051010 doi:10.1093/biomet/ast038
See Also
gam
, predict.gam
,
gam.check
, summary.gam
Examples
library(mgcv)
set.seed(0)
dat < gamSim(5,n=200,scale=2)
b<gam(y ~ x0 + s(x1) + s(x2) + s(x3),data=dat)
anova(b)
b1<gam(y ~ x0 + s(x1) + s(x2),data=dat)
anova(b,b1,test="F")