189 lines
6.1 KiB
R
189 lines
6.1 KiB
R
#-*- R -*-
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## Script from Fourth Edition of `Modern Applied Statistics with S'
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# Chapter 15 Spatial Statistics
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library(MASS)
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pdf(file="ch15.pdf", width=8, height=8, pointsize=9)
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options(width=65, digits=5)
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library(spatial)
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# 15.1 Spatial interpolation and smoothing
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par(mfrow=c(2,2), pty = "s")
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topo.ls <- surf.ls(2, topo)
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trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
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eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
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contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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title("Degree=2")
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topo.ls <- surf.ls(3, topo)
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trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
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eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
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contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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title("Degree=3")
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topo.ls <- surf.ls(4, topo)
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trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
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eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
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contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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title("Degree=4")
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topo.ls <- surf.ls(6, topo)
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trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
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eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
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contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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title("Degree=6")
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library(lattice)
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topo.ls <- surf.ls(4, topo)
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trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
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trsurf[c("x", "y")] <- expand.grid(x=trsurf$x, y=trsurf$y)
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plt1 <- levelplot(z ~ x * y, trsurf, aspect=1,
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at = seq(650, 1000, 10), xlab = "", ylab = "")
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plt2 <- wireframe(z ~ x * y, trsurf, aspect=c(1, 0.5),
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screen = list(z = -30, x = -60))
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print(plt1, position = c(0, 0, 0.5, 1), more=TRUE)
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print(plt2, position = c(0.45, 0, 1, 1))
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par(mfcol = c(2, 2), pty = "s")
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topo.loess <- loess(z ~ x * y, topo, degree = 2, span = 0.25,
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normalize = FALSE)
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topo.mar <- list(x = seq(0, 6.5, 0.1), y = seq(0, 6.5, 0.1))
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topo.lo <- predict(topo.loess, expand.grid(topo.mar), se = TRUE)
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eqscplot(topo.mar, xlab = "fit", ylab = "", type = "n")
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contour(topo.mar$x, topo.mar$y, topo.lo$fit,
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levels = seq(700, 1000, 25), add = TRUE)
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points(topo)
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eqscplot(topo.mar, xlab = "standard error", ylab = "", type = "n")
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contour(topo.mar$x,topo.mar$y,topo.lo$se.fit,
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levels = seq(5, 25, 5), add = TRUE)
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title("Loess degree = 2")
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points(topo)
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topo.loess <- loess(z ~ x * y, topo, degree = 1, span = 0.25, normalize = FALSE)
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topo.lo <- predict(topo.loess, expand.grid(topo.mar), se=TRUE)
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eqscplot(topo.mar, xlab = "fit", ylab = "", type = "n")
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contour(topo.mar$x,topo.mar$y,topo.lo$fit, levels = seq(700, 1000, 25),
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add = TRUE)
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points(topo)
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eqscplot(topo.mar, xlab = "standard error", ylab = "", type = "n")
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contour(topo.mar$x,topo.mar$y,topo.lo$se.fit, levels = seq(5, 25, 5),
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add = TRUE)
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title("Loess degree = 1")
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points(topo)
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library(interp) # was akima, interp.old()
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par(mfrow = c(1, 2), pty= "s")
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topo.int <- interp(topo$x, topo$y, topo$z)
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eqscplot(topo.int, xlab = "interp default", ylab = "", type = "n")
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contour(topo.int, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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topo.mar <- list(x = seq(0, 6.5, 0.1), y = seq(0, 6.5, 0.1))
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topo.int2 <- interp(topo$x, topo$y, topo$z, topo.mar$x, topo.mar$y,
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extrap = TRUE) # was ncp = 4.
