[Vinecopula-commits] r33 - / pkg/R pkg/inst pkg/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fr Okt 18 13:36:55 CEST 2013 

Author: ulf
Date: 2013-10-18 13:36:53 +0200 (Fri, 18 Oct 2013)
New Revision: 33

Added:
   VineCopula_1.2.zip
Modified:
   pkg.pdf
   pkg/R/BiCopSelect.r
   pkg/R/RVineAIC.r
   pkg/R/RVineClarkeTest.R
   pkg/R/RVineStructureSelect.r
   pkg/R/RVineVuongTest.R
   pkg/inst/ChangeLog
   pkg/man/BiCopPar2Beta.Rd
   pkg/man/RVineGofTest.Rd
   pkg/man/RVinePar2Beta.Rd
   pkg/man/RVineStructureSelect.Rd
   pkg/man/RvineMatrixCheck.Rd
Log:
Tobias hatte noch ein paar kleine Fehler gefunden im Code als auch in der Dokumentation. Ich hoffe ich habe jetzt alle Stellen erwischt, in der die Tawn copula einen Einfluss hat.

Added: VineCopula_1.2.zip
===================================================================
(Binary files differ)


Property changes on: VineCopula_1.2.zip
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Modified: pkg/R/BiCopSelect.r
===================================================================
--- pkg/R/BiCopSelect.r	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/R/BiCopSelect.r	2013-10-18 11:36:53 UTC (rev 33)
@@ -22,7 +22,7 @@
 
   }else{
   
-    if(!is.na(familyset[1]) && (!any(c(1,2,5,23,24,26:30,33,34,36:40) %in% familyset) || !any(c(1:10,13,14,16:20) %in% familyset))) stop("'familyset' has to include at least one bivariate copula family for positive and one for negative dependence.")
+    if(!is.na(familyset[1]) && (!any(c(1,2,5,23,24,26:30,33,34,36:40,104,114,204,214) %in% familyset) || !any(c(1:10,13,14,16:20,124,134,224,234) %in% familyset))) stop("'familyset' has to include at least one bivariate copula family for positive and one for negative dependence.")
 
     emp_tau = fasttau(data1,data2,weights)
 

Modified: pkg/R/RVineAIC.r
===================================================================
--- pkg/R/RVineAIC.r	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/R/RVineAIC.r	2013-10-18 11:36:53 UTC (rev 33)
@@ -13,8 +13,8 @@
 	if(n != dim(RVM)) stop("Dimensions of 'data' and 'RVM' do not match.")
   if(!is(RVM,"RVineMatrix")) stop("'RVM' has to be an RVineMatrix object.")
   
-	npar = sum(RVM$family >= 1, na.rm=TRUE) + sum(RVM$family %in% c(2,7:10,17:20,27:30,37:40),na.rm=TRUE)
-  npar_pair = (RVM$family>=1)+(RVM$family%in%c(2,7:10,17:20,27:30,37:40))
+	npar = sum(RVM$family >= 1, na.rm=TRUE) + sum(RVM$family %in% c(2,7:10,17:20,27:30,37:40,104,114,124,134,204,214,224,234),na.rm=TRUE)
+  npar_pair = (RVM$family>=1)+(RVM$family%in%c(2,7:10,17:20,27:30,37:40,104,114,124,134,204,214,224,234))
 
   like = RVineLogLik(data,RVM)
 
@@ -38,8 +38,8 @@
 	if(n != dim(RVM)) stop("Dimensions of 'data' and 'RVM' do not match.")
   if(is(RVM) != "RVineMatrix") stop("'RVM' has to be an RVineMatrix object.")
   
