[Vinecopula-commits] r98 - / pkg/R pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Do Mai 28 15:37:52 CEST 2015
Author: etobi
Date: 2015-05-28 15:37:47 +0200 (Thu, 28 May 2015)
New Revision: 98
Modified:
pkg.pdf
pkg/R/pairs.R
pkg/man/BB8Copula.Rd
pkg/man/BiCopLambda.Rd
pkg/man/RVineGofTest.Rd
pkg/man/RVinePIT.Rd
pkg/man/VineCopula-package.Rd
pkg/man/pairs.copuladata.Rd
Log:
some cosmetics and revision of pairs
Modified: pkg/R/pairs.R
===================================================================
--- pkg/R/pairs.R 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg/R/pairs.R 2015-05-28 13:37:47 UTC (rev 98)
@@ -6,44 +6,84 @@
diag.panel = dp.copuladata,
label.pos = 0.85,
cex.labels = 1,
- gap = 0) {
+ gap = 0,
+ method = "kendall",
+ ccols = terrain.colors(30),
+ margins = "norm",
+ margins.par = 0) {
## pairs plot for 'copuladata'
- # provide input data and set default labels, panel functions, etc.
- default <- list(x = as.matrix(x),
- labels = labels,
- lower.panel = lower.panel,
- upper.panel = upper.panel,
- diag.panel = diag.panel,
- label.pos = label.pos,
- cex.labels = cex.labels,
- gap = gap
- )
+ # panel functions
+ if (!is.null(lower.panel) && missing(lower.panel)) {
+ lp <- function(x, y, cc = ccols, mar = margins, marpar = margins.par, ...) {
+ lower.panel(x, y, cc = cc, mar = mar, marpar = marpar, ...)
+ }
+ } else {
+ lp <- lower.panel
+ }
+ if (!is.null(upper.panel) && missing(upper.panel)) {
+ up <- function(x, y, mthd = method, ...) {
+ upper.panel(x, y, mthd = mthd, ...)
+ }
+ } else {
+ up <- upper.panel
+ }
+ if (!is.null(diag.panel) && missing(diag.panel)) {
+ dp <- function(x, ...) {
+ diag.panel(x, ...)
+ }
+ } else {
+ dp <- diag.panel
+ }
# pairs plot (with panel functions as defined below or as provided by user)
- pars <- modifyList(list(xaxt = "n", yaxt = "n"), list(...))
- op <- do.call(par, pars)
- do.call(pairs, modifyList(default, list(...)))
+ op <- par(xaxt = "n", yaxt = "n")
+ #do.call(pairs, modifyList(default, list(...)))
+ pairs(x = as.matrix(x),
+ labels = labels,
+ ...,
+ lower.panel = lp,
+ upper.panel = up,
+ diag.panel = dp,
+ label.pos = label.pos,
+ cex.labels = cex.labels,
+ gap = gap)
on.exit(par(op))
}
## lower panel: empirical contour plot
-lp.copuladata <- function(x, y, ...) {
+lp.copuladata <- function(x, y, cc, mar, marpar, ...) {
+ # set number of levels and if contour labels are drawn
+ if (length(cc) == 1) {
+ nlvls <- 11
+ dl <- TRUE
+ } else {
+ nlvls <- length(cc)
+ dl <- FALSE
+ }
+ # set levels according to margins
+ if (mar %in% c("norm", "t", "exp")) {
+ lvls <- seq(0.0, 0.2, length.out = nlvls)
+ } else if (mar == "gamma") {
+ lvls <- seq(0.0, 0.1, length.out = nlvls)
+ } else if (mar == "unif") {
+ lvls <- seq(0.1, 1.5, length.out = nlvls)
+ }
# set default parameters
pars <- list(u1 = x,
u2 = y,
bw = 2,
size = 100,
- levels = seq(0.01, 0.2, length.out = 30),
- margins = "norm",
- margins.par = 0,
- xylim = NA,
- col = terrain.colors(30),
+ levels = lvls,
+ margins = mar,
+ margins.par = marpar,
+ xylim = NA,
axes = FALSE,
- drawlabels = FALSE)
+ drawlabels = dl)
# get non-default parameters
pars <- modifyList(pars, list(...))
