[Distr-commits] r1069 - in pkg: distrDoc distrDoc/inst distrDoc/man distrDoc/vignettes distrEllipse distrEllipse/R distrEllipse/inst distrEllipse/man distrEllipse/tests/Examples distrEx distrEx/R distrEx/inst distrEx/man distrEx/src distrEx/tests/Examples distrMod distrMod/R distrMod/inst distrMod/inst/scripts distrMod/man distrMod/tests/Examples distrRmetrics distrRmetrics/inst distrRmetrics/man distrRmetrics/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 6 18:18:17 CET 2015
Author: ruckdeschel
Date: 2015-11-06 18:18:16 +0100 (Fri, 06 Nov 2015)
New Revision: 1069
Added:
pkg/distrMod/R/checkEstClassForParamFamilyMethods.R
pkg/distrMod/R/returnlevelplot.R
pkg/distrMod/man/internal-methods.Rd
pkg/distrMod/man/returnlevelplot.Rd
Modified:
pkg/distrDoc/DESCRIPTION
pkg/distrDoc/inst/NEWS
pkg/distrDoc/man/0distrDoc-package.Rd
pkg/distrDoc/vignettes/distr.Rnw
pkg/distrEllipse/DESCRIPTION
pkg/distrEllipse/NAMESPACE
pkg/distrEllipse/R/01.R
pkg/distrEllipse/R/AllClasses.R
pkg/distrEllipse/R/AllShow.R
pkg/distrEllipse/R/EllipticalDistribution.R
pkg/distrEllipse/R/MVMixingDistribution.R
pkg/distrEllipse/R/MVNorm.R
pkg/distrEllipse/R/SphericalDistribution.R
pkg/distrEllipse/inst/NEWS
pkg/distrEllipse/man/0distrEllipse-package.Rd
pkg/distrEllipse/man/EllipticalDistribution-class.Rd
pkg/distrEllipse/man/MultivarDistrList-class.Rd
pkg/distrEllipse/man/MultivarMixingDistribution-class.Rd
pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save
pkg/distrEx/DESCRIPTION
pkg/distrEx/NAMESPACE
pkg/distrEx/R/CvMDist.R
pkg/distrEx/R/distrExIntegrate.R
pkg/distrEx/R/moved2RobExtremes.R
pkg/distrEx/inst/CITATION
pkg/distrEx/inst/NEWS
pkg/distrEx/inst/TOBEDONE
pkg/distrEx/man/0distrEx-package.Rd
pkg/distrEx/man/CvMDist.Rd
pkg/distrEx/man/DiscreteMVDistribution.Rd
pkg/distrEx/src/GLaw.c
pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save
pkg/distrMod/DESCRIPTION
pkg/distrMod/NAMESPACE
pkg/distrMod/R/0distrModUtils.R
pkg/distrMod/R/AllGeneric.R
pkg/distrMod/R/AllPlot.R
pkg/distrMod/R/Estimate.R
pkg/distrMod/R/Estimator.R
pkg/distrMod/R/MCEstimate.R
pkg/distrMod/R/MCEstimator.R
pkg/distrMod/R/MDEstimator.R
pkg/distrMod/R/MLEstimator.R
pkg/distrMod/R/ParamFamParameter.R
pkg/distrMod/R/confint.R
pkg/distrMod/R/existsPIC.R
pkg/distrMod/R/internalMleCalc.R
pkg/distrMod/R/mleCalc-methods.R
pkg/distrMod/R/modifyModel.R
pkg/distrMod/R/qqplot.R
pkg/distrMod/R/validParameter.R
pkg/distrMod/inst/NEWS
pkg/distrMod/inst/scripts/distrModExample.R
pkg/distrMod/inst/scripts/distrModExample1.R
pkg/distrMod/man/0distrMod-package.Rd
pkg/distrMod/man/L2ParamFamily-class.Rd
pkg/distrMod/man/MLEstimator.Rd
pkg/distrMod/man/existsPIC.Rd
pkg/distrMod/man/internalmleHelpers.Rd
pkg/distrMod/man/internals-qqplot.Rd
pkg/distrMod/man/mleCalc-methods.Rd
pkg/distrMod/man/qqplot.Rd
pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
pkg/distrRmetrics/DESCRIPTION
pkg/distrRmetrics/NAMESPACE
pkg/distrRmetrics/inst/CITATION
pkg/distrRmetrics/inst/NEWS
pkg/distrRmetrics/man/0distrRmetrics-package.Rd
pkg/distrRmetrics/tests/Examples/distrRmetrics-Ex.Rout.save
Log:
branch 2.6 reintegriert
Modified: pkg/distrDoc/DESCRIPTION
===================================================================
--- pkg/distrDoc/DESCRIPTION 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrDoc/DESCRIPTION 2015-11-06 17:18:16 UTC (rev 1069)