-	npar = sum(RVM$family >= 1, na.rm=TRUE) + sum(RVM$family %in% c(2,7:10,17:20,27:30,37:40),na.rm=TRUE)
-  npar_pair = (RVM$family>=1)+(RVM$family%in%c(2,7:10,17:20,27:30,37:40))
+	npar = sum(RVM$family >= 1, na.rm=TRUE) + sum(RVM$family %in% c(2,7:10,17:20,27:30,37:40,104,114,124,134,204,214,224,234),na.rm=TRUE)
+  npar_pair = (RVM$family>=1)+(RVM$family%in%c(2,7:10,17:20,27:30,37:40,104,114,124,134,204,214,224,234))
 
   like = RVineLogLik(data,RVM)
 

Modified: pkg/R/RVineClarkeTest.R
===================================================================
--- pkg/R/RVineClarkeTest.R	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/R/RVineClarkeTest.R	2013-10-18 11:36:53 UTC (rev 33)
@@ -11,8 +11,8 @@
 	Model1.ll = RVineLogLik(data,RVM1,separate=TRUE)$loglik
 	Model2.ll = RVineLogLik(data,RVM2,separate=TRUE)$loglik
   
-	anz.1 = sum(RVM1$family >= 1, na.rm=TRUE) + sum(RVM1$family %in% c(2,7:10,17:20,27:30,37:40),na.rm=TRUE)
-	anz.2 = sum(RVM2$family >= 1, na.rm=TRUE) + sum(RVM2$family %in% c(2,7:10,17:20,27:30,37:40),na.rm=TRUE)
+	anz.1 = sum(RVM1$family >= 1, na.rm=TRUE) + sum(RVM1$family %in% c(2,7:10,17:20,27:30,37:40, 104,114,124,134,204,214,224,234),na.rm=TRUE)
+	anz.2 = sum(RVM2$family >= 1, na.rm=TRUE) + sum(RVM2$family %in% c(2,7:10,17:20,27:30,37:40, 104,114,124,134,204,214,224,234),na.rm=TRUE)
  
   B = sum(Model1.ll-Model2.ll > 0)
   B.Schwarz = sum(Model1.ll-Model2.ll-(anz.1-anz.2)*log(N)/(2*N) > 0)

Modified: pkg/R/RVineStructureSelect.r
===================================================================
--- pkg/R/RVineStructureSelect.r	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/R/RVineStructureSelect.r	2013-10-18 11:36:53 UTC (rev 33)
@@ -11,7 +11,7 @@
   if(d<2) stop("Dimension has to be at least 2.")
   if(any(data>1) || any(data<0)) stop("Data has be in the interval [0,1].")
 	
-  if(!is.na(familyset[1])) for(i in 1:length(familyset)) if(!(familyset[i] %in% c(0,1:10,13,14,16:20,23,24,26:30,33,34,36:40))) stop("Copula family not implemented.")  
+  if(!is.na(familyset[1])) for(i in 1:length(familyset)) if(!(familyset[i] %in% c(0,1:10,13,14,16:20,23,24,26:30,33,34,36:40, 104,114,124,134,204,214,224,234))) stop("Copula family not implemented.")  
   if(selectioncrit != "AIC" && selectioncrit != "BIC") stop("Selection criterion not implemented.")
   if(level < 0 & level > 1) stop("Significance level has to be between 0 and 1.")
   	

Modified: pkg/R/RVineVuongTest.R
===================================================================
--- pkg/R/RVineVuongTest.R	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/R/RVineVuongTest.R	2013-10-18 11:36:53 UTC (rev 33)
@@ -11,8 +11,8 @@
 	Model1.ll = RVineLogLik(data,RVM1,separate=TRUE)$loglik
 	Model2.ll = RVineLogLik(data,RVM2,separate=TRUE)$loglik
   
-	anz.1 = sum(RVM1$family >= 1, na.rm=TRUE) + sum(RVM1$family %in% c(2,7,8,9,10,17,18,19,20,27,28,29,30,37,38,39,40),na.rm=TRUE)
-	anz.2 = sum(RVM2$family >= 1, na.rm=TRUE) + sum(RVM2$family %in% c(2,7,8,9,10,17,18,19,20,27,28,29,30,37,38,39,40),na.rm=TRUE)
+	anz.1 = sum(RVM1$family >= 1, na.rm=TRUE) + sum(RVM1$family %in% c(2,7,8,9,10,17,18,19,20,27,28,29,30,37,38,39,40, 104,114,124,134,204,214,224,234),na.rm=TRUE)
+	anz.2 = sum(RVM2$family >= 1, na.rm=TRUE) + sum(RVM2$family %in% c(2,7,8,9,10,17,18,19,20,27,28,29,30,37,38,39,40, 104,114,124,134,204,214,224,234),na.rm=TRUE)
 
   if(all(Model1.ll-Model2.ll==0)){  # models are the same
   	V = 0

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/inst/ChangeLog	2013-10-18 11:36:53 UTC (rev 33)
@@ -21,6 +21,7 @@
   
 - Bug fix:
   * RVineStructureSelect: Corrected code for the igraph package
+  * RVineTreePlot: Now a 3-dimensional R-vine can be plotted too.
 
