From noreply at r-forge.r-project.org Wed Jul 16 12:00:28 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 16 Jul 2014 12:00:28 +0200 (CEST) Subject: [spcopula-commits] r136 - in pkg: . R data demo man tests tests/Examples Message-ID: <20140716100028.CF9D91811D0@r-forge.r-project.org> Author: ben_graeler Date: 2014-07-16 12:00:26 +0200 (Wed, 16 Jul 2014) New Revision: 136 Added: pkg/data/EU_RB_2005.RData Modified: pkg/DESCRIPTION pkg/R/spCopula.R pkg/data/EU_RB.RData pkg/data/simulatedTriples.RData pkg/data/spCopDemo.RData pkg/demo/MRP.R pkg/demo/pureSpVineCopula.R pkg/demo/spCopula.R pkg/demo/stCoVarVineCop.R pkg/demo/stVineCopFit.R pkg/demo/tailDepFunctions.R pkg/man/EU_RB.Rd pkg/man/calcBins.Rd pkg/man/condCovariate.Rd pkg/man/condSpVine.Rd pkg/man/fitSpCopula.Rd pkg/man/getNeighbours.Rd pkg/man/getStNeighbours.Rd pkg/man/loglikByCopulasLags.Rd pkg/man/loglikByCopulasStLags.Rd pkg/man/neighbourhood-class.Rd pkg/man/neighbourhood.Rd pkg/man/rankTransform.Rd pkg/man/reduceNeighbours.Rd pkg/man/simulatedTriples.Rd pkg/man/spCopDemo.Rd pkg/man/spCopPredict.Rd pkg/man/spCopula-class.Rd pkg/man/spCopula.Rd pkg/man/spGaussCopPredict.Rd pkg/man/spGaussLogLik.Rd pkg/man/spVineCopula.Rd pkg/man/stCopPredict.Rd pkg/man/stNeighbourhood.Rd pkg/man/tailDepFun.Rd pkg/man/unitScatter.Rd pkg/tests/Examples/spcopula-Ex.Rout.save pkg/tests/spCopulaTest.R pkg/tests/spCopulaTest.Rout.save pkg/tests/stCopulaTest.R pkg/tests/stCopulaTest.Rout.save Log: - changes motivated by manuscript review Modified: pkg/DESCRIPTION =================================================================== --- pkg/DESCRIPTION 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/DESCRIPTION 2014-07-16 10:00:26 UTC (rev 136) @@ -2,7 +2,7 @@ Type: Package Title: copula driven spatial analysis Version: 0.2-0 -Date: 2014-08-05 +Date: 2014-07-16 Authors at R: c(person("Benedikt", "Graeler", role = c("aut", "cre"), email = "ben.graeler at uni-muenster.de"), person("Marius", "Appel",role = "ctb")) Modified: pkg/R/spCopula.R =================================================================== --- pkg/R/spCopula.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/R/spCopula.R 2014-07-16 10:00:26 UTC (rev 136) @@ -721,14 +721,15 @@ varSplit <- strsplit(neigh at var,"|",fixed=TRUE)[[1]] cond <- suppressWarnings(as.numeric(varSplit[length(varSplit)])) + coVar <- neigh at coVar if(is.na(cond)) { var <- paste(neigh at var,"|0",sep="") - coVar <- paste(neigh at coVar,"|0",sep="") + if(length(coVar)>0) + coVar <- paste(neigh at coVar,"|0",sep="") colnames(u1) <- paste(paste("N", rep(1:(ncol(u1)), each=length(var)), sep=""), rep(var,ncol(u1)),sep=".") } else { var <- paste(neigh at var,cond+1,sep="") - coVar <- neigh at coVar colnames(u1) <- paste(paste("N", rep(cond:(ncol(u1)+cond-1)+2, each=length(var)), sep=""), rep(var,ncol(u1)),sep=".") Modified: pkg/data/EU_RB.RData =================================================================== (Binary files differ) Added: pkg/data/EU_RB_2005.RData =================================================================== (Binary files differ) Property changes on: pkg/data/EU_RB_2005.RData ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: pkg/data/simulatedTriples.RData =================================================================== (Binary files differ) Modified: pkg/data/spCopDemo.RData =================================================================== (Binary files differ) Modified: pkg/demo/MRP.R =================================================================== --- pkg/demo/MRP.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/demo/MRP.R 2014-07-16 10:00:26 UTC (rev 136) @@ -1,5 +1,5 @@ ## get the data -data(simulatedTriples) +data("simulatedTriples") ## rank order transformation peakVol <- rankTransform(triples[,1],triples[,3]) Modified: pkg/demo/pureSpVineCopula.R =================================================================== --- pkg/demo/pureSpVineCopula.