@@ -1,14 +1,15 @@
Package: distrDoc
-Version: 2.5.1
-Date: 2015-02-04
-Title: Documentation for Packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod,
- and distrEllipse
-Description: provides documentation in form of a common vignette to packages distr, distrEx,
- distrMod, distrSim, distrTEst, distrTeach, and distrEllipse
-Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the documented packages in the initial phase --2005"),
- person("Matthias", "Kohl", role=c("aut", "cph")),
- person("Peter", "Ruckdeschel", role=c("cre", "cph"), email="Peter.Ruckdeschel at itwm.fraunhofer.de"),
- person("Thomas", "Stabla", role="ctb", comment="contributed as student to the documented packages in the initial phase --2005"))
+Version: 2.6
+Date: 2015-11-06
+Title: Documentation for 'distr' Family of R Packages
+Description: Provides documentation in form of a common vignette to packages distr, distrEx,
+ distrMod, distrSim, distrTEst, distrTeach, and distrEllipse.
+Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the
+ documented packages in the initial phase --2005"), person("Matthias", "Kohl",
+ role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "cph"),
+ email="peter.ruckdeschel at uni-oldenburg.de"), person("Thomas", "Stabla", role="ctb",
+ comment="contributed as student to the documented packages in the initial phase
+ --2005"))
Depends: R(>= 2.14.0)
Imports: distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0),
distrTeach(>= 2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods,
@@ -20,4 +21,4 @@
URL: http://distr.r-forge.r-project.org/
LastChangedDate: {$LastChangedDate$}
LastChangedRevision: {$LastChangedRevision$}
-SVNRevision: 993
+SVNRevision: 1055
Modified: pkg/distrDoc/inst/NEWS
===================================================================
--- pkg/distrDoc/inst/NEWS 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrDoc/inst/NEWS 2015-11-06 17:18:16 UTC (rev 1069)
@@ -8,13 +8,21 @@
information)
##############
-v 2.5.1
+v 2.6
##############
+
user-visible CHANGES:
+ title changed to title style / capitalization
+ updated CITATION file
++ removed some outdated references from uni-bayreuth
++ updated references in vignette distr.Rnw
++ mention that pattern substitution can now be switched on and off in all plot
+ functions according to argument withSubst
+under the hood
+ fixed \VignetteKeyword issue detected as in mail by K. Hornik 2015-02-03
++ added svn-properties to distr.Rnw
++ enhanced imports in DESCRIPTION by explicating second order imports
##############
v 2.5
Modified: pkg/distrDoc/man/0distrDoc-package.Rd
===================================================================
--- pkg/distrDoc/man/0distrDoc-package.Rd 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrDoc/man/0distrDoc-package.Rd 2015-11-06 17:18:16 UTC (rev 1069)
@@ -3,25 +3,27 @@
\alias{distrDoc}
\docType{package}
\title{
-distrDoc -- documentation for packages distr, distrEx, distrMod,
-distrTeach, distrSim, distrTEst
+distrDoc -- Documentation for 'distr' Family of R Packages
}
\description{
\pkg{distrDoc} provides documentation in form of a common vignette to
packages \pkg{distr}, \pkg{distrEx}, \pkg{distrSim}, \pkg{distrTEst},
-\pkg{distrTeach}, and \pkg{distrMod}.
+\pkg{distrTeach}, \pkg{distrMod}, and \pkg{distrEllipse}.