+ pars <- modifyList(modifyList(pars, list(col = NULL)), list(col = cc))
op <- par(usr = c(-3, 3, -3, 3), new = TRUE)
# call BiCopMetaContour
do.call(BiCopMetaContour, pars)
@@ -52,7 +92,7 @@
## upper panel: scatter plot (copula data) and correlation
-up.copuladata <- function(x, y, ...) {
+up.copuladata <- function(x, y, mthd, ...) {
# set default parameters
pars <- list(x = x,
y = y,
@@ -65,17 +105,14 @@
op <- par(usr = c(0, 1, 0, 1), new = TRUE)
# call points (to produce scatter plot)
do.call(points, pars)
- r <- cor(x = x, y = y, method = "kendall")
+ r <- cor(x = x, y = y, method = mthd)
txt <- format(x = r, digits = 2, nsmall = 2)[1]
# call text
- do.call(text, modifyList(list(x = 0.5,
- y = 0.5,
- labels = txt,
- cex = 1 + abs(r) * 3,
- col = "red"),
- list(...)
- )
- )
+ pars.txt <- list(x = 0.5,
+ y = 0.5,
+ labels = txt)
+ pars.txt <- modifyList(pars.txt, list(...))
+ do.call(text, modifyList(pars.txt, list(cex = 1 + abs(r) * 3, col = "red")))
on.exit(par(op))
}
@@ -86,14 +123,14 @@
pars <- list(x = x,
freq = FALSE,
add = TRUE,
- col = "grey",
- border = "black",
+ border = "white",
main = "")
# get non-default parameters
- pars <- modifyList(pars, list(...))
+ pars <- modifyList(modifyList(pars, list(...)), list(col = "grey"))
op <- par(usr = c(0, 1, 0, 1.6), new = TRUE)
# call hist
do.call(hist, pars)
+ box()
if (pars$freq == FALSE)
abline(h = 1, col = "black", lty = 3)
on.exit(par(op))
Modified: pkg/man/BB8Copula.Rd
===================================================================
--- pkg/man/BB8Copula.Rd 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg/man/BB8Copula.Rd 2015-05-28 13:37:47 UTC (rev 98)
@@ -37,8 +37,8 @@
\examples{
library(copula)
-persp(BB8Copula(c(1,0.5)), dCopula, zlim = c(0,10))
-persp(surBB8Copula(c(1,0.5)), dCopula, zlim = c(0,10))
-persp(r90BB8Copula(c(-1,-0.5)), dCopula, zlim = c(0,10))
-persp(r270BB8Copula(c(-1,-0.5)), dCopula, zlim = c(0,10))
+persp(BB8Copula(c(2,0.9)), dCopula, zlim = c(0,10))
+persp(surBB8Copula(c(2,0.9)), dCopula, zlim = c(0,10))
+persp(r90BB8Copula(c(-2,-0.9)), dCopula, zlim = c(0,10))
+persp(r270BB8Copula(c(-2,-0.9)), dCopula, zlim = c(0,10))
}
\ No newline at end of file
Modified: pkg/man/BiCopLambda.Rd
===================================================================
--- pkg/man/BiCopLambda.Rd 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg/man/BiCopLambda.Rd 2015-05-28 13:37:47 UTC (rev 98)
@@ -111,6 +111,7 @@
# lambda-function of estimated copula
fit <- BiCopSelect(dat[, 1], dat[, 2])
+par(mfrow = c(1, 1))
BiCopLambda(fit)
# simulate from rotated Clayton copula (90 degrees)
Modified: pkg/man/RVineGofTest.Rd
===================================================================
--- pkg/man/RVineGofTest.Rd 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg/man/RVineGofTest.Rd 2015-05-28 13:37:47 UTC (rev 98)
@@ -154,9 +154,9 @@
Preprint
\url{http://arxiv.org/abs/1306.0818}
-Schepsmeier, U. (2013)
-Efficient goodness-of-fit tests in multi-dimensional vine copula models.
