R: Thin plate spline regression

Tps {fields} | R Documentation

## Thin plate spline regression

### Description

Fits a thin plate spline surface to irregularly spaced data. The smoothing parameter is chosen by generalized cross-validation. The assumed model is additive Y = f(X) +e where f(X) is a d dimensional surface. This function also works for just a single dimension and is a special case of a spatial process estimate (Kriging). A "fast" version of this function uses a compactly supported Wendland covariance and computes the estimate for a fixed smoothing parameter.

### Usage

    Tps(x, Y, m = NULL, p = NULL, scale.type = "range", lon.lat = FALSE,
             miles = TRUE, method = "GCV", GCV = TRUE, ...)

    fastTps(x, Y, m = NULL, p = NULL,  theta, lon.lat=FALSE,
              find.trA = TRUE, lambda=0, ...)

### Arguments

`x` | Matrix of independent variables. Each row is a location or a set of independent covariates.
`Y` | Vector of dependent variables.
`m` | A polynomial function of degree (m-1) will be included in the model as the drift (or spatial trend) component. Default is the value such that 2m-d is greater than zero where d is the dimension of x.
`p` | Polynomial power for Wendland radial basis functions. Default is 2m-d where d is the dimension of x.
`scale.type` | The independent variables and knots are scaled to the specified scale.type. By default the scale type is "range", whereby the locations are transformed to the interval (0,1) by forming (x-min(x))/range(x) for each x. Scale type of "user" allows specification of an x.center and x.scale by the user. The default for "user" is mean 0 and standard deviation 1. Scale type of "unscaled" does not scale the data.
`theta` | The tapering range that is passed to the Wendland compactly supported covariance. The covariance (i.e. the radial basis function) is zero beyond range theta. The larger theta the closer this model will approximate the standard thin plate spline.
`lon.lat` | If TRUE locations are interpreted as lognitude and latitude and great circle distance is used to find distances among locations. The theta scale parameter for `fast.Tps` (setting the compact support of the Wendland function) in this case is in units of miles (see example and caution below).
`method` | Determines what "smoothing" parameter should be used. The default is to estimate standard GCV Other choices are: GCV.model, GCV.one, RMSE, pure error and REML. The differences are explained in the Krig help file.
`GCV` | If TRUE the decompositions are done to efficiently evaluate the estimate, GCV function and likelihood at multiple values of lambda.
`miles` | If TRUE great circle distances are in miles if FALSE distances are in kilometers
`lambda` | Smoothing parameter the ratio of error variance to process variance, default is zero which corresponds to interpolation. See fastTpsMLE to estimate this paramter from the data.
`find.trA` | If TRUE will estimate the effective degrees of freedom using a simple Monte Carlo method. This will add to the computational burden by approximately `NtrA` solutions of the linear system but the cholesky decomposition is reused.
`...` | For `Tps` any argument that is valid for the `Krig` function. Some of the main ones are listed below. For `fastTps` any argument that is suitable for the `mKrig` function see help on mKrig for these choices. Arguments for Tps: lambda Smoothing parameter that is the ratio of the error variance (sigma**2) to the scale parameter of the covariance function. If omitted this is estimated by GCV. Z Linear covariates to be included in fixed part of the model that are distinct from the default low order polynomial in `x` df The effective number of parameters for the fitted surface. Conversely, N- df, where N is the total number of observations is the degrees of freedom associated with the residuals. This is an alternative to specifying lambda and much more interpretable. cost Cost value used in GCV criterion. Corresponds to a penalty for increased number of parameters. The default is 1.0 and corresponds to the usual GCV. weights Weights are proportional to the reciprocal variance of the measurement error. The default is no weighting i.e. vector of unit weights. nstep.cv Number of grid points for minimum GCV search. x.center Centering values are subtracted from each column of the x matrix. Must have scale.type="user". x.scale Scale values that divided into each column after centering. Must have scale.type="user". rho Scale factor for covariance. sigma2 Variance of errors or if weights are not equal to 1 the variance is sigma**2/weight. verbose If true will print out all kinds of intermediate stuff. mean.obj Object to predict the mean of the spatial process. sd.obj Object to predict the marginal standard deviation of the spatial process. null.function An R function that creates the matrices for the null space model. The default is fields.mkpoly, an R function that creates a polynomial regression matrix with all terms up to degree m-1. (See Details) offset The offset to be used in the GCV criterion. Default is 0. This would be used when Krig/Tps is part of a backfitting algorithm and the offset has to be included to reflect other model degrees of freedom.