}
\details{
\tabular{ll}{
Package: \tab distrDoc \cr
-Version: \tab 2.5 \cr
-Date: \tab 2013-09-12 \cr
-Depends: \tab R(>= 2.6.0), tools, distr(>= 2.2.0), startupmsg, distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0), distrTeach(>=
-2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods \cr
-LazyLoad: \tab yes \cr
+Version: \tab 2.6 \cr
+Date: \tab 2015-11-06 \cr
+Depends: \tab R(>= 2.14.0) \cr
+Imports: \tab distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0),
+ distrTeach(>= 2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods,
+ SweaveListingUtils, startupmsg \cr
+Suggests: \tab Biobase \cr
+ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
URL: \tab http://distr.r-forge.r-project.org/\cr
-SVNRevision: \tab 913 \cr
+SVNRevision: \tab 1055 \cr
}}
Modified: pkg/distrDoc/vignettes/distr.Rnw
===================================================================
--- pkg/distrDoc/vignettes/distr.Rnw 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrDoc/vignettes/distr.Rnw 2015-11-06 17:18:16 UTC (rev 1069)
@@ -1343,6 +1343,7 @@
slot \code{param} of argument \code{x}
\item[\%D] time/date at which plot is/was generated
\end{itemize}
+This substitution can be switched off by means of argument \code{withSubst}.
As usual you may control title sizes and colors with
\code{cex.main} / \code{cex.inner} / \code{cex.sub} respectively with
\code{col} / \code{col.main} / \code{col.inner} / \code{col.sub}. Additionally
@@ -3566,7 +3567,7 @@
\begin{thebibliography}{8}
\bibitem{Beng:03}
-Bengtsson H.
+Bengtsson H. (2003):
\newblock The {R.oo} package - object-oriented programming with references using
standard {R} code.
\newblock In: Hornik K., Leisch F. and Zeileis A. (Eds.) {\em
@@ -3575,43 +3576,43 @@
\newblock Published as http://www.ci.tuwien.ac.at/Conferences/DSC-2003/
\bibitem{Cham:98}
-Chambers J.M.
+Chambers J.M. (1998):
\newblock {\em {Programming with data. A guide to the S language}\/}.
\newblock {Springer}.
\newblock http://cm.bell-labs.com/stat/Sbook/index.html
\bibitem{OOPGent}
-Gentleman R.
+Gentleman R. (2003):
\newblock {\em Object Orientated Programming. Slides of a Short Course held in
Auckland\/}.
\newblock http://www.stat.auckland.ac.nz/S-Workshop/Gentleman/Methods.pdf
\bibitem{MK:05}
-Kohl M.
+Kohl M. (2005):
\newblock {\em Numerical Contributions to the Asymptotic Theory of Robustness\/}.
\newblock {Dissertation}, Universit\"at Bayreuth.
\newblock See also http://stamats.de/ThesisMKohl.pdf
\bibitem{K:R:S:04}
-Kohl M., Ruckdeschel P. and Stabla T.
-\newblock {General Purpose Convolution Algorithm for Distributions in S4-Classes
+Ruckdeschel P. and Kohl, M. (2014):
+\newblock {General Purpose Convolution Algorithm for Distributions in S4-Classes
by means of FFT}.
-\newblock unpublished manual
+\newblock {\em J. Statist. Software\/}, {\bf 59}(4): 1--25.
\bibitem{NumR:92}
-Press W.H., Teukolsky S.A., Vetterling W.T. and Flannery B.P.
+Press W.H., Teukolsky S.A., Vetterling W.T. and Flannery B.P. (1992):
\newblock {\em {Numerical recipes in C. The art of scientific computing.}\/}
\newblock {Cambridge Univ. Press}, 2. Aufl.
\bibitem{Ric:88}
-Rice J.A.
+Rice J.A. (1988):
\newblock {\em {Mathematical statistics and data analysis}\/}.
\newblock The Wadsworth \& Brooks/Cole Statistics/Probability Series.
{Wadsworth \& Brooks/Cole Advanced Books \& Software}, Pacific Grove,
California.
\bibitem{R:K:S:C:04}
-Ruckdeschel P., Kohl M., Stabla T., and Camphausen F.
+Ruckdeschel P., Kohl M., Stabla T., and Camphausen F. (2006):
\newblock {S4 Classes for Distributions.}
\newblock {\em R-News\/}, {\bf 6}(2): 10--13.
\newblock http://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf
Modified: pkg/distrEllipse/DESCRIPTION
===================================================================
--- pkg/distrEllipse/DESCRIPTION 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/DESCRIPTION 2015-11-06 17:18:16 UTC (rev 1069)
@@ -1,18 +1,19 @@
Package: distrEllipse
-Version: 2.5
-Date: 2013-09-12
-Title: S4 classes for elliptically contoured distributions
+Version: 2.6
+Date: 2015-11-06
+Title: S4 Classes for Elliptically Contoured Distributions
+Description: Distribution (S4-)classes for elliptically contoured distributions (based on
+ package 'distr').