-\url{http://arxiv.org/abs/1309.5808}
+Schepsmeier, U. (2015)
+Efficient information based goodness-of-fit tests for vine copula models with fixed margins.
+Journal of Multivariate Analysis 138, 34-52.
White, H. (1982)
Maximum likelihood estimation of misspecified models,
Modified: pkg/man/RVinePIT.Rd
===================================================================
--- pkg/man/RVinePIT.Rd 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg/man/RVinePIT.Rd 2015-05-28 13:37:47 UTC (rev 98)
@@ -46,9 +46,9 @@
Remarks on a Multivariate Transformation. The Annals
of Mathematical Statistics 23 (3), 470-472.
-Schepsmeier, U. (2013)
-Efficient goodness-of-fit tests in multi-dimensional vine copula models.
-\url{http://arxiv.org/abs/1309.5808}
+Schepsmeier, U. (2015)
+Efficient information based goodness-of-fit tests for vine copula models with fixed margins.
+Journal of Multivariate Analysis 138, 34-52.
}
\examples{
Modified: pkg/man/VineCopula-package.Rd
===================================================================
--- pkg/man/VineCopula-package.Rd 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg/man/VineCopula-package.Rd 2015-05-28 13:37:47 UTC (rev 98)
@@ -14,7 +14,7 @@
}
\section{Remark}{
-The package VineCopula is a continuation of the package CDVine by U. Schepsmeier and E. C. Brechmann (see Brechmann and Schepsmeier (2013)).
+The package \code{VineCopula} is a continuation of the package \code{CDVine} by U. Schepsmeier and E. C. Brechmann (see Brechmann and Schepsmeier (2013)).
It includes all functions implemented in CDVine for the bivariate case (BiCop-functions).
}
@@ -159,7 +159,7 @@
Schepsmeier, U. and J. Stoeber (2012).
Derivatives and Fisher information of bivariate copulas.
-Statistical Papers, 55 (2), 525-542.
+Statistical Papers, 55 (2), 525-542. \cr
\url{http://link.springer.com/article/10.1007/s00362-013-0498-x}.
Schepsmeier, U. (2013)
@@ -168,11 +168,11 @@
\url{http://arxiv.org/abs/1306.0818}
Schepsmeier, U. (2015)
-Efficient information based goodness-of-fit tests for vine copula models with fixed margins.
-Journal of Multivariate Analysis 138, 34–52.
+Efficient information based goodness-of-fit tests for vine copula models with fixed margins.
+Journal of Multivariate Analysis 138, 34-52.
Stoeber, J. and U. Schepsmeier (2013).
-Estimating standard errors in regular vine copula models. Computational Statistics, 28 (6), 2679-2707
+Estimating standard errors in regular vine copula models. Computational Statistics, 28 (6), 2679-2707 \cr
\url{http://link.springer.com/article/10.1007/s00180-013-0423-8#}.
