################################################### ### chunk number 1: ################################################### rm(list=ls()) .owidth <- getOption("width") options("width"=70) owarn <- options("warn")$warn options(warn=1) .epsNo <- 0 ################################################### ### chunk number 2: figreset eval=FALSE ################################################### ## .iwidth <- 4 ## .iheight <- 4 ## .ipointsize <- 10 ## .pwd <- 0.95 ## grey_gamma <- 2.2 ################################################### ### chunk number 3: ################################################### .iwidth <- 4 .iheight <- 4 .ipointsize <- 10 .pwd <- 0.95 grey_gamma <- 2.2 ################################################### ### chunk number 4: afig eval=FALSE ################################################### ## .epsNo <- .epsNo + 1; file <- paste("Fig-hlo-", .epsNo, ".eps", sep="") ## postscript(file=file, onefile = TRUE, paper="special", width = .iwidth, height = .iheight, pointsize = .ipointsize, horizontal=FALSE) ## def.par <- par(no.readonly = TRUE) ################################################### ### chunk number 5: zfig eval=FALSE ################################################### ## par(def.par) ## dev.null <- dev.off() ## system(paste("../scripts/mungeEps.sh", file, "3 > outfile ; mv outfile", file, sep=" ")) ## cat("\\includegraphics[width=", .pwd, "\\textwidth]{", file, "}", sep="") ## cat("\n") ################################################### ### chunk number 6: zfigr eval=FALSE ################################################### ## par(def.par) ## dev.null <- dev.off() ## system(paste("../scripts/mungeEps.sh", file, "3 > outfile ; mv outfile", file, sep=" ")) ## cat("\\includegraphics[width=", .pwd, "\\textwidth,angle=90]{", file, "}", sep="") ## cat("\n") ################################################### ### chunk number 7: afig_l eval=FALSE ################################################### ## .epsNo <- .epsNo + 1; file <- paste("Fig-hlo-", .epsNo, ".eps", sep="") ## postscript(file=file, onefile = TRUE, paper="special", width = .iwidth, height = .iheight, pointsize = .ipointsize, horizontal=FALSE) ################################################### ### chunk number 8: zfig_l eval=FALSE ################################################### ## dev.null <- dev.off() ## #system(paste("./mungeEps.sh", file, "3 > outfile ; mv outfile", file, sep=" ")) ## cat("\\includegraphics[width=", .pwd, "\\textwidth]{", file, "}", sep="") ## cat("\n") ################################################### ### chunk number 9: ################################################### library("pkgDepTools") # library("Biobase") library("Rgraphviz") allDeps <- makeDepGraph("http://cran.ii.uib.no", type="source", keep.builtin=FALSE, dosize=FALSE) allDepsOnMe <- reverseEdgeDirections(allDeps) categoryNodes <- c("sp", names(acc(allDepsOnMe, "sp")[[1]])) categoryGraph <- subGraph(categoryNodes, allDepsOnMe) nn <- makeNodeAttrs(categoryGraph, shape="ellipse") fc <- rep("#ffffff", numNodes(categoryGraph)) names(fc) <- names(nn$label) ours <- match(c("sp", "DCluster", "gstat", "maptools", "rgdal", "spdep", "spgrass6", "spgwr", "splancs"), nn$label) fc[ours] <- "#e0e0e0" nn$fillcolor <- fc ################################################### ### chunk number 10: ################################################### .iwidth <- 7 .iheight <- 4 .ipointsize <- 10 .pwd <- 1.4 .epsNo <- .epsNo + 1; file <- paste("Fig-hlo-", .epsNo, ".eps", sep="") postscript(file=file, onefile = TRUE, paper="special", width = .iwidth, height = .iheight, pointsize = .ipointsize, horizontal=FALSE) def.par <- par(no.readonly = TRUE) plot(categoryGraph, nodeAttrs=nn) par(def.par) dev.null <- dev.off() system(paste("../scripts/mungeEps.sh", file, "3 > outfile ; mv outfile", file, sep=" ")) cat("\\includegraphics[width=", .pwd, "\\textwidth,angle=90]{", file, "}", sep="") cat("\n") .iwidth <- 4 .iheight <- 4 .ipointsize <- 10 .pwd <- 0.95 grey_gamma <- 2.2 ################################################### ### chunk number 11: ################################################### library(maptools) library(maps) library(rgdal) ################################################### ### chunk number 12: ################################################### .iwidth <- 6 .iheight <- 3.5 .ipointsize <- 10 .epsNo <- .epsNo + 1; file <- paste("Fig-hlo-", .epsNo, ".eps", sep="") postscript(file=file, onefile = TRUE, paper="special", width = .iwidth, height = .iheight, pointsize = .ipointsize, horizontal=FALSE) def.par <- par(no.readonly = TRUE) # volc.tab = read.table("data.xy") volc.tab = read.table("hsd_data/data1964al.xy") volc = SpatialPoints(volc.tab[c(2,1)]) llCRS <- CRS("+proj=longlat +ellps=WGS84") proj4string(volc) <- llCRS prj_new = CRS("+proj=moll") volc_proj = spTransform(volc, prj_new) wrld <- map("world", interior=FALSE, xlim=c(-179,179), ylim=c(-89,89), plot=FALSE) wrld_p <- pruneMap(wrld, xlim=c(-179,179)) wrld_sp <- map2SpatialLines(wrld_p, proj4string=llCRS) wrld_proj <- spTransform(wrld_sp, prj_new) #save(c("wrld_proj", "wrld_sp"), file = "hsd_data/wrld.RData") #load("hsd_data/wrld.RData") wrld_grd <- gridlines(wrld_sp, easts=c(-179,seq(-150,150,50),179.5), norths=seq(-75,75,15), ndiscr=100) wrld_grd_proj <- spTransform(wrld_grd, prj_new) at_sp <- gridat(wrld_sp, easts=0, norths=seq(-75,75,15), offset=0.3) at_proj <- spTransform(at_sp, prj_new) opar = par(no.readonly = TRUE) par(mar=c(1,1,1,1)+0.1, xpd=NA) plot(wrld_proj, col="grey50") plot(wrld_grd_proj, add=TRUE, lty=3, col="grey50") points(volc_proj, cex = .8, pch = 3) text(coordinates(at_proj), pos=at_proj$pos, offset=at_proj$offset, labels=parse(text=as.character(at_proj$lab)), cex=0.6) #legend(c(-18000000,-11000000), c(-6000000,-2500000), pch=3, cex = .2, legend=c("volcano"), bty="n") par(opar) # $ par(def.par) dev.null <- dev.off() system(paste("../scripts/mungeEps.sh", file, "3 > outfile ; mv outfile", file, sep=" ")) cat("\\includegraphics[width=", .pwd, "\\textwidth]{", file, "}", sep="") cat("\n") .iwidth <- 4 .iheight <- 4 .ipointsize <- 10 .pwd <- 0.95 grey_gamma <- 2.2 ################################################### ### chunk number 13: ################################################### .iwidth <- 5 .iheight <- 3.5 .ipointsize <- 9 .epsNo <- .epsNo + 1; file <- paste("Fig-hlo-", .epsNo, ".eps", sep="") postscript(file=file, onefile = TRUE, paper="special", width = .iwidth, height = .iheight, pointsize = .ipointsize, horizontal=FALSE) def.par <- par(no.readonly = TRUE) opar = par(no.readonly = TRUE) par(mar = rep(1,4)) library(sp) data(volcano) grys <- grey.colors(8, 0.55, 0.95, grey_gamma) layout(matrix(c(1,2,1,3,1,4),3,2,byrow=TRUE), c(3,1)) image(volcano, axes=F, col=grys, asp=1, main="a") contour(volcano, add=T) box() image(volcano, axes=F, col='white', asp=1, main="b") library(maptools) x2 = ContourLines2SLDF(contourLines(volcano)) plot(x2, add=T) box() image(volcano, axes=F, col='white', asp=1, main="c") plot(SpatialPolygons(list(Polygons(list(Polygon(coordinates(x2[x2$level == 140,]))), ID="x"))), add = T) box() #image(volcano, axes=F, col='white', asp=1, main="d") image(volcano, axes=F, col=grys, asp=1, main="d") x3l1 = coordinates(x2[x2$level == 160,])[[1]][[1]] x3l2 = coordinates(x2[x2$level == 160,])[[1]][[2]] #plot(SpatialPolygons(list(Polygons(list(Polygon(x3l1,hole=F), Polygon(x3l2,hole=T)), ID=c("x")))), # pbg = 'white', col = grey(.5), add = T) x3 = SpatialPolygons(list(Polygons(list(Polygon(x3l1,hole=F), Polygon(x3l2,hole=T)), ID=c("x")))) SP2TRI = function(x, debug = TRUE){ p = x@polygons[[1]] # object of class Polygons p1 = p@Polygons[[1]] # outer Polygon p2 = p@Polygons[[2]] # inner Polygon stopifnot(!p1@hole) stopifnot(p2@hole) # find nearest point allcoords = rbind(p1@coords, p2@coords) n1 = nrow(p1@coords) n2 = nrow(p2@coords) dists = as.matrix(dist(allcoords))[((n1+1):(n1+n2)),1:n1] wm = which.min(dists)[1] ind1 = (wm %/% n2) + 1 ind2 = wm %% n2 if (debug) print(c(ind1,ind2)) #plot polygon points: p1c = p1@coords p2c = p2@coords #plot shortest distance: if (debug) lines(rbind(p1c[ind1,], p2c[ind2,])) if (debug) points(rbind(p1c, p2c)) p = rbind(p1c[c(ind1:n1,1:ind1),], p2c[c(ind2:n2,1:ind2),], p1c[ind1,]) #polygon(p, col = 'red', border = NULL) polygon(p, angle=45, border = NA, density = 12) } plot(x3, col = 'transparent', add = T) SP2TRI(x3, F) box() par(opar) # $ par(def.par) dev.null <- dev.off() system(paste("../scripts/mungeEps.sh", file, "3 > outfile ; mv outfile", file, sep=" ")) cat("\\includegraphics[width=", .pwd, "\\textwidth]{", file, "}", sep="") cat("\n") layout(matrix(1)) .iwidth <- 4 .iheight <- 4 .ipointsize <- 10 .pwd <- 0.95 grey_gamma <- 2.2 ################################################### ### chunk number 14: ################################################### sI <- capture.output(print(sessionInfo())) cat(paste("%", sI[1:(length(sI)/2)], sep=" "), sep="\n") sT <- capture.output(print(Sys.time())) cat("%", sT, "\n")