On Monday 26 October 2009, Frank E Harrell Jr wrote:
Dylan Beaudette wrote:
Hi,
Using the latest rms package I am able to make nice plots of model
predictions +/- desired confidence intervals like this:
# need this
library(rms)
# setup data
d - data.frame(x=rnorm(100), y=rnorm(100))
dd - datadist(d)
options(datadist='dd')
# fit model
l - ols(y ~ rcs(x), data=d)
# predict along original limits of data
l.pred - Predict(l)
# plot of fit and conf. int.
xYplot(Cbind(yhat, lower, upper) ~ x, data=l.pred, method='filled',
col.fill=grey(0.9), col=1, type='l')
Is there any way in which I can turn this figure on its side, by plotting
x ~ y... something like this:
# doesn't work
xYplot(x ~ Cbind(yhat, lower, upper), data=l.pred, method='filled',
lable.curves=FALSE, col.fill=grey(0.9), col=1, type='l')
# standard lattice, but without the fancy filled area
xyplot(x ~ yhat + lower + upper, data=l.pred, type='l', lty=c(1,2,2),
col=1)
Any suggestions? If it is not possible, then I will try and manually make
the figure with basic lattice functions.
Cheers,
Dylan
Dylan,
Cbind is for the left hand side of the formula. I suggest you look at
one of the books that covers lattice graphics, or the online resources
for lattice to customize this. The output from Predict is suitable for
several graphics models.
Frank
Thanks Frank. I was able to cobble together a replacement; note that it
depends on the original structure of my data, and is therefore not a general
solution.
Cheers,
Dylan
panel.yx - function(x, y, subscripts, groups, upper, lower, ...) {
# extract this panel's data
d - data.frame(yhat=x, top=y, upper=upper[subscripts],
lower=lower[subscripts], groups=groups[subscripts])
# levels in the groups, for color matching
ll - levels(d$groups)
# add grid
panel.grid(h=-1, v=-1, lty=3, col=1)
# add conf. intervals
by(d, d$groups, function(d_i) {
# make conf.int polygon
panel.polygon(x=c(d_i$lower, rev(d_i$upper)), y=c(d_i$top, rev(d_i$top)),
col=grey(0.85), border=NA, alpha=0.5)
})
# add main lines
by(d, d$groups, function(d_i) {
# lookup color
m - match(unique(d_i$group), ll)
# add line
panel.lines(d_i$yhat, d_i$top, lwd=trellis.par.get('superpose.line')$lwd,
col=trellis.par.get('superpose.line')$col[m])
})
}
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
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