[spcopula-commits] r136 - in pkg: . R data demo man tests tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jul 16 12:00:28 CEST 2014
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
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