 - Documentation update
 

Modified: pkg/man/BiCopPar2Beta.Rd
===================================================================
--- pkg/man/BiCopPar2Beta.Rd	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/man/BiCopPar2Beta.Rd	2013-10-18 11:36:53 UTC (rev 33)
@@ -15,7 +15,6 @@
   \item{family}{An integer defining the bivariate copula family:\cr
 		\code{0} = independence copula \cr
 	        \code{1} = Gaussian copula \cr
-	        \code{2} = Student t copula (t-copula) \cr
 	        \code{3} = Clayton copula \cr
 	        \code{4} = Gumbel copula \cr
 	        \code{5} = Frank copula \cr
@@ -53,6 +52,7 @@
     \code{214} = rotated Tawn type 2 copula (180 degrees) \cr
     \code{224} = rotated Tawn type 2 copula (90 degrees)  \cr
     \code{234} = rotated Tawn type 2 copula (270 degrees) \cr
+    Note that the Student's t-copula is not allowed since the CDF of the t-copula is not implemented (see \code{\link{BiCopCDF}}).
 		}
   \item{par}{Copula parameter.}
   \item{par2}{Second parameter for the two parameter BB1, BB6, BB7, BB8, Tawn type 1 and type 2 copulas (default: \code{par2 = 0}).}

Modified: pkg/man/RVineGofTest.Rd
===================================================================
--- pkg/man/RVineGofTest.Rd	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/man/RVineGofTest.Rd	2013-10-18 11:36:53 UTC (rev 33)
@@ -14,7 +14,24 @@
 \arguments{
   \item{data}{An N x d data matrix (with uniform margins).} 
   \item{RVM}{\code{\link{RVineMatrix}} objects of the R-vine model under the null hypothesis. \cr
-  Note that the pair-copula families in the R-vine Matrix object have to be a member of the vector \code{(0,1:6,13,14,16,23,24,26,33,34,36)}}
+  Only the following copula families are allowed in \code{RVM$family} due to restrictions in \code{\link{RVineGrad}} and \code{\link{RVineHessian}}  \cr
+  	\code{0} = independence copula \cr
+		\code{1} = Gaussian copula \cr
+		\code{2} = Student t copula (t-copula)\cr
+		\code{3} = Clayton copula \cr
+		\code{4} = Gumbel copula \cr
+		\code{5} = Frank copula \cr
+		\code{6} = Joe copula \cr 
+		\code{13} = rotated Clayton copula (180 degrees; ``survival Clayton'') \cr
+		\code{14} = rotated Gumbel copula (180 degrees; ``survival Gumbel'') \cr
+		\code{16} = rotated Joe copula (180 degrees; ``survival Joe'') \cr 
+		\code{23} = rotated Clayton copula (90 degrees) \cr
+		\code{24} = rotated Gumbel copula (90 degrees) \cr
+		\code{26} = rotated Joe copula (90 degrees) \cr
+		\code{33} = rotated Clayton copula (270 degrees) \cr
+		\code{34} = rotated Gumbel copula (270 degrees) \cr
+		\code{36} = rotated Joe copula (270 degrees) \cr
+		}
   \item{method}{A string indicating the goodness-of-fit method:\cr
 		\code{"White"} = goodness-of-fit test based on White's information matrix equality (default) \cr
 		\code{"IR"} = goodness-of-fit test based on the information ratio \cr
@@ -30,7 +47,7 @@
 		\code{"AD"} = Anderson-Darling test statistic (only univariate for \code{"Breymann"}, \code{"Berg"} and \code{"Berg2"})
 		}
 	\item{B}{an integer for the number of bootstrap steps (default \code{B=200})\cr
-	For \code{B = 0} the asymptotic p-value is returned if available, otherwise only the the test statistic is returned.\cr
+	For \code{B = 0} the asymptotic p-value is returned if available, otherwise only the test statistic is returned.\cr
     WARNING: If \code{B} is chosen too large, computations will take very long.}
 	\item{alpha}{an integer of the set \code{2,4,6,...} for the \code{"Berg2"} goodness-of-fit test (default \code{alpha=2})}
 }
@@ -68,7 +85,7 @@
 }
 where \eqn{\boldsymbol{H}(\theta)} is the expected Hessian matrix and \eqn{\boldsymbol{C}(\theta)} is the expected outer product of the score function. \cr
 For the calculation of the test statistic we use the consistent maximum likelihood estimator \eqn{\hat{\theta}} and the sample counter parts of \eqn{\boldsymbol{H}(\theta)} and \eqn{\boldsymbol{C}(\theta)}. \cr
-The correction of the Covariance-Matrix in the test statistic for the uncertainty in the margins is skipped. The implemented tests assumes that where is no uncertainty in the margins. The correction can be found in Wanling and Prokhorov (2011) for bivariate copulas and in Schepsmeier (2013) for vine copulas. It involves multi-dimensional integrals. \cr
+The correction of the Covariance-Matrix in the test statistic for the uncertainty in the margins is skipped. The implemented test assumes that there is no uncertainty in the margins. The correction can be found in Wanling and Prokhorov (2011) for bivariate copulas and in Schepsmeier (2013) for vine copulas. It involves multi-dimensional integrals. \cr
 