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/demo/pureSpVineCopula.R 2014-07-16 10:00:26 UTC (rev 136) @@ -1,10 +1,10 @@ ## librarys ## -library(spcopula) -# library(evd) -library(sp) +library("spcopula") +# library("evd") +library("sp") ## meuse - spatial poionts data.frame ## -data(meuse) +data("meuse") coordinates(meuse) = ~x+y spplot(meuse,"zinc", col.regions=bpy.colors(5)) Modified: pkg/demo/spCopula.R =================================================================== --- pkg/demo/spCopula.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/demo/spCopula.R 2014-07-16 10:00:26 UTC (rev 136) @@ -1,10 +1,10 @@ ## librarys ## -library(spcopula) -library(sp) -# library(evd) +library("spcopula") +library("sp") +# library("evd") ## meuse - spatial poionts data.frame ## -data(meuse) +data("meuse") coordinates(meuse) = ~x+y spplot(meuse,"zinc", col.regions=bpy.colors(5)) Modified: pkg/demo/stCoVarVineCop.R =================================================================== --- pkg/demo/stCoVarVineCop.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/demo/stCoVarVineCop.R 2014-07-16 10:00:26 UTC (rev 136) @@ -5,9 +5,9 @@ # copula family candidates is limited. These chnages have been neces- # sary to maintain the "runability" of this demo. ###################################################################### -library(spcopula) -library(evd) -data(EU_RB) +library("spcopula") +library("evd") +data("EU_RB") # estimate a GEV at each location for PM10 and EMEP parPM10 <- matrix(NA, length(EU_RB at sp), 3) Modified: pkg/demo/stVineCopFit.R =================================================================== --- pkg/demo/stVineCopFit.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/demo/stVineCopFit.R 2014-07-16 10:00:26 UTC (rev 136) @@ -2,8 +2,8 @@ ## selected smaller subset of the original data to reduce calculation demands. ## Thus, results are likely to differ (a little) from the original study. -library(spcopula) -load(url("http://ifgi.uni-muenster.de/~b_grae02/publications/EU_RB_2005.RData")) +library("spcopula") +data("EU_RB_2005") ## spatio-temporal copula # binning, using only 90 out of all temporal instances Modified: pkg/demo/tailDepFunctions.R =================================================================== --- pkg/demo/tailDepFunctions.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/demo/tailDepFunctions.R 2014-07-16 10:00:26 UTC (rev 136) @@ -1,5 +1,5 @@ -library(spcopula) -data(simulatedTriples) +library("spcopula") +data("simulatedTriples") rtPair <- 1-as.matrix(rankTransform(triples[,c(1,3)])) Modified: pkg/man/EU_RB.Rd =================================================================== --- pkg/man/EU_RB.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/EU_RB.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -7,7 +7,7 @@ \description{ Daily mean PM10 concentrations over Europe in June and July 2005 } -\usage{data(EU_RB)} +\usage{data("EU_RB")} \format{ The format is: Formal class 'STSDF' [package "spacetime"] with 5 slots @@ -29,7 +29,7 @@ .. .. .. .. ..$ : chr [1:2] "min" "max" .. .. ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots .. .. .. .. ..@ projargs: chr " +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs" - ..@ time :An ?xts? object on 2005-06-01/2005-07-31 containing: + ..@ time :An 'xts' object on 2005-06-01/2005-07-31 containing: Data: int [1:61, 1] 5266 5267 5268 5269 5270 5271 5272 5273 5274 5275 ... - attr(*, "dimnames")=List of 2 ..$ : NULL @@ -49,7 +49,7 @@ http://acm.eionet.europa.eu/reports/ETCACM_TP_2011_10_spatio-temp_AQinterpolation } \examples{ -data(EU_RB) +data("EU_RB") str(EU_RB) } \keyword{datasets} Modified: pkg/man/calcBins.Rd =================================================================== --- pkg/man/calcBins.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/calcBins.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -56,8 +56,8 @@ \code{\link{VineCopula-package}} } \examples{ -library(sp) -data(meuse) +library("sp") +data("meuse") coordinates(meuse) = ~x+y meuse$rtZinc <- rank(meuse$zinc)/(length(meuse)+1) Modified: pkg/man/condCovariate.Rd =================================================================== --- pkg/man/condCovariate.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/condCovariate.