Depends: R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-1), distr(>= 2.2),
distrEx(>= 2.2), distrSim(>= 2.2)
Suggests: distrMod(>= 2.2), distrTEst(>= 2.2)
-Author: Peter Ruckdeschel
-Description: Distribution (S4-)classes for elliptically contoured distributions (based on
- package distr)
-Maintainer: Peter Ruckdeschel <Peter.Ruckdeschel at itwm.fraunhofer.de>
+Imports: startupmsg, stats
+Authors at R: person("Peter", "Ruckdeschel", role=c("cre", "cph"),
+ email="peter.ruckdeschel at uni-oldenburg.de")
ByteCompile: yes
License: LGPL-3
URL: http://distr.r-forge.r-project.org/
Encoding: latin1
LastChangedDate: {$LastChangedDate: 2009-03-31 15:31:30 +0200 (Di, 31 Mrz 2009) $}
LastChangedRevision: {$LastChangedRevision: 447 $}
-SVNRevision: 913
+SVNRevision: 1055
Modified: pkg/distrEllipse/NAMESPACE
===================================================================
--- pkg/distrEllipse/NAMESPACE 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/NAMESPACE 2015-11-06 17:18:16 UTC (rev 1069)
@@ -1,9 +1,12 @@
import("methods")
+importFrom("graphics", "lines", "pairs", "points")
+importFrom("stats", "qchisq")
importFrom("setRNG", "setRNG")
import("mvtnorm")
import("distr")
import("distrEx")
import("distrSim")
+importFrom("startupmsg", "buildStartupMessage", "infoShow")
export("SphericalDistribution", "EllipticalDistribution",
"MVNorm", "MVt", "MultivarDistrList",
Modified: pkg/distrEllipse/R/01.R
===================================================================
--- pkg/distrEllipse/R/01.R 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/R/01.R 2015-11-06 17:18:16 UTC (rev 1069)
@@ -35,3 +35,37 @@
{
infoShow(pkg = "distrEllipse", filename="MASKING", library = library)
}
+
+#------------------------------------
+#### utilities copied from package distr v.2.6 svn-rev 943
+#------------------------------------
+.isInteger <- function(x, tol = .Machine$double.eps) abs(as.integer(x)-x)< tol
+.isNatural <- function(x, tol = .Machine$double.eps) .isInteger(x, tol) & (x>0)
+
+.inArgs <- function(arg, fct)
+ {as.character(arg) %in% names(formals(fct))}
+
+.isEqual <- function(p0, p1, tol = min( getdistrOption("TruncQuantile")/2,
+ .Machine$double.eps^.7
+ ))
+ abs(p0-p1)< tol
+
+#------------------------------------------------------------------------------
+# issue warnings in show / print as to Arith or print
+#------------------------------------------------------------------------------
+.IssueWarn <- function(Arith,Sim){
+ msgA1 <- msgA2 <- msgS1 <- msgS2 <- NULL
+ if(Arith && getdistrOption("WarningArith")){
+ msgA1 <- gettext(
+ "arithmetics on distributions are understood as operations on r.v.'s\n")
+ msgA2 <- gettext(
+ "see 'distrARITH()'; for switching off this warning see '?distroptions'")
+ }
+ if(Sim && getdistrOption("WarningSim")){
+ msgS1 <- gettext(
+ "slots d,p,q have been filled using simulations; ")
+ msgS2 <- gettext(
+ "for switching off this warning see '?distroptions'")
+ }
+ return(list(msgA=c(msgA1,msgA2), msgS = c(msgS1,msgS2)))
+ }
Modified: pkg/distrEllipse/R/AllClasses.R
===================================================================
--- pkg/distrEllipse/R/AllClasses.R 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/R/AllClasses.R 2015-11-06 17:18:16 UTC (rev 1069)
@@ -37,7 +37,7 @@
contains = "EllipticalParameter",
validity = function(object){
dim0 <- length(object at loc)
- if(!distr:::.isNatural(object at df)) stop("'df' must be an integer")
+ if(!.isNatural(object at df)) stop("'df' must be an integer")
if(!length(object at ncp)==1) stop("wrong dimension for ncp")
if(!nrow(object at scale)==dim0) stop("wrong dimensions")
else return(TRUE)
Modified: pkg/distrEllipse/R/AllShow.R