 \code{method="IR"}: \cr
 As the White test the information matrix ratio test is based on the expected Hessian matrix \eqn{\boldsymbol{H}(\theta)} and the expected outer product of the score function \eqn{\boldsymbol{C}(\theta)}. \cr

Modified: pkg/man/RVinePar2Beta.Rd
===================================================================
--- pkg/man/RVinePar2Beta.Rd	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/man/RVinePar2Beta.Rd	2013-10-18 11:36:53 UTC (rev 33)
@@ -1,51 +1,52 @@
-\name{RVinePar2Beta}      
-\alias{RVinePar2Beta}
-
-\title{Blomqvist's beta values of an R-vine copula model}
-
-\description{
-This function computes the values of Blomqvist's beta corresponding to the parameters of an R-vine copula model.
-}
-
-\usage{
-RVinePar2Beta(RVM)
-}
-
-\arguments{
-  \item{RVM}{An \code{\link{RVineMatrix}} object.}
-}
-
-\value{
-Matrix with the same structure as the family and parameter matrices of the \code{\link{RVineMatrix}} object \code{RVM} where the entries
-are values of Blomqvist's beta corresponding to the families and parameters of the R-vine copula model given by \code{RVM}.
-}
-
-\author{Jeffrey Dissmann}
-
-\seealso{\code{\link{RVineMatrix}}, \code{\link{BiCopPar2Beta}}}
-
-\examples{
-# define 5-dimensional R-vine tree structure matrix
-Matrix = c(5,2,3,1,4,0,2,3,4,1,0,0,3,4,1,0,0,0,4,1,0,0,0,0,1)
-Matrix = matrix(Matrix,5,5)
-
-# define R-vine pair-copula family matrix
-family = c(0,1,3,4,4,0,0,3,4,1,0,0,0,4,1,0,0,0,0,3,0,0,0,0,0)
-family = matrix(family,5,5)
-
-# define R-vine pair-copula parameter matrix
-par = c(0,0.2,0.9,1.5,3.9,0,0,1.1,1.6,0.9,0,0,0,1.9,0.5,
-        0,0,0,0,4.8,0,0,0,0,0)
-par = matrix(par,5,5)
-
-# define second R-vine pair-copula parameter matrix
-par2 = matrix(0,5,5)
-
-# define RVineMatrix object
-RVM = RVineMatrix(Matrix=Matrix,family=family,par=par,par2=par2,
-                  names=c("V1","V2","V3","V4","V5"))
-
-# compute the Blomqvist's beta values
-BlomBeta = RVinePar2Beta(RVM)
-}
-
+\name{RVinePar2Beta}      
+\alias{RVinePar2Beta}
+
+\title{Blomqvist's beta values of an R-vine copula model}
+
+\description{
+This function computes the values of Blomqvist's beta corresponding to the parameters of an R-vine copula model.
+}
+
+\usage{
+RVinePar2Beta(RVM)
+}
+
+\arguments{
+  \item{RVM}{An \code{\link{RVineMatrix}} object. \cr
+  Note that the Student's t-copula is not allowed since the CDF of the t-copula is not implemented (see \code{\link{BiCopCDF}} and \code{\link{BiCopPar2Beta}}).}
+}
+
+\value{
+Matrix with the same structure as the family and parameter matrices of the \code{\link{RVineMatrix}} object \code{RVM} where the entries
+are values of Blomqvist's beta corresponding to the families and parameters of the R-vine copula model given by \code{RVM}.
+}
+
+\author{Ulf Schepsmeier}
+
+\seealso{\code{\link{RVineMatrix}}, \code{\link{BiCopPar2Beta}}}
+
+\examples{
+# define 5-dimensional R-vine tree structure matrix
+Matrix = c(5,2,3,1,4,0,2,3,4,1,0,0,3,4,1,0,0,0,4,1,0,0,0,0,1)
+Matrix = matrix(Matrix,5,5)
+
+# define R-vine pair-copula family matrix
+family = c(0,1,3,4,4,0,0,3,4,1,0,0,0,4,1,0,0,0,0,3,0,0,0,0,0)
+family = matrix(family,5,5)
+
+# define R-vine pair-copula parameter matrix
+par = c(0,0.2,0.9,1.5,3.9,0,0,1.1,1.6,0.9,0,0,0,1.9,0.5,
+        0,0,0,0,4.8,0,0,0,0,0)
+par = matrix(par,5,5)
+
+# define second R-vine pair-copula parameter matrix
+par2 = matrix(0,5,5)
+
+# define RVineMatrix object
+RVM = RVineMatrix(Matrix=Matrix,family=family,par=par,par2=par2,
+                  names=c("V1","V2","V3","V4","V5"))
+
+# compute the Blomqvist's beta values
+BlomBeta = RVinePar2Beta(RVM)
+}
+