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -25,8 +25,8 @@ \seealso{\code{\linkS4class{stNeighbourhood}}} \examples{ -library(sp) -library(spacetime) +library("sp") +library("spacetime") sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2) Modified: pkg/man/condSpVine.Rd =================================================================== --- pkg/man/condSpVine.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/condSpVine.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -35,7 +35,7 @@ \code{\linkS4class{spVineCopula}} } \examples{ -data(spCopDemo) +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) Modified: pkg/man/fitSpCopula.Rd =================================================================== --- pkg/man/fitSpCopula.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/fitSpCopula.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -38,15 +38,15 @@ } \examples{ # reload some spatial data -library(sp) -data(meuse) +library("sp") +data("meuse") coordinates(meuse) <- ~x+y # drop margins meuse$marZinc <- plnorm(meuse$zinc, mean(log(meuse$zinc)), sd(log(meuse$zinc))) # load data from a provided binning -data(spCopDemo) +data("spCopDemo") fitSpCopula(bins, meuse, 600) } Modified: pkg/man/getNeighbours.Rd =================================================================== --- pkg/man/getNeighbours.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/getNeighbours.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -29,7 +29,7 @@ See \code{\link{neighbourhood}} for the native constructor of a \code{\linkS4class{neighbourhood}} class. } \examples{ -library(sp) +library("sp") spdf <- data.frame(x=c(112,154,212,289,345),y=c(124,198,85,168,346),measure=rlnorm(5)) coordinates(spdf) <- ~x+y Modified: pkg/man/getStNeighbours.Rd =================================================================== --- pkg/man/getStNeighbours.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/getStNeighbours.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -41,8 +41,8 @@ See \code{\link{stNeighbourhood}} for the native constructor of a \code{\linkS4class{stNeighbourhood}} class. The pure spatial version can be found at \code{\link{getNeighbours}}. } \examples{ -library(sp) -library(spacetime) +library("sp") +library("spacetime") sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2) Modified: pkg/man/loglikByCopulasLags.Rd =================================================================== --- pkg/man/loglikByCopulasLags.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/loglikByCopulasLags.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -33,15 +33,15 @@ \examples{ # load spatial data -library(sp) -data(meuse) +library("sp") +data("meuse") coordinates(meuse) <- ~x+y # drop margins meuse$marZinc <- plnorm(meuse$zinc, mean(log(meuse$zinc)), sd(log(meuse$zinc))) # load parts of the workspace from demo(spCopula) -data(spCopDemo) +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) Modified: pkg/man/loglikByCopulasStLags.Rd =================================================================== --- pkg/man/loglikByCopulasStLags.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/loglikByCopulasStLags.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -31,15 +31,15 @@ \examples{ # the spatial case # load spatial data -library(sp) -data(meuse) +library("sp") +data("meuse") coordinates(meuse) <- ~x+y # drop margins meuse$marZinc <- plnorm(meuse$zinc, mean(log(meuse$zinc)), sd(log(meuse$zinc))) # load parts of the workspace from demo(spCopula) -data(spCopDemo) +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) Modified: pkg/man/neighbourhood-class.Rd =================================================================== --- pkg/man/neighbourhood-class.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/neighbourhood-class.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -38,7 +38,7 @@ \code{\link{getNeighbours}} } \examples{ -library(sp) +library("sp") spdf <- data.frame(x=c(112,154,212,289),y=c(124,198,85,168),measure=rlnorm(4)) coordinates(spdf) <- ~x+y Modified: pkg/man/neighbourhood.Rd =================================================================== --- pkg/man/neighbourhood.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/neighbourhood.