[spcopula-commits] r148 - / pkg pkg/R pkg/man pkg/tests pkg/tests/Examples

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Aug 18 11:56:11 CEST 2015


Author: ben_graeler
Date: 2015-08-18 11:56:11 +0200 (Tue, 18 Aug 2015)
New Revision: 148

Added:
   .Rprofile
Modified:
   pkg/DESCRIPTION
   pkg/NAMESPACE
   pkg/R/tailDependenceFunctions.R
   pkg/man/bivTailDepFun.Rd
   pkg/tests/Examples/spcopula-Ex.Rout.save
   pkg/tests/spCopulaTest.Rout.save
   pkg/tests/stCopulaTest.Rout.save
Log:
- changed (again) naming of tail dependence functions to the more descriptive name bivJointDepFun - the bivariate joint dependence functions
- updated Rout.save files

Added: .Rprofile
===================================================================
--- .Rprofile	                        (rev 0)
+++ .Rprofile	2015-08-18 09:56:11 UTC (rev 148)
@@ -0,0 +1 @@
+options(repos = c(CRAN="http://cran.uni-muenster.de"))

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2015-08-14 13:14:05 UTC (rev 147)
+++ pkg/DESCRIPTION	2015-08-18 09:56:11 UTC (rev 148)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Copula Driven Spatio-Temporal Analysis
 Version: 0.2-1
-Date: 2015-08-14
+Date: 2015-08-18
 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/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2015-08-14 13:14:05 UTC (rev 147)
+++ pkg/NAMESPACE	2015-08-18 09:56:11 UTC (rev 148)
@@ -61,8 +61,8 @@
 
 # fitting
 export(fitCorFun, loglikByCopulasLags, loglikByCopulasStLags, fitSpCopula, composeSpCopula)
-export(bivTailDepFun, lowerBivTailDepFun, upperBivTailDepFun)
-export(empBivTailDepFun, lowerEmpBivTailDepFun, upperEmpBivTailDepFun)
+export(bivJointDepFun, lowerBivJointDepFun, upperBivJointDepFun)
+export(empBivJointDepFun, lowerEmpBivJointDepFun, upperEmpBivJointDepFun)
 
 # MRP functions
 export(genEmpKenFun, genInvKenFun)

Modified: pkg/R/tailDependenceFunctions.R
===================================================================
--- pkg/R/tailDependenceFunctions.R	2015-08-14 13:14:05 UTC (rev 147)
+++ pkg/R/tailDependenceFunctions.R	2015-08-18 09:56:11 UTC (rev 148)
@@ -1,45 +1,45 @@
-# adopted from http://www.r-bloggers.com/copulas-and-tail-dependence-part-1/, 04.11.2013
+# adopted from http://freakonometrics.hypotheses.org/2435, 
 
-lowerEmpBivTailDepFun <- function(u) {
+lowerEmpBivJointDepFun <- function(u) {
   stopifnot(ncol(u) == 2)
   empFun <- function(x) sum((u[,1]<=x)&(u[,2]<=x))/sum(u[,1]<=x)
   function(x) sapply(x,empFun)
 }
 
-upperEmpBivTailDepFun <- function(u) {
+upperEmpBivJointDepFun <- function(u) {
   stopifnot(ncol(u) == 2)
   empFun <- function(x) sum((u[,1]>=x)&(u[,2]>=x))/sum(u[,1]>=x)
   function(x) sapply(x,empFun)
 }
 
-empBivTailDepFun <- function(u) {
+empBivJointDepFun <- function(u) {
   stopifnot(ncol(u) == 2)
   
   function(z) {
     res <- z
-    res[z>0.5] <- upperEmpBivTailDepFun(u)(z[z>0.5])
-    res[z<=0.5] <- lowerEmpBivTailDepFun(u)(z[z<=0.5])
+    res[z>0.5] <- upperEmpBivJointDepFun(u)(z[z>0.5])
+    res[z<=0.5] <- lowerEmpBivJointDepFun(u)(z[z<=0.5])
     return(res)
   }
 }
 