White, H. (1982)
Modified: pkg/man/pairs.copuladata.Rd
===================================================================
--- pkg/man/pairs.copuladata.Rd 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg/man/pairs.copuladata.Rd 2015-05-28 13:37:47 UTC (rev 98)
@@ -12,22 +12,48 @@
lower.panel = lp.copuladata,
upper.panel = up.copuladata,
diag.panel = dp.copuladata,
- label.pos = 0.85, cex.labels = 1, gap = 0)
+ label.pos = 0.85, cex.labels = 1, gap = 0,
+ method = "kendall", ccols = terrain.colors(30),
+ margins = "norm", margins.par = 0)
}
\arguments{
\item{x}{\code{copuladata} object.}
\item{labels}{variable names/labels.}
\item{\dots}{other graphical parameters (see \code{\link[graphics]{par}}).}
- \item{lower.panel}{panel function to be used on the lower diagonal panels}
- \item{upper.panel}{panel function to be used on the upper diagonal panels}
- \item{diag.panel}{panel function to be used on the diagonal panels}
+ \item{lower.panel}{panel function to be used on the lower diagonal panels (if not supplied, a default function is used)}
+ \item{upper.panel}{panel function to be used on the upper diagonal panels (if not supplied, a default function is used)}
+ \item{diag.panel}{panel function to be used on the diagonal panels (if not supplied, a default function is used)}
\item{label.pos}{y position of labels in the diagonal panel; default: \code{label.pos = 0.85}.}
\item{cex.labels}{magnification to be used for the labels of the diagonal panel; default: \code{cex.labels = 1}.}
\item{gap}{distance between subplots, in margin lines; default: \code{gap = 0}.}
+If the default panel function \code{upper.panel} is used, the following parameters can be set additionally:
+\item{method}{a character string indicating which correlation coefficients are computed. One of \code{"pearson"}, \code{"kendall"} (default), or \code{"spearman"}}
+If the default panel function \code{lower.panel} (see \code{\link{BiCopMetaContour}}) is used, the following parameters can be set additionally:
+\item{ccols}{colour to be used for the contour plots; default: \code{ccols = terrain.colors(30)}.}
+\item{margins}{character; margins for the contour plots. Possible margins are:\cr
+ \code{"norm"} = standard normal margins (default)\cr
+ \code{"t"} = Student t margins with degrees of freedom as specified by \code{margins.par}\cr
+ \code{"gamma"} = Gamma margins with shape and scale as specified by \code{margins.par}\cr
+ \code{"exp"} = Exponential margins with rate as specified by \code{margins.par}\cr
+ \code{"unif"} = uniform margins}
+ \item{margins.par}{parameter(s) of the distribution of the margins (of the contour plots) if necessary (default: \code{margins.par = 0}), i.e.,
+ \itemize{
+ \item a positive real number for the degrees of freedom of Student t margins (see \code{\link{dt}}),
+ \item a 2-dimensional vector of positive real numbers for the shape and scale parameters of Gamma margins (see \code{\link{dgamma}}),
+ \item a positive real number for the rate parameter of exponential margins (see \code{\link{dexp}}).
+ }}
}
+\note{
+If the default panel functions are used \cr
+\itemize{
+\item \code{col} changes only the colour of the points in the scatter plot (\code{upper.panel}) \cr
+\item \code{cex} changes only the magnification of the points in the scatter plot (\code{upper.panel})
+}
+}
+
\author{Tobias Erhardt}
\seealso{\code{\link[graphics]{pairs}}, \code{\link{as.copuladata}}, \code{\link{BiCopMetaContour}}}
@@ -36,19 +62,22 @@
data(daxreturns)
data <- as.copuladata(daxreturns)
+sel <- c(4,5,14,15)
## pairs plot with default settings
-pairs(data[1:5])
+pairs(data[sel])
## pairs plot with custom settings
nlevels <- 20
-pairs(data[1:5], cex = 2, pch = 1,
+pairs(data[sel], cex = 2, pch = 1, col = "black",
diag.panel = NULL, label.pos = 0.5,
- cex.labels = 2.5, gap = 1)
+ cex.labels = 2.5, gap = 1,
