plot.gam {mgcv}R Documentation

Default GAM plotting

Description

Takes a fitted gam object produced by gam() and plots the component smooth functions that make it up, on the scale of the linear predictor. Optionally produces term plots for parametric model components as well.

Usage

## S3 method for class 'gam':
plot(x,residuals=FALSE,rug=TRUE,se=TRUE,pages=0,select=NULL,scale=-1,
         n=100,n2=40,pers=FALSE,theta=30,phi=30,jit=FALSE,xlab=NULL,
         ylab=NULL,main=NULL,ylim=NULL,xlim=NULL,too.far=0.1,
         all.terms=FALSE,shade=FALSE,shade.col="gray80",
         shift=0,trans=I,...)

Arguments

x a fitted gam object as produced by gam().
residuals If TRUE then partial residuals are added to plots of 1-D smooths. If FALSE then no residuals are added. If this is an array of the correct length then it is used as the array of residuals to be used for producing partial residuals. If TRUE then the residuals are the working residuals from the IRLS iteration weighted by the IRLS weights. Partial residuals for a smooth term are the residuals that would be obtained by dropping the term concerned from the model, while leaving all other estimates fixed (i.e. the estimates for the term plus the residuals).
rug when TRUE (default) then the covariate to which the plot applies is displayed as a rug plot at the foot of each plot of a 1-d smooth, and the locations of the covariates are plotted as points on the contour plot representing a 2-d smooth.
se when TRUE (default) upper and lower lines are added to the 1-d plots at 2 standard errors above and below the estimate of the smooth being plotted while for 2-d plots, surfaces at +1 and -1 standard errors are contoured and overlayed on the contour plot for the estimate. If a positive number is supplied then this number is multiplied by the standard errors when calculating standard error curves or surfaces. See also shade, below.
pages (default 0) the number of pages over which to spread the output. For example, if pages=1 then all terms will be plotted on one page with the layout performed automatically. Set to 0 to have the routine leave all graphics settings as they are.
select Allows the plot for a single model term to be selected for printing. e.g. if you just want the plot for the second smooth term set select=2.
scale set to -1 (default) to have the same y-axis scale for each plot, and to 0 for a different y axis for each plot. Ignored if ylim supplied.
n number of points used for each 1-d plot - for a nice smooth plot this needs to be several times the estimated degrees of freedom for the smooth. Default value 100.
n2 Square root of number of points used to grid estimates of 2-d functions for contouring.
pers Set to TRUE if you want perspective plots for 2-d terms.
theta One of the perspective plot angles.
phi The other perspective plot angle.
jit Set to TRUE if you want rug plots for 1-d terms to be jittered.
xlab If supplied then this will be used as the x label for all plots.
ylab If supplied then this will be used as the y label for all plots.
main Used as title (or z axis label) for plots if supplied.
ylim If supplied then this pair of numbers are used as the y limits for each plot.
xlim If supplied then this pair of numbers are used as the x limits for each plot.
too.far If greater than 0 then this is used to determine when a location is too far from data to be plotted when plotting 2-D smooths. This is useful since smooths tend to go wild away from data. The data are scaled into the unit square before deciding what to exclude, and too.far is a distance within the unit square.
all.terms if set to TRUE then the partial effects of parametric model components are also plotted, via a call to termplot. Only terms of order 1 can be plotted in this way.
shade Set to TRUE to produce shaded regions as confidence bands for smooths (not avaliable for parametric terms, which are plotted using termplot).
shade.col define the color used for shading confidence bands.
shift constant to add to each smooth (on the scale of the linear predictor) before plotting. Can be useful for some diagnostics, or with trans.
trans function to apply to each smooth (after any shift), before plotting. shift and trans are occasionally useful as a means for getting plots on the response scale, when the model consists only of a single smooth.
... other graphics parameters to pass on to plotting commands.

Details

Produces default plot showing the smooth components of a fitted GAM, and optionally parametric terms as well, when these can be handled by termplot.