 ##
 
-lowerBivTailDepFun <- function(copula) {
+lowerBivJointDepFun <- function(copula) {
   stopifnot(copula at dimension == 2)
   function(z) pCopula(cbind(z,z),copula)/z
 }
 
-upperBivTailDepFun <- function(copula) {
+upperBivJointDepFun <- function(copula) {
   stopifnot(copula at dimension == 2)
   function(z) (1-2*z+pCopula(cbind(z,z),copula))/(1-z)
 }
 
-bivTailDepFun <- function(copula) {
+bivJointDepFun <- function(copula) {
   function(z) {
     res <- z
-    res[z>0.5] <- upperBivTailDepFun(copula)(z[z>0.5])
-    res[z<=0.5] <- lowerBivTailDepFun(copula)(z[z<=0.5])
+    res[z>0.5] <- upperBivJointDepFun(copula)(z[z>0.5])
+    res[z<=0.5] <- lowerBivJointDepFun(copula)(z[z<=0.5])
     return(res)
   }
 }
\ No newline at end of file

Modified: pkg/man/bivTailDepFun.Rd
===================================================================
--- pkg/man/bivTailDepFun.Rd	2015-08-14 13:14:05 UTC (rev 147)
+++ pkg/man/bivTailDepFun.Rd	2015-08-18 09:56:11 UTC (rev 148)
@@ -1,26 +1,34 @@
-\name{bivTailDepFun}
-\alias{bivTailDepFun}
-\alias{lowerBivTailDepFun}
-\alias{upperBivTailDepFun}
+\name{bivJointDepFun}
+\alias{bivJointDepFun}
+\alias{lowerBivJointDepFun}
+\alias{upperBivJointDepFun}
 
-\alias{empBivTailDepFun}
-\alias{lowerEmpBivTailDepFun}
-\alias{upperEmpBivTailDepFun}
+\alias{empBivJointDepFun}
+\alias{lowerEmpBivJointDepFun}
+\alias{upperEmpBivJointDepFun}
 
 \title{
-Tail dependence functions
+Bivariate joint dependence functions
 }
 \description{
-Functions returning a (empirical) tail dependence function for a bivariate copula (sample). The tail dependence functions can be upper, lower or joint, where values below 0.5 are calculated from the lower tail dependence function and values larger 0.5 for the upper tail dependence function. The definition follows the one by Nelsen (2006, Theorem 5.4.2.). For tail dependence of multivariate copulas, see the papers by Joe et al. (2010) and Nikoloulopoulos et al. (2012).
+Functions returning a (empirical) joint shortfall/exceedance dependence function for a bivariate copula (sample). The functions can be lower (shortfall), upper (exceedance), or both, where values below 0.5 are calculated from the lower joint dependence function and values larger 0.5 from the upper joint dependence function. The definition follows the one by Nelsen for the tail dependence index (2006, Theorem 5.4.2.):
+
+lower joint dependence (shortfall):
+\eqn{\frac{P(U \leq u | V \leq u)}{P(V \leq v)}=\frac{C(u,u)}{u}}{P(U <= u | V <= u)/P(V <= u) = C(u,u)/u}
+
+upper joint dependence (exceedance):
+\eqn{\frac{P(U \geq u | V \geq u)}{P(V \geq v)}=1-2u+\frac{C(u,u)}{1-u}}{P(U >= u | V >= u)/P(V >= u) = 1 - 2u + C(u,u)/(1-u)}
+
+Taking the limits of the above for \eqn{u \rightarrow 0}{u -> 0} and \eqn{u \rightarrow 1}{u -> 1} respectively yields the lower and upper tail index. For tail dependence of multivariate copulas, see the papers by Joe et al. (2010) and Nikoloulopoulos et al. (2012).
 }
 \usage{
-bivTailDepFun(copula)
-lowerBivTailDepFun(copula)
-upperBivTailDepFun(copula)
+bivJointDepFun(copula)
+lowerBivJointDepFun(copula)
+upperBivJointDepFun(copula)
 