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -24,7 +24,7 @@ \code{\linkS4class{neighbourhood}}, \code{\link{getNeighbours}} } \examples{ -library(sp) +library("sp") spdf <- data.frame(x=c(112,154,212,289),y=c(124,198,85,168),measure=rlnorm(4)) coordinates(spdf) <- ~x+y Modified: pkg/man/rankTransform.Rd =================================================================== --- pkg/man/rankTransform.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/rankTransform.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -23,7 +23,7 @@ Benedikt Graeler } \examples{ -data(simulatedTriples) +data("simulatedTriples") str(rankTransform(triples)) } \keyword{ function} \ No newline at end of file Modified: pkg/man/reduceNeighbours.Rd =================================================================== --- pkg/man/reduceNeighbours.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/reduceNeighbours.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -35,8 +35,8 @@ } \examples{ -library(sp) -library(spacetime) +library("sp") +library("spacetime") sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2,3,4) Modified: pkg/man/simulatedTriples.Rd =================================================================== --- pkg/man/simulatedTriples.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/simulatedTriples.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -8,7 +8,7 @@ The dataset contains of the annual extreme rainfall events used in the study: \dQuote{Graeler, B., M. J. van den Berg, S. Vandenberghe, A. Petroselli, S. Grimaldi, B. De Baets, & N. E. C. Verhoest (2013): Multivariate return periods in hydrology: a critical and practical review focusing on synthetic design hydrograph estimation. Hydrology and Earth System Sciences, 17, 1281-1296.}. } -\usage{data(simulatedTriples)} +\usage{data("simulatedTriples")} \format{ The format is: peak, duration, volume @@ -17,7 +17,7 @@ Graeler, B., M. J. van den Berg, S. Vandenberghe, A. Petroselli, S. Grimaldi, B. De Baets, & N. E. C. Verhoest (2013): Multivariate return periods in hydrology: a critical and practical review focusing on synthetic design hydrograph estimation. Hydrology and Earth System Sciences, 17, 1281-1296. } \examples{ -data(simulatedTriples) +data("simulatedTriples") str(triples) } \keyword{datasets} Modified: pkg/man/spCopDemo.Rd =================================================================== --- pkg/man/spCopDemo.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/spCopDemo.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -21,11 +21,11 @@ \description{ This workspace is produced by the call \code{demo(spCopula)} and used in a couple of examples throughout the package. } -\usage{data(spCopDemo)} +\usage{data("spCopDemo")} \references{ Graeler, B. & E. Pebesma (2011): The pair-copula construction for spatial data: a new approach to model spatial dependency. Poster at: Spatial Statistics 2011 - Mapping global change. Enschede, The Netherlands, 23-25 March 2011. DOI: 10.1016/j.proenv.2011.07.036.} \examples{ -data(spCopDemo) +data("spCopDemo") ls() } \keyword{datasets} Modified: pkg/man/spCopPredict.Rd =================================================================== --- pkg/man/spCopPredict.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/spCopPredict.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -38,14 +38,14 @@ \code{\link{condSpVine}} } \examples{ -library(sp) -data(meuse.grid) +library("sp") +data("meuse.grid") coordinates(meuse.grid) <- ~x+y gridded(meuse.grid) <- TRUE -data(meuse) +data("meuse") coordinates(meuse) <- ~x+y -data(spCopDemo) +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) Modified: pkg/man/spCopula-class.Rd =================================================================== --- pkg/man/spCopula-class.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/spCopula-class.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -48,7 +48,7 @@ \examples{ # data from demo(spcopula_estimation) -data(spCopDemo) +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) Modified: pkg/man/spCopula.Rd =================================================================== --- pkg/man/spCopula.