vis.gam {mgcv}R Documentation

Visualization of GAM objects

Description

Produces perspective or contour plot views of gam model predictions, fixing all but the values in view to the values supplied in cond.

Usage

vis.gam(x,view=NULL,cond=list(),n.grid=30,too.far=0,col=NA,
        color="heat",contour.col=NULL,se=-1,type="link",
        plot.type="persp",zlim=NULL,nCol=50,...)

Arguments

x

a gam object, produced by gam()

view

an array containing the names of the two main effect terms to be displayed on the x and y dimensions of the plot. If omitted the first two suitable terms will be used. Note that variables coerced to factors in the model formula won't work as view variables, and vis.gam can not detect that this has happened when setting defaults.

cond

a named list of the values to use for the other predictor terms (not in view). Variables omitted from this list will have the closest observed value to the median for continuous variables, or the most commonly occuring level for factors. Parametric matrix variables have all the entries in each column set to the observed column entry closest to the column median.

n.grid

The number of grid nodes in each direction used for calculating the plotted surface.

too.far

plot grid nodes that are too far from the points defined by the variables given in view can be excluded from the plot. too.far determines what is too far. The grid is scaled into the unit square along with the view variables and then grid nodes more than too.far from the predictor variables are excluded.

col

The colours for the facets of the plot. If this is NA then if se>0 the facets are transparent, otherwise the colour scheme specified in color is used. If col is not NA then it is used as the facet colour.

color

the colour scheme to use for plots when se<=0. One of "topo", "heat", "cm", "terrain", "gray" or "bw". Schemes "gray" and "bw" also modify the colors used when se>0.

contour.col

sets the colour of contours when using plot.type="contour". Default scheme used if NULL.

se

if less than or equal to zero then only the predicted surface is plotted, but if greater than zero, then 3 surfaces are plotted, one at the predicted values minus se standard errors, one at the predicted values and one at the predicted values plus se standard errors.

type

"link" to plot on linear predictor scale and "response" to plot on the response scale.

plot.type

one of "contour" or "persp".

zlim

a two item array giving the lower and upper limits for the z-axis scale. NULL to choose automatically.

nCol

The number of colors to use in color schemes.

...

other options to pass on to persp, image or contour. In particular ticktype="detailed" will add proper axes labelling to the plots.

Details

The x and y limits are determined by the ranges of the terms named in view. If se<=0 then a single (height colour coded, by default) surface is produced, otherwise three (by default see-through) meshes are produced at mean and +/- se standard errors. Parts of the x-y plane too far from data can be excluded by setting too.far

All options to the underlying graphics functions can be reset by passing them as extra arguments ...: such supplied values will always over-ride the default values used by vis.gam.

Value

Simply produces a plot.

WARNINGS

The routine can not detect that a variable has been coerced to factor within a model formula, and will therefore fail if such a variable is used as a view variable. When setting default view variables it can not detect this situation either, which can cause failures if the coerced variables are the first, otherwise suitable, variables encountered.

Author(s)

Simon Wood simon.wood@r-project.org

Based on an original idea and design by Mike Lonergan.

See Also

persp and 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)
y<-x0^2+x1*x2 +runif(n,-0.3,0.3)
g<-gam(y~s(x0,x1,x2))
old.par<-par(mfrow=c(2,2))
# display the prediction surface in x0, x1 ....
vis.gam(g,ticktype="detailed",color="heat",theta=-35)  
vis.gam(g,se=2,theta=-35) # with twice standard error surfaces
vis.gam(g, view=c("x1","x2"),cond=list(x0=0.75)) # different view 
vis.gam(g, view=c("x1","x2"),cond=list(x0=.75),theta=210,phi=40,
        too.far=.07)
# ..... areas where there is no data are not plotted

# contour examples....
vis.gam(g, view=c("x1","x2"),plot.type="contour",color="heat")
vis.gam(g, view=c("x1","x2"),plot.type="contour",color="terrain")
vis.gam(g, view=c("x1","x2"),plot.type="contour",color="topo")
vis.gam(g, view=c("x1","x2"),plot.type="contour",color="cm")


par(old.par)

# Examples with factor and "by" variables

fac<-rep(1:4,20)
x<-runif(80)
y<-fac+2*x^2+rnorm(80)*0.1
fac<-factor(fac)
b<-gam(y~fac+s(x))

vis.gam(b,theta=-35,color="heat") # factor example

z<-rnorm(80)*0.4   
y<-as.numeric(fac)+3*x^2*z+rnorm(80)*0.1
b<-gam(y~fac+s(x,by=z))

vis.gam(b,theta=-35,color="heat",cond=list(z=1)) # by variable example

vis.gam(b,view=c("z","x"),theta= -135) # plot against by variable


[Package mgcv version 1.8-31 Index]