-empBivTailDepFun(u)
-lowerEmpBivTailDepFun(u)
-upperEmpBivTailDepFun(u)
+empBivJointDepFun(u)
+lowerEmpBivJointDepFun(u)
+upperEmpBivJointDepFun(u)
 }
 
 \arguments{
@@ -33,7 +41,7 @@
 }
 
 \value{
-A function taking arguments from the unit interval (0,1) and returning the corresponding tail index.
+A function taking arguments from the unit interval (0,1) and returning the corresponding index.
 }
 \references{
 Definition: 
@@ -48,7 +56,7 @@
 
 Plots inspired by:
 
-\url{http://freakonometrics.blog.free.fr/index.php?post/2012/09/11/Copulas-and-statistical-inference}
+\url{http://freakonometrics.hypotheses.org/2435}
 }
 \author{
 Benedikt Graeler
@@ -59,7 +67,7 @@
 data("simulatedTriples")
 X <- rankTransform(triples[,c(1,3)])
   
-tdfEmp <- empBivTailDepFun(X)
+tdfEmp <- empBivJointDepFun(X)
 plot(tdfEmp,ylim=c(0,1),
      ylab="tail dependence index")  
 abline(v=0.5, col="grey")
@@ -67,15 +75,15 @@
 smplTau <- cor(X,method="kendall")[1,2]
 
 # Gauss
-tdfGauss <- bivTailDepFun(normalCopula(sin(smplTau*pi/2)))
+tdfGauss <- bivJointDepFun(normalCopula(sin(smplTau*pi/2)))
 curve(tdfGauss,add=TRUE,col="blue")
 
 # survival Gumbel
-tdfGumbel <- bivTailDepFun(surGumbelCopula(1/(1-smplTau)))
+tdfGumbel <- bivJointDepFun(surGumbelCopula(1/(1-smplTau)))
 curve(tdfGumbel,add=TRUE,col="darkgreen")
 
 # survival BB6 copula
-tdfBB6 <- bivTailDepFun(surBB6Copula(c(4.65,2.28)))
+tdfBB6 <- bivJointDepFun(surBB6Copula(c(4.65,2.28)))
 curve(tdfBB6,add=TRUE,col="red")
 
