| vis.gam {mgcv} | R Documentation |
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 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. Names must be names from
names(x$model). i.e. terms are used, rather than variables.
|
cond |
a named list of the values to use for the other predictor terms
(not in view). Terms omitted from
this list will have their values set to their mean for continuous variables,
or first level for factors. Names must correspond to names(x$model).
|
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. |
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
defualt values used by vis.gam.
Simply produces a plot.
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)
# 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")
# ..... areas where there is no data are not plotted
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= 35) # plot against by variable