+ method = "pearson", ccols = heat.colors(nlevels),
+ margins = "gamma", margins.par = c(1,1))
## pairs plot with own panel functions
-up.copuladata <- function(x, y) {
- # lower panel: empirical contour plot
+up <- function(x, y) {
+ # upper panel: empirical contour plot
op <- par(usr = c(-3, 3, -3, 3), new = TRUE)
BiCopMetaContour(x, y, bw = 2, levels = c(0.01, 0.05, 0.1, 0.15, 0.2),
# exponential margins
@@ -57,8 +86,8 @@
on.exit(par(op))
}
-lp.copuladata <- function(x, y) {
- # upper panel: scatter plot (copula data) and correlation
+lp <- function(x, y) {
+ # lower panel: scatter plot (copula data) and correlation
op <- par(usr = c(0, 1, 0, 1), new = TRUE)
points(x, y, pch = 1, col = "black")
r <- cor(x, y, method = "spearman") # Spearman's rho
@@ -67,16 +96,15 @@
on.exit(par(op))
}
-dp.copuladata <- function(x) {
+dp <- function(x) {
# diagonal panel: histograms (copula data)
op <- par(usr = c(0, 1, 0, 1.5), new = TRUE)
- hist(x, freq = FALSE, add = TRUE, col = "brown", border = "white", main = "")
+ hist(x, freq = FALSE, add = TRUE, col = "brown", border = "black", main = "")
abline(h = 1, col = "black", lty = 2)
on.exit(par(op))
}
nlevels <- 20
-pairs(data[1:5],
- lower.panel = lp.copuladata, upper.panel = up.copuladata,
- diag.panel = dp.copuladata, gap = 0.5)
+pairs(data[sel],
+ lower.panel = lp, upper.panel = up, diag.panel = dp, gap = 0.5)
}
Modified: pkg.pdf
===================================================================
--- pkg.pdf 2015-05-27 18:06:14 UTC (rev 97)
+++ pkg.pdf 2015-05-28 13:37:47 UTC (rev 98)
@@ -7,15622 +7,16913 @@
(VineCopula-package)
endobj
5 0 obj
-<< /S /GoTo /D (Rfn.BB1Copula.1) >>
+<< /S /GoTo /D (Rfn.as.copuladata.1) >>
endobj
8 0 obj
-(BB1Copula)
+(as.copuladata)
endobj
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-<< /S /GoTo /D (Rfn.BB1Copula.Rdash.class.1) >>
+<< /S /GoTo /D (Rfn.BB1Copula.1) >>
endobj
12 0 obj
-(BB1Copula-class)
+(BB1Copula)
endobj
13 0 obj
-<< /S /GoTo /D (Rfn.BB6Copula.1) >>
+<< /S /GoTo /D (Rfn.BB1Copula.Rdash.class.1) >>
endobj
16 0 obj
-(BB6Copula)
+(BB1Copula-class)
endobj
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-<< /S /GoTo /D (Rfn.BB6Copula.Rdash.class.1) >>
+<< /S /GoTo /D (Rfn.BB6Copula.1) >>
endobj
20 0 obj
-(BB6Copula-class)
+(BB6Copula)
endobj
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-<< /S /GoTo /D (Rfn.BB7Copula.1) >>
+<< /S /GoTo /D (Rfn.BB6Copula.Rdash.class.1) >>
endobj
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-(BB7Copula)
+(BB6Copula-class)
endobj
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-<< /S /GoTo /D (Rfn.BB7Copula.Rdash.class.1) >>
+<< /S /GoTo /D (Rfn.BB7Copula.1) >>
endobj
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-(BB7Copula-class)
+(BB7Copula)
endobj
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-<< /S /GoTo /D (Rfn.BB8Copula.1) >>
+<< /S /GoTo /D (Rfn.BB7Copula.Rdash.class.1) >>
endobj
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-(BB8Copula)
+(BB7Copula-class)
endobj
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-<< /S /GoTo /D (Rfn.BB8Copula.Rdash.class.1) >>
+<< /S /GoTo /D (Rfn.BB8Copula.1) >>
endobj
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-(BB8Copula-class)
+(BB8Copula)
endobj
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-<< /S /GoTo /D (Rfn.BetaMatrix.1) >>
+<< /S /GoTo /D (Rfn.BB8Copula.Rdash.class.1) >>
endobj
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-(BetaMatrix)
+(BB8Copula-class)
endobj
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-<< /S /GoTo /D (Rfn.BiCopCDF.1) >>
+<< /S /GoTo /D (Rfn.BetaMatrix.1) >>
endobj
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-(BiCopCDF)
+(BetaMatrix)
endobj
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-<< /S /GoTo /D (Rfn.BiCopChiPlot.1) >>
+<< /S /GoTo /D (Rfn.BiCop.1) >>
endobj
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-(BiCopChiPlot)
+(BiCop)
endobj
