Visualization of GAM objects
Produces perspective or contour plot views of gam model
predictions, fixing all but the values in view to the values supplied in cond.
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,...)x |
a |
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 |
cond |
a named list of the values to use for the other predictor terms
(not in |
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 |
col |
The colours for the facets of the plot. If this is |
color |
the colour scheme to use for plots when |
contour.col |
sets the colour of contours when using |
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 |
type |
|
plot.type |
one of |
zlim |
a two item array giving the lower and upper limits for the z-axis
scale. |
nCol |
The number of colors to use in color schemes. |
... |
other options to pass on to |
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.
Simply produces a plot.
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.
Simon Wood simon.wood@r-project.org
Based on an original idea and design by Mike Lonergan.
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 variablePlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.