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/spCopula.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -38,7 +38,7 @@ See also \code{\link{calcBins}} or \code{\link{loglikByCopulasLags}} and \code{demo(spcopula_estimation)}. } \examples{ -data(spCopDemo) +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) Modified: pkg/man/spGaussCopPredict.Rd =================================================================== --- pkg/man/spGaussCopPredict.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/spGaussCopPredict.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -48,7 +48,7 @@ } \examples{ # load data from the Meuse demo -data(spCopDemo) +data("spCopDemo") # calculate the correlation function based on Kendall's tau calcKTauPol <- fitCorFun(bins, degree=1) @@ -62,12 +62,12 @@ } # get some prediction data -library(sp) -data(meuse.grid) +library("sp") +data("meuse.grid") coordinates(meuse.grid) <- ~x+y gridded(meuse.grid) <- TRUE -data(meuse) +data("meuse") coordinates(meuse) <- ~x+y meuse$rtZinc <- rank(meuse$zinc)/(length(meuse)+1) Modified: pkg/man/spGaussLogLik.Rd =================================================================== --- pkg/man/spGaussLogLik.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/spGaussLogLik.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -28,10 +28,10 @@ } \examples{ -library(spcopula) +library("spcopula") # load data from the Meuse demo -data(spCopDemo) +data("spCopDemo") # calculate the correlation function based on Kendall's tau calcKTauPol <- fitCorFun(bins, degree=1) @@ -45,8 +45,8 @@ } # get the neighbours -library(sp) -data(meuse) +library("sp") +data("meuse") coordinates(meuse) <- ~x+y meuse$rtZinc <- rank(meuse$zinc)/(length(meuse)+1) Modified: pkg/man/spVineCopula.Rd =================================================================== --- pkg/man/spVineCopula.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/spVineCopula.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -25,7 +25,7 @@ } \examples{ # a spatial C-vine copula (with independent dummy copulas in the upper vine) -data(spCopDemo) +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) @@ -36,7 +36,7 @@ distances=bins$meanDists, spDepFun=calcKTauPol, unit="m") -library(VineCopula) +library("VineCopula") RVM <- RVineMatrix(matrix(c(1,0,0,2,2,0,3,3,3),3,byrow=TRUE)) spVineCopula(spCop, vineCopula(RVM)) } Modified: pkg/man/stCopPredict.Rd =================================================================== --- pkg/man/stCopPredict.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/stCopPredict.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -34,8 +34,8 @@ \code{\link{condStVine}} and \code{\link{spCopPredict}} for the spatial version. } \examples{ -library(sp) -library(spacetime) +library("sp") +library("spacetime") spCopT0 <- spCopula(components=list(claytonCopula(8), claytonCopula(4), claytonCopula(2), claytonCopula(1), Modified: pkg/man/stNeighbourhood.Rd =================================================================== --- pkg/man/stNeighbourhood.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/stNeighbourhood.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -24,8 +24,8 @@ \code{\linkS4class{stNeighbourhood}}, \code{\link{getStNeighbours}} } \examples{ -library(sp) -library(spacetime) +library("sp") +library("spacetime") sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2) Modified: pkg/man/tailDepFun.Rd =================================================================== --- pkg/man/tailDepFun.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/tailDepFun.