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-<< /S /GoTo /D (Rfn.BiCopDeriv.1) >>
+<< /S /GoTo /D (Rfn.BiCopCDF.1) >>
endobj
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+(BiCopCDF)
endobj
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-<< /S /GoTo /D (Rfn.BiCopDeriv2.1) >>
+<< /S /GoTo /D (Rfn.BiCopChiPlot.1) >>
endobj
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+(BiCopChiPlot)
endobj
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-<< /S /GoTo /D (Rfn.BiCopEst.1) >>
+<< /S /GoTo /D (Rfn.BiCopDeriv.1) >>
endobj
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+(BiCopDeriv)
endobj
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-<< /S /GoTo /D (Rfn.BiCopGofTest.1) >>
+<< /S /GoTo /D (Rfn.BiCopDeriv2.1) >>
endobj
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+(BiCopDeriv2)
endobj
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-<< /S /GoTo /D (Rfn.BiCopHfunc.1) >>
+<< /S /GoTo /D (Rfn.BiCopEst.1) >>
endobj
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+(BiCopEst)
endobj
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-<< /S /GoTo /D (Rfn.BiCopHfuncDeriv.1) >>
+<< /S /GoTo /D (Rfn.BiCopGofTest.1) >>
endobj
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endobj
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endobj
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+(BiCopHfunc)
endobj
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endobj
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+(BiCopHfuncDeriv)
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-<< /S /GoTo /D (Rfn.BiCopKPlot.1) >>
+<< /S /GoTo /D (Rfn.BiCopHfuncDeriv2.1) >>
endobj
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+(BiCopHfuncDeriv2)
endobj
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+<< /S /GoTo /D (Rfn.BiCopIndTest.1) >>
endobj
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+(BiCopIndTest)
endobj
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-<< /S /GoTo /D (Rfn.BiCopMetaContour.1) >>
+<< /S /GoTo /D (Rfn.BiCopKPlot.1) >>
endobj
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+(BiCopKPlot)
endobj
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-<< /S /GoTo /D (Rfn.BiCopName.1) >>
+<< /S /GoTo /D (Rfn.BiCopLambda.1) >>
endobj
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endobj
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+<< /S /GoTo /D (Rfn.BiCopMetaContour.1) >>
endobj
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+(BiCopMetaContour)
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+<< /S /GoTo /D (Rfn.BiCopName.1) >>
endobj
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+(BiCopName)
endobj
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endobj
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+<< /S /GoTo /D (Rfn.BiCopPar2TailDep.1) >>
endobj
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+(BiCopPar2TailDep)
endobj
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+<< /S /GoTo /D (Rfn.BiCopPar2Tau.1) >>
endobj
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+(BiCopPar2Tau)
endobj
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+<< /S /GoTo /D (Rfn.BiCopPDF.1) >>
endobj
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endobj
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+<< /S /GoTo /D (Rfn.BiCopSelect.1) >>
endobj
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endobj
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-<< /S /GoTo /D (Rfn.BiCopVuongClarke.1) >>
+<< /S /GoTo /D (Rfn.BiCopSim.1) >>
endobj
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+(BiCopSim)
endobj
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-<< /S /GoTo /D (Rfn.C2RVine.1) >>
+<< /S /GoTo /D (Rfn.BiCopTau2Par.1) >>
endobj
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vinecopula -r 98
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