 legend("bottomleft",c("empircal","Gauss","surv. Gumbel","surv. BB6"),

Modified: pkg/tests/Examples/spcopula-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/spcopula-Ex.Rout.save	2015-08-14 13:14:05 UTC (rev 147)
+++ pkg/tests/Examples/spcopula-Ex.Rout.save	2015-08-18 09:56:11 UTC (rev 148)
@@ -1,40 +1,27 @@
-
-R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
-Copyright (C) 2015 The R Foundation for Statistical Computing
-Platform: x86_64-w64-mingw32/x64 (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-  Natural language support but running in an English locale
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> pkgname <- "spcopula"
-> source(file.path(R.home("share"), "R", "examples-header.R"))
-> options(warn = 1)
-> options(pager = "console")
-> base::assign(".ExTimings", "spcopula-Ex.timings", pos = 'CheckExEnv')
-> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
-> base::assign(".format_ptime",
-+ function(x) {
-+   if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
-+   if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
-+   options(OutDec = '.')
-+   format(x[1L:3L], digits = 7L)
-+ },
-+ pos = 'CheckExEnv')
-> 
-> ### * </HEADER>
-> library('spcopula')
-Loading required package: copula
+
+R version 3.2.2 (2015-08-14) -- "Fire Safety"
+Copyright (C) 2015 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> pkgname <- "spcopula"
+> source(file.path(R.home("share"), "R", "examples-header.R"))
+> options(warn = 1)
+> library('spcopula')
+Loading required package: copula
 > 
 > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
 > cleanEx()
@@ -43,7 +30,6 @@
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: EU_RB
 > ### Title: Daily mean PM10 concentrations over Europe in June and July 2005
 > ### Aliases: EU_RB
@@ -71,7 +57,7 @@
   .. .. .. .. ..$ : chr [1:2] "min" "max"
   .. .. ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
   .. .. .. .. ..@ 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
@@ -83,15 +69,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("EU_RB", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("EU_RB_2005")
 > ### * EU_RB_2005
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: EU_RB_2005
 > ### Title: Daily mean PM10 concentrations over Europe in 2005 as used in
 > ###   the JSS manuscript
@@ -128,7 +111,7 @@
   .. .. .. .. ..$ : chr [1:2] "min" "max"
   .. .. ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
   .. .. .. .. ..@ 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:
+  ..@ 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
@@ -140,15 +123,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("EU_RB_2005", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("asCopula-class")
 > ### * asCopula-class
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: asCopula-class
 > ### Title: Class '"asCopula"'
 > ### Aliases: asCopula-class dduCopula,matrix,asCopula-method
@@ -177,15 +157,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("asCopula-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("asCopula")
 > ### * asCopula
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: asCopula
 > ### Title: Constructor of an asymmetric copula with cubic and quadratic
 > ###   sections (Nelsen 2006).
@@ -198,15 +175,56 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("asCopula", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
+> nameEx("bivTailDepFun")
+> ### * bivTailDepFun
+> 
+> flush(stderr()); flush(stdout())
+> 
+> ### Name: bivJointDepFun
+> ### Title: Bivariate joint dependence functions
+> ### Aliases: bivJointDepFun lowerBivJointDepFun upperBivJointDepFun
+> ###   empBivJointDepFun lowerEmpBivJointDepFun upperEmpBivJointDepFun
+> 
+> ### ** Examples
+> 
+> library("VineCopula")
+> data("simulatedTriples")
+> X <- rankTransform(triples[,c(1,3)])
+>   
+> tdfEmp <- empBivJointDepFun(X)
+> plot(tdfEmp,ylim=c(0,1),
++      ylab="tail dependence index")  
+> abline(v=0.5, col="grey")
+> 
+> smplTau <- cor(X,method="kendall")[1,2]
+> 
+> # Gauss
+> tdfGauss <- bivJointDepFun(normalCopula(sin(smplTau*pi/2)))
+> curve(tdfGauss,add=TRUE,col="blue")
+> 
+> # survival Gumbel
+> tdfGumbel <- bivJointDepFun(surGumbelCopula(1/(1-smplTau)))
+> curve(tdfGumbel,add=TRUE,col="darkgreen")
+> 
+> # survival BB6 copula
+> tdfBB6 <- bivJointDepFun(surBB6Copula(c(4.65,2.28)))
+> curve(tdfBB6,add=TRUE,col="red")
+> 
+> legend("bottomleft",c("empircal","Gauss","surv. Gumbel","surv. BB6"),
++        col=c("black","blue","darkgreen","red"),lty=1)
+> 
+> 
+> 
+> cleanEx()
+
+detaching ‘package:VineCopula’
+
 > nameEx("calcBins")
 > ### * calcBins
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: calcBins
 > ### Title: A function calculating the spatial/spatio-temporal bins
 > ### Aliases: calcBins calcBins-methods calcBins,Spatial-method
@@ -225,18 +243,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("calcBins", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:sp'
+detaching ‘package:sp’
 
 > nameEx("composeSpCopula")
 > ### * composeSpCopula
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: composeSpCopula
 > ### Title: Composing a bivariate Spatial Copula
 > ### Aliases: composeSpCopula
@@ -256,15 +271,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("composeSpCopula", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("condCovariate")
 > ### * condCovariate
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: condCovariate
 > ### Title: Conditioning of a Covariate
 > ### Aliases: condCovariate
@@ -293,18 +305,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("condCovariate", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:spacetime', 'package:sp'
+detaching ‘package:spacetime’, ‘package:sp’
 