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eqscplot(topo.int2, xlab = "interp", ylab = "", type = "n")
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contour(topo.int2, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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# 15.2 Kriging
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par(mfrow = c(2, 2), pty = "s")
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topo.ls <- surf.ls(2, topo)
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trsurf <- trmat(topo.ls, 0, 6.5, 0, 6.5, 30)
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eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
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contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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title("LS trend surface")
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topo.gls <- surf.gls(2, expcov, topo, d = 0.7)
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trsurf <- trmat(topo.gls, 0, 6.5, 0, 6.5, 30)
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eqscplot(trsurf, , xlab = "", ylab = "", type = "n")
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contour(trsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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title("GLS trend surface")
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prsurf <- prmat(topo.gls, 0, 6.5, 0, 6.5, 50)
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eqscplot(prsurf, , xlab = "", ylab = "", type = "n")
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contour(prsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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title("Kriging prediction")
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sesurf <- semat(topo.gls, 0, 6.5, 0, 6.5, 30)
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eqscplot(sesurf, , xlab = "", ylab = "", type = "n")
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contour(sesurf, levels = c(20, 25), add = TRUE)
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points(topo)
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title("Kriging s.e.")
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par(mfrow = c(2, 2), pty = "m")
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topo.kr <- surf.ls(2, topo)
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correlogram(topo.kr, 25)
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d <- seq(0, 7, 0.1)
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lines(d, expcov(d, 0.7))
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variogram(topo.kr, 25)
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## left panel of Figure 15.7
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topo.kr <- surf.gls(2, expcov, topo, d=0.7)
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correlogram(topo.kr, 25)
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lines(d, expcov(d, 0.7))
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lines(d, gaucov(d, 1.0, 0.3), lty = 3) # try nugget effect
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## right panel
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topo.kr <- surf.ls(0, topo)
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correlogram(topo.kr, 25)
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lines(d, gaucov(d, 2, 0.05))
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par(mfrow = c(2, 2), pty = "s")
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## top row of Figure 15.8
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topo.kr <- surf.gls(2, gaucov, topo, d = 1, alph = 0.3)
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prsurf <- prmat(topo.kr, 0, 6.5, 0, 6.5, 50)
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eqscplot(prsurf, , xlab = "fit", ylab = "", type = "n")
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contour(prsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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sesurf <- semat(topo.kr, 0, 6.5, 0, 6.5, 25)
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eqscplot(sesurf, , xlab = "standard error", ylab = "", type = "n")
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contour(sesurf, levels = c(15, 20, 25), add = TRUE)
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points(topo)
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## bottom row of Figure 15.8
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topo.kr <- surf.gls(0, gaucov, topo, d = 2, alph = 0.05,
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nx = 10000)
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prsurf <- prmat(topo.kr, 0, 6.5, 0, 6.5, 50)
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eqscplot(prsurf, , xlab = "fit", ylab = "", type = "n")
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contour(prsurf, levels = seq(600, 1000, 25), add = TRUE)
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points(topo)
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sesurf <- semat(topo.kr, 0, 6.5, 0, 6.5, 25)
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eqscplot(sesurf, , xlab = "standard error", ylab = "", type = "n")
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contour(sesurf, levels = c(15, 20, 25), add = TRUE)
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points(topo)
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# 15.3 Point process analysis
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library(spatial)
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pines <- ppinit("pines.dat")
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par(mfrow = c(2, 2), pty = "s")
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plot(pines, xlim = c(0, 10), ylim = c(0, 10),
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xlab = "", ylab = "", xaxs = "i", yaxs = "i")
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plot(Kfn(pines,5), type = "s", xlab = "distance", ylab = "L(t)")
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lims <- Kenvl(5, 100, Psim(72))
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lines(lims$x, lims$l, lty = 2)
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lines(lims$x, lims$u, lty = 2)
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ppregion(pines)
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plot(Kfn(pines, 1.5), type = "s",
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xlab = "distance", ylab = "L(t)")
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lims <- Kenvl(1.5, 100, Strauss(72, 0.2, 0.7))
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lines(lims$x, lims$a, lty = 2)
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lines(lims$x, lims$l, lty = 2)
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lines(lims$x, lims$u, lty = 2)
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pplik(pines, 0.7)
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lines(Kaver(1.5, 100, Strauss(72, 0.15, 0.7)), lty = 3)
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# End of ch15
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