Modified: pkg/man/RVineStructureSelect.Rd
===================================================================
--- pkg/man/RVineStructureSelect.Rd	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/man/RVineStructureSelect.Rd	2013-10-18 11:36:53 UTC (rev 33)
@@ -50,7 +50,15 @@
 		\code{37} = rotated BB1 copula (270 degrees) \cr
 		\code{38} = rotated BB6 copula (270 degrees) \cr
 		\code{39} = rotated BB7 copula (270 degrees) \cr
-		\code{40} = rotated BB8 copula (270 degrees) 
+		\code{40} = rotated BB8 copula (270 degrees) \cr
+    \code{104} = Tawn type 1 copula \cr
+    \code{114} = rotated Tawn type 1 copula (180 degrees) \cr
+    \code{124} = rotated Tawn type 1 copula (90 degrees)  \cr
+    \code{134} = rotated Tawn type 1 copula (270 degrees) \cr
+    \code{204} = Tawn type 2 copula  \cr
+    \code{214} = rotated Tawn type 2 copula (180 degrees) \cr
+    \code{224} = rotated Tawn type 2 copula (90 degrees)  \cr
+    \code{234} = rotated Tawn type 2 copula (270 degrees) \cr
 		}
   \item{type}{Type of the vine model to be specified:\cr
     \code{0} or \code{"RVine"} = R-vine (default)\cr

Modified: pkg/man/RvineMatrixCheck.Rd
===================================================================
--- pkg/man/RvineMatrixCheck.Rd	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg/man/RvineMatrixCheck.Rd	2013-10-18 11:36:53 UTC (rev 33)
@@ -12,7 +12,7 @@
 
 \arguments{
   \item{M}{A dxd vine matrix: only lower triangle is used;
-For the check, M is assumed to be in natural order, i.e. 1:d on diagonal.
+For the check, M is assumed to be in natural order, i.e. d:1 on diagonal.
 Further M[j-1,j]=j-1 and M[j,j]=j
 }
 }

Modified: pkg.pdf
===================================================================
--- pkg.pdf	2013-10-17 13:14:59 UTC (rev 32)
+++ pkg.pdf	2013-10-18 11:36:53 UTC (rev 33)
@@ -310,13 +310,11 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/vinecopula -r 33

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