 > nameEx("condSpVine")
 > ### * condSpVine
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: condSpVine
 > ### Title: Conditions a spatial vine copula for conditional prediction
 > ### Aliases: condSpVine
@@ -354,18 +363,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("condSpVine", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:VineCopula'
+detaching ‘package:VineCopula’
 
 > nameEx("condStCoVarVine")
 > ### * condStCoVarVine
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: condStCoVarVine
 > ### Title: conditional distribution function of spatio-temporal covariate
 > ###   vine copula
@@ -403,18 +409,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("condStCoVarVine", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:VineCopula'
+detaching ‘package:VineCopula’
 
 > nameEx("condStVine")
 > ### * condStVine
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: condStVine
 > ### Title: Conditions a spatio-temporal vine copula for conditional
 > ###   prediction
@@ -450,18 +453,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("condStVine", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:VineCopula'
+detaching ‘package:VineCopula’
 
 > nameEx("cqsCopula-class")
 > ### * cqsCopula-class
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: cqsCopula-class
 > ### Title: Class '"cqsCopula"'
 > ### Aliases: cqsCopula-class dduCopula,matrix,cqsCopula-method
@@ -490,15 +490,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("cqsCopula-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("cqsCopula")
 > ### * cqsCopula
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: cqsCopula
 > ### Title: Constructor of a symmetric copula with cubic quadratic sections.
 > ### Aliases: cqsCopula
@@ -510,15 +507,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("cqsCopula", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("criticalLevel")
 > ### * criticalLevel
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: criticalLevel
 > ### Title: Calculating the critical level for a given Kendall Return Period
 > ### Aliases: criticalLevel
@@ -531,15 +525,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("criticalLevel", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("criticalPair")
 > ### * criticalPair
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: criticalPair
 > ### Title: Calculate Critical Pairs
 > ### Aliases: criticalPair
@@ -553,15 +544,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("criticalPair", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("criticalTriple")
 > ### * criticalTriple
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: criticalTriple
 > ### Title: calculate critical triples
 > ### Aliases: criticalTriple
@@ -578,15 +566,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("criticalTriple", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("dduCopula")
 > ### * dduCopula
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: dduCopula
 > ### Title: partial derivatives of copulas
 > ### Aliases: dduCopula ddvCopula
@@ -624,15 +609,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("dduCopula", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("dependencePlot")
 > ### * dependencePlot
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: dependencePlot
 > ### Title: Kernel smoothed scatter plot
 > ### Aliases: dependencePlot
@@ -644,15 +626,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("dependencePlot", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("empiricalCopula-class")
 > ### * empiricalCopula-class
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: empiricalCopula-class
 > ### Title: Class '"empiricalCopula"'
 > ### Aliases: empiricalCopula-class
@@ -677,15 +656,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("empiricalCopula-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("empiricalCopula")
 > ### * empiricalCopula
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: empiricalCopula
 > ### Title: Constructor of an empirical copula class
 > ### Aliases: empiricalCopula
@@ -737,15 +713,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("empiricalCopula", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("fitCorFun")
 > ### * fitCorFun
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: fitCorFun
 > ### Title: Automated fitting of a correlation function to the correlogram
 > ### Aliases: fitCorFun
@@ -791,15 +764,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("fitCorFun", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("fitSpCopula")
 > ### * fitSpCopula
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: fitSpCopula
 > ### Title: Spatial Copula Fitting
 > ### Aliases: fitSpCopula
@@ -966,18 +936,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("fitSpCopula", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:sp'
+detaching ‘package:sp’
 
