summary.gam               package:mgcv               R Documentation

Summary for a GAM fit

Description:

     Takes a fitted 'gam' object produced by 'gam()' and produces
     various useful summaries from it.

Usage:

     ## S3 method for class 'gam':
     summary(object, dispersion=NULL, freq=TRUE, ...)

     ## S3 method for class 'summary.gam':
     print(x,digits = max(3, getOption("digits") - 3), 
                       signif.stars = getOption("show.signif.stars"),...)

Arguments:

  object: a fitted 'gam' object as produced by 'gam()'.

       x: a 'summary.gam' object produced by 'summary.gam()'.

dispersion: A known dispersion parameter. 'NULL' to use estimate or
          default (e.g. 1 for Poisson).

    freq: By default p-values for individual terms are calculated using
          the frequentist estimated covariance matrix of the parameter
          estimators. If this is set to FALSE then the Bayesian
          covariance matrix of the parameters is used instead. See
          details. 

  digits: controls number of digits printed in output.

signif.stars: Should significance stars be printed alongside output.

     ...: other arguments.

Details:

     Model degrees of freedom are taken as the trace of the influence
     (or hat) matrix A for the model fit. Residual degrees of freedom
     are taken as number of data minus model degrees of freedom.  Let
     P_i be the matrix  giving the parameters of the ith smooth when
     applied to the data (or pseudodata in the generalized case) and
     let X  be the design matrix of the model. Then tr(XP_i) is the edf
     for the ith term. Clearly this definition causes  the edf's to add
     up properly! 

     'print.summary.gam' tries to print various bits of summary
     information useful for term selection in a pretty way.

     If 'freq=FALSE' then the Bayesian parameter covariance matrix,
     'object$Vp', is used to calculate test statistics for terms, and
     the degrees of freedom for reference distributions is taken as the
     estimated degrees of freedom for the term concerned. This is not
     easy to justify theoretically, and the resulting `Bayesian
     p-values' are difficult to interpret and often have much worse
     frequentist performance than the default p-values.

Value:

     'summary.gam' produces a list of summary information for a fitted
     'gam' object. 

 p.coeff: is an array of estimates of the strictly parametric model
          coefficients.

     p.t: is an array of the 'p.coeff''s divided by their standard
          errors.

    p.pv: is an array of p-values for the null hypothesis that the
          corresponding parameter is zero.  Calculated with reference
          to the t distribution with the estimated residual degrees of
          freedom for the model fit if the dispersion parameter has
          been estimated, and the standard normal if not.

       m: The number of smooth terms in the model.

  chi.sq: An array of test statistics for assessing the significance of
          model smooth terms. If p_i  is the parameter vector for the
          ith smooth term, and this term has estimated covariance
          matrix V_i then the  statistic is p_i'V_i^{k-}p_i, where
          V_i^{k-} is the rank k  pseudo-inverse of V_i, and k is
          estimated rank of  V_i.

    s.pv: An array of approximate p-values for the null hypotheses that
          each smooth term is zero. Be warned, these are only
          approximate. In the case of known dispersion parameter, they
          are obtained by comparing the chi.sq statistic given above to
          the  chi-squared distribution with k degrees of freedom,
          where k is the estimated rank of  V_i. If the dispersion
          parameter is unknown (in  which case it will have been
          estimated) the statistic is compared to an F distribution
          with k upper d.f.  and lower d.f. given by the residual
          degrees of freedom for the model .  Typically the p-values
          will be somewhat too low, because they are conditional on the
          smoothing parameters, which are usually uncertain, but note
          that the statistic can also have low power if the rank, k, is
          too high relative to the EDF of the term! 

      se: array of standard error estimates for all parameter
          estimates.

    r.sq: The adjusted r-squared for the model. Defined as the
          proportion of variance explained, where original variance and
           residual variance are both estimated using unbiased
          estimators. This quantity can be negative if your model is
          worse than a one  parameter constant model, and can be higher
          for the smaller of two nested models! Note that proportion
          null deviance  explained is probably more appropriate for
          non-normal errors.

dev.expl: The proportion of the null deviance explained by the model.

     edf: array of estimated degrees of freedom for the model terms.

residual.df: estimated residual degrees of freedom.

       n: number of data.

     gcv: minimized GCV score for the model, if GCV used.

    ubre: minimized UBRE score for the model, if UBRE used.

   scale: estimated (or given) scale parameter.

  family: the family used.

 formula: the original GAM formula.

dispersion: the scale parameter.

pTerms.df: the degrees of freedom associated with each parameteric term
          (excluding the constant).

pTerms.chi.sq: a Wald statistic for testing the null hypothesis that
          the each parametric term is zero.

pTerms.pv: p-values associated with the tests that each term is zero.
          For penalized fits these are approximate, being conditional
          on the smoothing parameters. The reference distribution is an
          appropriate chi-squared when the scale parameter is known,
          and is based on an F when it is not.

cov.unscaled: The estimated covariance matrix of the parameters (or
          estimators if 'freq=TRUE'), divided by scale parameter.

cov.scaled: The estimated covariance matrix of the parameters
          (estimators if 'freq=TRUE').

 p.table: significance table for parameters

 s.table: significance table for smooths

 p.Terms: significance table for parametric model terms

WARNING:

     The supplied p-values will often be underestimates if smoothing
     parameters have been estimated as part of model fitting.

Author(s):

     Simon N. Wood simon.wood@r-project.org with substantial
     improvements by Henric Nilsson.

References:

     Wood S.N. (2006) Generalized Additive Models: An Introduction with
     R. Chapman and Hall/CRC Press.

See Also:

     'gam', 'predict.gam', 'gam.check', 'anova.gam'

Examples:

     library(mgcv)
     set.seed(0)
     n<-200
     sig2<-4
     x0 <- runif(n, 0, 1)
     x1 <- runif(n, 0, 1)
     x2 <- runif(n, 0, 1)
     x3 <- runif(n, 0, 1)
     pi <- asin(1) * 2
     y <- 2 * sin(pi * x0)
     y <- y + exp(2 * x1) - 3.75887
     y <- y + 0.2 * x2^11 * (10 * (1 - x2))^6 + 10 * (10 * x2)^3 * (1 - x2)^10
     e <- rnorm(n, 0, sqrt(abs(sig2)))
     y <- y + e
     b<-gam(y~s(x0)+s(x1)+s(x2)+s(x3))
     plot(b,pages=1)
     summary(b)
     # now check the p-values by using a pure regression spline.....
     b.d<-round(summary(b)$edf)+1 ## get edf per smooth
     b.d<-pmax(b.d,3) # can't have basis dimension less than 3!
     bc<-gam(y~s(x0,k=b.d[1],fx=TRUE)+s(x1,k=b.d[2],fx=TRUE)+
             s(x2,k=b.d[3],fx=TRUE)+s(x3,k=b.d[4],fx=TRUE))
     plot(bc,pages=1)
     summary(bc)
     # p-value check - increase k to make this useful!
     n<-200;p<-0;k<-20
     for (i in 1:k)
     { b<-gam(y~s(x,z),data=data.frame(y=rnorm(n),x=runif(n),z=runif(n)))
       p[i]<-summary(b)$s.p[1]
     }
     plot(((1:k)-0.5)/k,sort(p))
     abline(0,1,col=2)