### Details

Both of these functions are special cases of using the `Krig` and `mKrig` functions. See the help on each of these for more information on the calling arguments and what is returned.

A thin plate spline is result of minimizing the residual sum of squares subject to a constraint that the function have a certain level of smoothness (or roughness penalty). Roughness is quantified by the integral of squared m-th order derivatives. For one dimension and m=2 the roughness penalty is the integrated square of the second derivative of the function. For two dimensions the roughness penalty is the integral of

(Dxx(f))**22 + 2(Dxy(f))**2 + (Dyy(f))**22

(where Duv denotes the second partial derivative with respect to u and v.) Besides controlling the order of the derivatives, the value of m also determines the base polynomial that is fit to the data. The degree of this polynomial is (m-1).

The smoothing parameter controls the amount that the data is smoothed. In the usual form this is denoted by lambda, the Lagrange multiplier of the minimization problem. Although this is an awkward scale, lambda =0 corresponds to no smoothness constraints and the data is interpolated. lambda=infinity corresponds to just fitting the polynomial base model by ordinary least squares.

This estimator is implemented by passing the right generalized covariance function based on radial basis functions to the more general function Krig. One advantage of this implementation is that once a Tps/Krig object is created the estimator can be found rapidly for other data and smoothing parameters provided the locations remain unchanged. This makes simulation within R efficient (see example below). Tps does not currently support the knots argument where one can use a reduced set of basis functions. This is mainly to simplify the code and a good alternative using knots would be to use a valid covariance from the Matern family and a large range parameter.

CAUTION about `lon.lat=TRUE`: The option to use great circle distance to define the radial basis functions (`lon.lat=TRUE`) is very useful for small geographic domains where the spherical geometry is well approximated by a plane. However, for large domains the spherical distortion be large enough that the basis function no longer define a positive definite system and Tps will report a numerical error. An alternative is to switch to a three dimensional thin plate spline the locations being the direction cosines. This will give approximate great circle distances for locations that are close and also the numerical methods will always have a positive definite matrices.

Here is an example using this idea for `RMprecip` and also some examples of building grids and evaluating the Tps results on them:

    # a useful function:
      dircos<- function(x1){
                 coslat1 <- cos((x1[, 2] * pi)/180)
                 sinlat1 <- sin((x1[, 2] * pi)/180)
                 coslon1 <- cos((x1[, 1] * pi)/180)
                 sinlon1 <- sin((x1[, 1] * pi)/180)
                 cbind(coslon1*coslat1, sinlon1*coslat1, sinlat1)}
    # fit in 3-d to direction cosines
      out<- Tps(dircos(RMprecip$x),RMprecip$y)
      xg<-make.surface.grid(fields.x.to.grid(RMprecip$x))
      fhat<- predict( out, dircos(xg))
    # coerce to image format from prediction vector and grid points.
      out.p<- as.surface( xg, fhat)
      surface( out.p)
    # compare to the automatic
      out0<- Tps(RMprecip$x,RMprecip$y, lon.lat=TRUE)
      surface(out0)

The function `fastTps` is really a convenient wrapper function that calls `mKrig` with the Wendland covariance function. This is experimental and some care needs to exercised in specifying the taper range and power ( `p`) which describes the polynomial behavior of the Wendland at the origin. Note that unlike Tps the locations are not scaled to unit range and this can cause havoc in smoothing problems with variables in very different units. So rescaling the locations `x<- scale(x)` is a good idea for putting the variables on a common scale for smoothing. This function does have the potential to approximate estimates of Tps for very large spatial data sets. See `wendland.cov` and help on the SPAM package for more background. Also, the function `predictSurface.fastTps` has been made more efficient for the case of k=2 and m=2.

See also the mKrig function for handling larger data sets and also for an example of combining Tps and mKrig for evaluation on a huge grid.

### Value

A list of class Krig. This includes the fitted values, the predicted surface evaluated at the observation locations, and the residuals. The results of the grid search minimizing the generalized cross validation function are returned in gcv.grid. Note that the GCV/REML optimization is done even if lambda or df is given. Please see the documentation on Krig for details of the returned arguments.

### References

See "Nonparametric Regression and Generalized Linear Models" by Green and Silverman. See "Additive Models" by Hastie and Tibshirani.

### See Also

Krig, summary.Krig, predict.Krig, predictSE.Krig, predictSurface, predictSurface.fastTps, plot.Krig, mKrig `surface.Krig`, `sreg`

### Examples

    #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")

    ## End(Not run)
    ## 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)

    ## End(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()

    ## End(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()

    ## End(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")

    ## End(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)

[Package fields version 9.6.1 Index]