 > nameEx("genEmpCop")
 > ### * genEmpCop
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: genEmpCop
 > ### Title: Generate an empirical copula
 > ### Aliases: genEmpCop
@@ -998,15 +965,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("genEmpCop", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("genEmpKenFun")
 > ### * genEmpKenFun
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: genEmpKenFun
 > ### Title: Generates an empirical Kendall distribution function
 > ### Aliases: genEmpKenFun
@@ -1020,15 +984,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("genEmpKenFun", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("genInvKenFun")
 > ### * genInvKenFun
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: genInvKenFun
 > ### Title: Generate the inverse Kendall distribution function
 > ### Aliases: genInvKenFun
@@ -1046,15 +1007,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("genInvKenFun", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("getKendallDistr")
 > ### * getKendallDistr
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: getKendallDistr
 > ### Title: Retrieving the Kendall Distribution function for a given copula
 > ### Aliases: getKendallDistr getKendallDistr,claytonCopula-method
@@ -1072,15 +1030,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("getKendallDistr", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("getNeighbours")
 > ### * getNeighbours
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: getNeighbours
 > ### Title: Creating Local Neighbourhoods
 > ### Aliases: getNeighbours
@@ -1099,18 +1054,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("getNeighbours", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:sp'
+detaching ‘package:sp’
 
 > nameEx("getStNeighbours")
 > ### * getStNeighbours
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: getStNeighbours
 > ### Title: Creating Local Spatio-Temporal Neighbourhoods
 > ### Aliases: getStNeighbours
@@ -1137,18 +1089,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("getStNeighbours", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:spacetime', 'package:sp'
+detaching ‘package:spacetime’, ‘package:sp’
 
 > nameEx("kendallDistribution")
 > ### * kendallDistribution
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: kendallDistribution
 > ### Title: The Kendall distribution
 > ### Aliases: kendallDistribution kendallDistribution,claytonCopula-method
@@ -1167,15 +1116,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("kendallDistribution", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("kendallRP")
 > ### * kendallRP
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: kendallRP
 > ### Title: calculating the Kendall Return Period
 > ### Aliases: kendallRP
@@ -1188,15 +1134,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("kendallRP", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 > nameEx("loglikByCopulasLags")
 > ### * loglikByCopulasLags
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: loglikByCopulasLags
 > ### Title: Log-likelihoods by copula family and spatial lag class
 > ### Aliases: loglikByCopulasLags
@@ -1364,18 +1307,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("loglikByCopulasLags", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:sp'
+detaching ‘package:sp’
 
 > nameEx("loglikByCopulasStLags")
 > ### * loglikByCopulasStLags
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: loglikByCopulasStLags
 > ### Title: Log-likelihoods by copula family and spatio-temporal lag class
 > ### Aliases: loglikByCopulasStLags
@@ -1543,18 +1483,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("loglikByCopulasStLags", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:sp'
+detaching ‘package:sp’
 
 > nameEx("neighbourhood-class")
 > ### * neighbourhood-class
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: neighbourhood-class
 > ### Title: Class 'neighbourhood'
 > ### Aliases: neighbourhood-class names,neighbourhood-method
@@ -1574,18 +1511,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("neighbourhood-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:sp'
+detaching ‘package:sp’
 
 > nameEx("neighbourhood")
 > ### * neighbourhood
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: neighbourhood
 > ### Title: Constructor of the 'neighbourhood' class.
 > ### Aliases: neighbourhood
@@ -1612,18 +1546,15 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("neighbourhood", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
 > cleanEx()
 
-detaching 'package:sp'
+detaching ‘package:sp’
 
 > nameEx("qCopula_u")
 > ### * qCopula_u
 > 
 > flush(stderr()); flush(stdout())
 > 
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
 > ### Name: qCopula_u
 > ### Title: The inverse of a bivariate copula given u or v
 > ### Aliases: qCopula_u qCopula_u,copula-method qCopula_v
@@ -1644,15 +1575,12 @@
 > 
 > 
 > 
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/spcopula -r 148


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