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -43,7 +43,7 @@ } \examples{ -data(simulatedTriples) +data("simulatedTriples") X <- rankTransform(triples[,c(1,3)]) tdfEmp <- empTailDepFun(X) Modified: pkg/man/unitScatter.Rd =================================================================== --- pkg/man/unitScatter.Rd 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/man/unitScatter.Rd 2014-07-16 10:00:26 UTC (rev 136) @@ -28,7 +28,7 @@ Benedikt Graeler } \examples{ -data(loss) +data("loss") rt_loss <- rankTransform(loss[,1:2]) unitScatter(smpl=rt_loss) } Modified: pkg/tests/Examples/spcopula-Ex.Rout.save =================================================================== --- pkg/tests/Examples/spcopula-Ex.Rout.save 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/tests/Examples/spcopula-Ex.Rout.save 2014-07-16 10:00:26 UTC (rev 136) @@ -1,5 +1,5 @@ -R version 3.1.0 alpha (2014-03-13 r65184) -- "Unsuffered Consequences" +R version 3.1.1 (2014-07-10) -- "Sock it to Me" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) @@ -39,7 +39,7 @@ > > ### ** Examples > -> data(EU_RB) +> data("EU_RB") > str(EU_RB) Formal class 'STFDF' [package "spacetime"] with 4 slots ..@ data :'data.frame': 11834 obs. of 2 variables: @@ -72,6 +72,60 @@ > > > cleanEx() +> nameEx("EU_RB_2005") +> ### * EU_RB_2005 +> +> flush(stderr()); flush(stdout()) +> +> ### Name: EU_RB_2005 +> ### Title: Daily mean PM10 concentrations over Europe in 2005 as used in +> ### the JSS manuscript +> ### Aliases: EU_RB_2005 +> ### Keywords: datasets +> +> ### ** Examples +> +> data("EU_RB_2005") +> str(EU_RB_2005) +Formal class 'STFDF' [package "spacetime"] with 4 slots + ..@ data :'data.frame': 70810 obs. of 3 variables: + .. ..$ PM10 : num [1:70810] 28 7 11.9 12.9 14.6 30 31.1 8.4 37.8 37.8 ... + .. ..$ EMEP : num [1:70810] 6.36 4.13 5.84 4.93 5.86 ... + .. ..$ logResidKrige: num [1:70810] 12.8 12.4 10.6 11.6 17.1 ... + ..@ sp :Formal class 'SpatialPointsDataFrame' [package "sp"] with 5 slots + .. .. ..@ data :'data.frame': 194 obs. of 8 variables: + .. .. .. ..$ station_altitude : int [1:194] 525 581 918 560 172 117 665 1137 330 330 ... + .. .. .. ..$ station_european_code: Factor w/ 7734 levels "AD0942A","AD0944A",..: 12 61 112 69 73 14 194 184 23 25 ... + .. .. .. ..$ country_iso_code : Factor w/ 39 levels "AD","AL","AT",..: 3 3 3 3 3 3 3 3 3 3 ... + .. .. .. ..$ station_start_date : Factor w/ 2344 levels "1900-01-01","1951-04-01",..: 1117 377 296 411 649 134 658 429 672 684 ... + .. .. .. ..$ station_end_date : Factor w/ 811 levels "","1900-01-01",..: 1 1 1 1 1 1 1 1 1 736 ... + .. .. .. ..$ type_of_station : Factor w/ 5 levels "","Background",..: 2 2 2 2 2 2 2 2 2 2 ... + .. .. .. ..$ station_type_of_area : Factor w/ 5 levels "","rural","suburban",..: 2 2 2 2 2 2 2 2 2 2 ... + .. .. .. ..$ street_type : Factor w/ 5 levels "","Canyon street: L/H < 1.5",..: 1 1 5 4 4 1 4 1 2 1 ... + .. .. ..@ coords.nrs : num(0) + .. .. ..@ coords : num [1:194, 1:2] 4592866 4761515 4658756 4690954 4799839 ... + .. .. .. ..- attr(*, "dimnames")=List of 2 + .. .. .. .. ..$ : NULL + .. .. .. .. ..$ : chr [1:2] "coords.x1" "coords.x2" + .. .. ..@ bbox : num [1:2, 1:2] 2749697 1647732 6412269 4604814 + .. .. .. ..- attr(*, "dimnames")=List of 2 + .. .. .. .. ..$ : chr [1:2] "coords.x1" "coords.x2" + .. .. .. .. ..$ : chr [1:2] "min" "max" + .. .. ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots + .. .. .. .. ..@ projargs: chr " +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs" + ..@ time :An 'xts' object on 2005-01-01/2005-12-31 containing: + Data: int [1:365, 1] 5115 5116 5117 5118 5119 5120 5121 5122 5123 5124 ... + - attr(*, "dimnames")=List of 2 + ..$ : NULL + ..$ : chr "..1" + Indexed by objects of class: [POSIXct,POSIXt] TZ: GMT + xts Attributes: + NULL + ..@ endTime: POSIXct[1:365], format: "2005-01-02 01:00:00" "2005-01-03 01:00:00" ... +> +> +> +> cleanEx() > nameEx("asCopula-class") > ### * asCopula-class > @@ -137,8 +191,8 @@ > > ### ** Examples > -> library(sp) -> data(meuse) +> library("sp") +> data("meuse") > coordinates(meuse) = ~x+y > meuse$rtZinc <- rank(meuse$zinc)/(length(meuse)+1) > @@ -187,8 +241,8 @@ > > ### ** Examples > -> library(sp) -> library(spacetime) +> library("sp") +> library("spacetime") > > sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) > time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2) @@ -225,7 +279,7 @@ > > ### ** Examples > -> data(spCopDemo) +> data("spCopDemo") > > calcKTauPol <- fitCorFun(bins, degree=3) @@ -670,15 +724,15 @@ > ### ** Examples > > # reload some spatial data -> library(sp) -> data(meuse) +> library("sp") +> data("meuse") > coordinates(meuse) <- ~x+y > > # drop margins > meuse$marZinc <- plnorm(meuse$zinc, mean(log(meuse$zinc)), sd(log(meuse$zinc))) > > # load data from a provided binning -> data(spCopDemo) +> data("spCopDemo") > > fitSpCopula(bins, meuse, 600) @@ -935,7 +989,7 @@ > > ### ** Examples > -> library(sp) +> library("sp") > spdf <- data.frame(x=c(112,154,212,289,345),y=c(124,198,85,168,346),measure=rlnorm(5)) > coordinates(spdf) <- ~x+y > @@ -962,8 +1016,8 @@ > > ### ** Examples > -> library(sp) -> library(spacetime) +> library("sp") +> library("spacetime") > > sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) > time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2) @@ -1040,15 +1094,15 @@ > ### ** Examples > > # load spatial data -> library(sp) -> data(meuse) +> library("sp") +> data("meuse") > coordinates(meuse) <- ~x+y > > # drop margins > meuse$marZinc <- plnorm(meuse$zinc, mean(log(meuse$zinc)), sd(log(meuse$zinc))) > > # load parts of the workspace from demo(spCopula) -> data(spCopDemo) +> data("spCopDemo") > > calcKTauPol <- fitCorFun(bins, degree=3) @@ -1216,15 +1270,15 @@ > > # the spatial case > # load spatial data -> library(sp) -> data(meuse) +> library("sp") +> data("meuse") > coordinates(meuse) <- ~x+y > > # drop margins > meuse$marZinc <- plnorm(meuse$zinc, mean(log(meuse$zinc)), sd(log(meuse$zinc))) > > # load parts of the workspace from demo(spCopula) -> data(spCopDemo) +> data("spCopDemo") > > calcKTauPol <- fitCorFun(bins, degree=3) @@ -1392,7 +1446,7 @@ > > ### ** Examples > -> library(sp) +> library("sp") > spdf <- data.frame(x=c(112,154,212,289),y=c(124,198,85,168),measure=rlnorm(4)) > coordinates(spdf) <- ~x+y > @@ -1419,7 +1473,7 @@ > > ### ** Examples > -> library(sp) +> library("sp") > spdf <- data.frame(x=c(112,154,212,289),y=c(124,198,85,168),measure=rlnorm(4)) > coordinates(spdf) <- ~x+y > @@ -1480,7 +1534,7 @@ > > ### ** Examples > -> data(simulatedTriples) +> data("simulatedTriples") > str(rankTransform(triples)) 'data.frame': 494 obs. of 3 variables: $ peak : num 0.00202 0.00404 0.00606 0.00808 0.0101 ... @@ -1501,8 +1555,8 @@ > > ### ** Examples > -> library(sp) -> library(spacetime) +> library("sp") +> library("spacetime") > > sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) > time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2,3,4) @@ -1556,7 +1610,7 @@ > > ### ** Examples > -> data(simulatedTriples) +> data("simulatedTriples") > str(triples) 'data.frame': 494 obs. of 3 variables: $ peak : num 0.167 0.335 0.488 0.586 0.753 ... @@ -1579,7 +1633,7 @@ > > ### ** Examples > -> data(spCopDemo) +> data("spCopDemo") > ls() [1] "bestFitTau" "bins" "calcKTauPol" "meuseSpVine" "spCop" > @@ -1598,14 +1652,14 @@ > > ### ** Examples > -> library(sp) -> data(meuse.grid) +> library("sp") +> data("meuse.grid") > coordinates(meuse.grid) <- ~x+y > gridded(meuse.grid) <- TRUE > -> data(meuse) +> data("meuse") > coordinates(meuse) <- ~x+y -> data(spCopDemo) +> data("spCopDemo") > > calcKTauPol <- fitCorFun(bins, degree=3) @@ -1699,7 +1753,7 @@ > ### ** Examples > > # data from demo(spcopula_estimation) -> data(spCopDemo) +> data("spCopDemo") > > calcKTauPol <- fitCorFun(bins, degree=3) @@ -1748,7 +1802,7 @@ > > ### ** Examples > -> data(spCopDemo) +> data("spCopDemo") > > calcKTauPol <- fitCorFun(bins, degree=3) @@ -1788,7 +1842,7 @@ > ### ** Examples > > # load data from the Meuse demo -> data(spCopDemo) +> data("spCopDemo") > > # calculate the correlation function based on Kendall's tau > calcKTauPol <- fitCorFun(bins, degree=1) @@ -1811,12 +1865,12 @@ + } > > # get some prediction data -> library(sp) -> data(meuse.grid) +> library("sp") +> data("meuse.grid") > coordinates(meuse.grid) <- ~x+y > gridded(meuse.grid) <- TRUE > -> data(meuse) +> data("meuse") > coordinates(meuse) <- ~x+y > > meuse$rtZinc <- rank(meuse$zinc)/(length(meuse)+1) @@ -1885,10 +1939,10 @@ > > ### ** Examples > -> library(spcopula) +> library("spcopula") > > # load data from the Meuse demo -> data(spCopDemo) +> data("spCopDemo") > > # calculate the correlation function based on Kendall's tau > calcKTauPol <- fitCorFun(bins, degree=1) @@ -1911,8 +1965,8 @@ + } > > # get