For plots of 1-d smooths, the x axis of each plot is labelled with the covariate name, while the y axis is labelled s(cov,edf) where cov is the covariate name, and edf the estimated (or user defined for regression splines) degrees of freedom of the smooth.

Contour plots are produced for 2-d smooths with the x-axes labelled with the first covariate name and the y axis with the second covariate name. The main title of the plot is something like s(var1,var2,edf), indicating the variables of which the term is a function, and the estimated degrees of freedom for the term. When se=TRUE, estimator variability is shown by overlaying contour plots at plus and minus 1 s.e. relative to the main estimate. If se is a positive number then contour plots are at plus or minus se multiplied by the s.e. Contour levels are chosen to try and ensure reasonable separation of the contours of the different plots, but this is not always easy to achieve. Note that these plots can not be modified to the same extent as the other plot.

Smooths of more than 2 variables are not currently dealt with, but simply generate a warning, but see vis.gam.

Fine control of plots for parametric terms can be obtained by calling termplot directly, taking care to use its terms argument.

Value

The function simply generates plots.

WARNING

Note that the behaviour of this function is not identical to plot.gam() in S-PLUS.

Plots of 2-D smooths with standard error contours shown can not easily be customized.

The function can not deal with smooths of more than 2 variables!

Author(s)

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

Henric Nilsson henric.nilsson@statisticon.se donated the code for the shade option.

The design is inspired by the S function of the same name described in Chambers and Hastie (1993) (but is not a clone).

References

Chambers and Hastie (1993) Statistical Models in S. Chapman & Hall.

Gu and Wahba (1991) Minimizing GCV/GML scores with multiple smoothing parameters via the Newton method. SIAM J. Sci. Statist. Comput. 12:383-398

Wood, S.N. (2000) Modelling and Smoothing Parameter Estimation with Multiple Quadratic Penalties. J.R.Statist.Soc.B 62(2):413-428

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

Wood, S.N. (2004) Stable and efficient multiple smoothing parameter estimation for generalized additive models. J. Amer. Statist. Ass. 99:637-686

http://www.maths.bath.ac.uk/~sw283/

See Also

gam, predict.gam, vis.gam

Examples

library(mgcv)
set.seed(0)
## fake some data...

f1 <- function(x) {exp(2 * x)}
f2 <- function(x) { 
  0.2*x^11*(10*(1-x))^6+10*(10*x)^3*(1-x)^10 
}
f3 <- function(x) {x*0}

n<-200
sig2<-4
x0 <- rep(1:4,50)
x1 <- runif(n, 0, 1)
x2 <- runif(n, 0, 1)
x3 <- runif(n, 0, 1)
e <- rnorm(n, 0, sqrt(sig2))
y <- 2*x0 + f1(x1) + f2(x2) + f3(x3) + e
x0 <- factor(x0)

## fit and plot...
b<-gam(y~x0+s(x1)+s(x2)+s(x3))
plot(b,pages=1,residuals=TRUE,all.terms=TRUE,shade=TRUE,shade.col=2)

## just parametric term alone...
termplot(b,terms="x0",se=TRUE)

## more use of color...
op <- par(mfrow=c(2,2),bg="blue")
x <- 0:1000/1000
for (i in 1:3) {
  plot(b,select=i,rug=FALSE,col="green",
    col.axis="white",col.lab="white",all.terms=TRUE)
  for (j in 1:2) axis(j,col="white",labels=FALSE)
  box(col="white")
  eval(parse(text=paste("fx <- f",i,"(x)",sep="")))
  fx <- fx-mean(fx)
  lines(x,fx,col=2) ## overlay `truth' in red
}
par(op)

## example with 2-d plots...
b1<-gam(y~x0+s(x1,x2)+s(x3))
op<-par(mfrow=c(2,2))
plot(b1,all.terms=TRUE)
par(op) 

[Package mgcv version 1.3-23 Index]