# NOT RUN {
#2-d example
fit<- Tps(ChicagoO3$x, ChicagoO3$y) # fits a surface to ozone measurements.
set.panel(2,2)
plot(fit) # four diagnostic plots of fit and residuals.
set.panel()
# summary of fit and estiamtes of lambda the smoothing parameter
summary(fit)
surface( fit) # Quick image/contour plot of GCV surface.
# NOTE: the predict function is quite flexible:
look<- predict( fit, lambda=2.0)
# evaluates the estimate at lambda =2.0 _not_ the GCV estimate
# it does so very efficiently from the Krig fit object.
look<- predict( fit, df=7.5)
# evaluates the estimate at the lambda values such that
# the effective degrees of freedom is 7.5
# compare this to fitting a thin plate spline with
# lambda chosen so that there are 7.5 effective
# degrees of freedom in estimate
# Note that the GCV function is still computed and minimized
# but the lambda values used correpsonds to 7.5 df.
fit1<- Tps(ChicagoO3$x, ChicagoO3$y,df=7.5)
set.panel(2,2)
plot(fit1) # four diagnostic plots of fit and residuals.
# GCV function (lower left) has vertical line at 7.5 df.
set.panel()
# The basic matrix decompositions are the same for
# both fit and fit1 objects.
# predict( fit1) is the same as predict( fit, df=7.5)
# predict( fit1, lambda= fit$lambda) is the same as predict(fit)
# predict onto a grid that matches the ranges of the data.
out.p<-predictSurface( fit)
image( out.p)
# the surface function (e.g. surface( fit)) essentially combines
# the two steps above
# predict at different effective
# number of parameters
out.p<-predictSurface( fit,df=10)
# }
# NOT RUN {
# predicting on a grid along with a covariate
data( COmonthlyMet)
# predicting average daily minimum temps for spring in Colorado
# NOTE to create an 4km elevation grid:
# data(PRISMelevation); CO.elev1 <- crop.image(PRISMelevation, CO.loc )
# then use same grid for the predictions: CO.Grid1<- CO.elev1[c("x","y")]
obj<- Tps( CO.loc, CO.tmin.MAM.climate, Z= CO.elev)
out.p<-predictSurface( obj,
grid.list=CO.Grid, ZGrid= CO.elevGrid)
image.plot( out.p)
US(add=TRUE, col="grey")
contour( CO.elevGrid, add=TRUE, levels=c(2000), col="black")
# }
# NOT RUN {
#A 1-d example with confidence intervals
out<-Tps( rat.diet$t, rat.diet$trt) # lambda found by GCV
out
plot( out$x, out$y)
xgrid<- seq( min( out$x), max( out$x),,100)
fhat<- predict( out,xgrid)
lines( xgrid, fhat,)
SE<- predictSE( out, xgrid)
lines( xgrid,fhat + 1.96* SE, col="red", lty=2)
lines(xgrid, fhat - 1.96*SE, col="red", lty=2)
#
# compare to the ( much faster) B spline algorithm
# sreg(rat.diet$t, rat.diet$trt)
# Here is a 1-d example with 95 percent CIs where sreg would not
# work:
# sreg would give the right estimate here but not the right CI's
x<- seq( 0,1,,8)
y<- sin(3*x)
out<-Tps( x, y) # lambda found by GCV
plot( out$x, out$y)
xgrid<- seq( min( out$x), max( out$x),,100)
fhat<- predict( out,xgrid)
lines( xgrid, fhat, lwd=2)
SE<- predictSE( out, xgrid)
lines( xgrid,fhat + 1.96* SE, col="red", lty=2)
lines(xgrid, fhat - 1.96*SE, col="red", lty=2)
# }
# NOT RUN {
# More involved example adding a covariate to the fixed part of model
# }
# NOT RUN {
set.panel( 1,3)
# without elevation covariate
out0<-Tps( RMprecip$x,RMprecip$y)
surface( out0)
US( add=TRUE, col="grey")
# with elevation covariate
out<- Tps( RMprecip$x,RMprecip$y, Z=RMprecip$elev)
# NOTE: out$d[4] is the estimated elevation coefficient
# it is easy to get the smooth surface separate from the elevation.
out.p<-predictSurface( out, drop.Z=TRUE)
surface( out.p)
US( add=TRUE, col="grey")
# and if the estimate is of high resolution and you get by with
# a simple discretizing -- does not work in this case!
quilt.plot( out$x, out$fitted.values)
#
# the exact way to do this is evaluate the estimate
# on a grid where you also have elevations
# An elevation DEM from the PRISM climate data product (4km resolution)
data(RMelevation)
grid.list<- list( x=RMelevation$x, y= RMelevation$y)
fit.full<- predictSurface( out, grid.list, ZGrid= RMelevation)
# this is the linear fixed part of the second spatial model:
# lon,lat and elevation
fit.fixed<- predictSurface( out, grid.list, just.fixed=TRUE, ZGrid= RMelevation)
# This is the smooth part but also with the linear lon lat terms.
fit.smooth<-predictSurface( out, grid.list, drop.Z=TRUE)
#
set.panel( 3,1)
fit0<- predictSurface( out0, grid.list)
image.plot( fit0)
title(" first spatial model (w/o elevation)")
image.plot( fit.fixed)
title(" fixed part of second model (lon,lat,elev linear model)")
US( add=TRUE)
image.plot( fit.full)
title("full prediction second model")
set.panel()
# }
# NOT RUN {
###
### fast Tps
# m=2 p= 2m-d= 2
#
# Note: theta =3 degrees is a very generous taper range.
# Use some trial theta value with rdist.nearest to determine a
# a useful taper. Some empirical studies suggest that in the
# interpolation case in 2 d the taper should be large enough to
# about 20 non zero nearest neighbors for every location.
fastTps( RMprecip$x,RMprecip$y,m=2,lambda= 1e-2, theta=3.0) -> out2
# note that fastTps produces an mKrig object so one can use all the
# the overloaded functions that are defined for the mKrig class.
# summary of what happened note estimate of effective degrees of
# freedom
print( out2)
# }
# NOT RUN {
set.panel( 1,2)
surface( out2)
#
# now use great circle distance for this smooth
# Here "theta" for the taper support is the great circle distance in degrees latitude.
# Typically for data analysis it more convenient to think in degrees. A degree of
# latitude is about 68 miles (111 km).
#
fastTps( RMprecip$x,RMprecip$y,m=2,lambda= 1e-2,lon.lat=TRUE, theta= 3.0) -> out3
print( out3) # note the effective degrees of freedom is different.
surface(out3)
set.panel()
# }
# NOT RUN {
# }
# NOT RUN {
#
# simulation reusing Tps/Krig object
#
fit<- Tps( rat.diet$t, rat.diet$trt)
true<- fit$fitted.values
N<- length( fit$y)
temp<- matrix( NA, ncol=50, nrow=N)
sigma<- fit$shat.GCV
for ( k in 1:50){
ysim<- true + sigma* rnorm(N)
temp[,k]<- predict(fit, y= ysim)
}
matplot( fit$x, temp, type="l")
# }
# NOT RUN {
#
#4-d example
fit<- Tps(BD[,1:4],BD$lnya,scale.type="range")
# plots fitted surface and contours
# default is to hold 3rd and 4th fixed at median values
surface(fit)
# }
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