the neighbours -> library(sp) -> data(meuse) +> library("sp") +> data("meuse") > coordinates(meuse) <- ~x+y > > meuse$rtZinc <- rank(meuse$zinc)/(length(meuse)+1) @@ -2249,7 +2303,7 @@ > ### ** Examples > > # a spatial C-vine copula (with independent dummy copulas in the upper vine) -> data(spCopDemo) +> data("spCopDemo") > > calcKTauPol <- fitCorFun(bins, degree=3) @@ -2278,7 +2332,7 @@ parameter at boundary ==> returning indepCopula() parameter at boundary ==> returning indepCopula() > -> library(VineCopula) +> library("VineCopula") > RVM <- RVineMatrix(matrix(c(1,0,0,2,2,0,3,3,3),3,byrow=TRUE)) > spVineCopula(spCop, vineCopula(RVM)) Spatial vine copula family with 1 spatial tree(s). @@ -2369,8 +2423,8 @@ > > ### ** Examples > -> library(sp) -> library(spacetime) +> library("sp") +> library("spacetime") > > spCopT0 <- spCopula(components=list(claytonCopula(8), claytonCopula(4), + claytonCopula(2), claytonCopula(1), @@ -2535,8 +2589,8 @@ > > ### ** Examples > -> library(sp) -> library(spacetime) +> library("sp") +> library("spacetime") > > sp <- SpatialPoints(matrix(c(181000,181100,333500,333600),2)) > time <- as.POSIXct("2014-03-18")+60*60*24*c(0,1,2) @@ -2638,7 +2692,7 @@ > > ### ** Examples > -> data(simulatedTriples) +> data("simulatedTriples") > X <- rankTransform(triples[,c(1,3)]) > > tdfEmp <- empTailDepFun(X) @@ -2733,7 +2787,7 @@ > > ### ** Examples > -> data(loss) +> data("loss") > rt_loss <- rankTransform(loss[,1:2]) > unitScatter(smpl=rt_loss) > @@ -2743,7 +2797,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 15.31 0.21 15.71 NA NA +Time elapsed: 17.44 0.42 25.01 NA NA > grDevices::dev.off() null device 1 Modified: pkg/tests/spCopulaTest.R =================================================================== --- pkg/tests/spCopulaTest.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/tests/spCopulaTest.R 2014-07-16 10:00:26 UTC (rev 136) @@ -1,5 +1,5 @@ -library(spcopula) -data(spCopDemo) +library("spcopula") +data("spCopDemo") calcKTauPol <- fitCorFun(bins, degree=3) spCop <- spCopula(components=list(normalCopula(), tCopula(), Modified: pkg/tests/spCopulaTest.Rout.save =================================================================== --- pkg/tests/spCopulaTest.Rout.save 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/tests/spCopulaTest.Rout.save 2014-07-16 10:00:26 UTC (rev 136) @@ -1,5 +1,5 @@ -R version 3.1.0 alpha (2014-03-13 r65184) -- "Unsuffered Consequences" +R version 3.1.1 (2014-07-10) -- "Sock it to Me" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) @@ -15,10 +15,10 @@ 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. -> library(spcopula) +> library("spcopula") Loading required package: copula Loading required package: VineCopula -> data(spCopDemo) +> data("spCopDemo") > calcKTauPol <- fitCorFun(bins, degree=3) Call: @@ -63,4 +63,4 @@ > > proc.time() user system elapsed - 6.59 0.14 6.91 + 6.92 0.17 7.19 Modified: pkg/tests/stCopulaTest.R =================================================================== --- pkg/tests/stCopulaTest.R 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/tests/stCopulaTest.R 2014-07-16 10:00:26 UTC (rev 136) @@ -1,4 +1,4 @@ -library(spcopula) +library("spcopula") spCopT0 <- spCopula(components=list(claytonCopula(8), claytonCopula(4), claytonCopula(2), claytonCopula(1), claytonCopula(0.5), indepCopula()), Modified: pkg/tests/stCopulaTest.Rout.save =================================================================== --- pkg/tests/stCopulaTest.Rout.save 2014-05-08 11:14:55 UTC (rev 135) +++ pkg/tests/stCopulaTest.Rout.save 2014-07-16 10:00:26 UTC (rev 136) @@ -1,5 +1,5 @@ -R version 3.1.0 alpha (2014-03-13 r65184) -- "Unsuffered Consequences" +R version 3.1.1 (2014-07-10) -- "Sock it to Me" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) @@ -15,7 +15,7 @@ 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. -> library(spcopula) +> library("spcopula") Loading required package: copula Loading required package: VineCopula > spCopT0 <- spCopula(components=list(claytonCopula(8), claytonCopula(4), @@ -56,4 +56,4 @@ > > proc.time() user system elapsed - 5.63 0.14 5.83 + 6.03 0.24 6.33