===================================================================
--- pkg/distrEllipse/R/AllShow.R 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/R/AllShow.R 2015-11-06 17:18:16 UTC (rev 1069)
@@ -35,7 +35,7 @@
function(object){
cls <- class(object)[1]
cat(showobj(object, className = cls))
- ws <- distr:::.IssueWarn(object at .withArith, object at .withSim)
+ ws <- .IssueWarn(object at .withArith, object at .withSim)
if(!is.null(ws$msgA)) warning(ws$msgA)
if(!is.null(ws$msgS)) warning(ws$msgS)
}
Modified: pkg/distrEllipse/R/EllipticalDistribution.R
===================================================================
--- pkg/distrEllipse/R/EllipticalDistribution.R 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/R/EllipticalDistribution.R 2015-11-06 17:18:16 UTC (rev 1069)
@@ -17,7 +17,7 @@
stop("distr must have pos. support")
dr <- d(radDistr)
- dlog <- if(distr:::.inArgs("log", dr))
+ dlog <- if(.inArgs("log", dr))
quote(dr(r, log = TRUE)) else quote(log(dr(r)))
if(is(radDistr,"AbscontDistribution")){
@@ -130,6 +130,17 @@
## functionals:
setMethod("E", signature(object = "EllipticalDistribution",
+ fun = "function", cond = "missing"),
+ function(object,fun){
+ x <- r(object)(1e5)
+ fx1 <- fun(x[,1])
+ dfx <- dim(fx1)
+ ffun <- function(x) c(fun(x))
+ mfun <- rowMeans(apply(x,2,ffun))
+ if(is.null(dfx)) return(mfun)
+ return(array(mfun,dim=dfx))
+ })
+setMethod("E", signature(object = "EllipticalDistribution",
fun = "missing", cond = "missing"),
function(object,...) location(object))
setMethod("var", signature(x = "EllipticalDistribution"),
Modified: pkg/distrEllipse/R/MVMixingDistribution.R
===================================================================
--- pkg/distrEllipse/R/MVMixingDistribution.R 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/R/MVMixingDistribution.R 2015-11-06 17:18:16 UTC (rev 1069)
@@ -1,4 +1,3 @@
-.isEqual <- distr:::.isEqual
MultivarMixingDistribution <- function(..., Dlist, mixCoeff #,
# withSimplify = getdistrOption("simplifyD")
@@ -11,8 +10,6 @@
ldots <- c(ldots, Dlist.L)
}
l <- length(ldots)
- print(ldots)
- print(ldots[[2]])
mixDistr <- do.call(MultivarDistrList,args=ldots)
if(is(mixDistr,"UnivarDistrList"))
return(UnivarMixingDistribution(Dlist = mixDistr, mixCoeff = mixCoeff))
@@ -126,38 +123,45 @@
})
}
+
setMethod("E", signature(object = "MultivarMixingDistribution",
- fun = "ANY", cond = "ANY"),
- function(object, fun, cond, ...) {
- dots <- match.call(call = sys.call(sys.parent(1)),
- expand.dots = FALSE)$"..."
-
+ fun = "missing", cond = "missing"), function(object, ...) {
l <- length(object at mixCoeff)
- argL <- NULL
- if(!missing(fun)) argL <- list(fun=fun)
- if(!missing(cond)) argL <- c(argL, list(cond = cond))
- res <- object at mixCoeff[1]*do.call("E",
- args = c(list(object=object at mixDistr[[1]]),
- argL, dots))
- di <- dim(res)
- lres <- length(res)
- if(l>1){
- cdo <- if(lres >1) cbind else c
- res <- cdo(c(res), sapply(2:l, function(i)
- object at mixCoeff[i]*do.call("E",
- args = c(list(object=object at mixDistr[[i]]),
- argL, dots))))
+ res <- object at mixCoeff[1]*E(object=object at mixDistr[[1]], ...)
+ if(l==1) return(res)
+ for(i in 2:l){
+ res0 <- object at mixCoeff[i]*E(object=object at mixDistr[[i]], ...)
+ res <- res + res0
}
- if(!is.null(di))
- res <- array(res, dim=c(di,l))
- di <- dim(res)
-
- ldi <- if(length(di)>1) 1:(length(di)-1) else 1
- if(length(di) > 1)
- return(apply(res,ldi,sum))
- else return(sum(res))
+ return(res)
})
+setMethod("E", signature(object = "MultivarMixingDistribution",
+ fun = "function", cond = "missing"),
+ function(object, fun, ...) {
+ l <- length(object at mixCoeff)
+ res <- object at mixCoeff[1]*E(object=object at mixDistr[[1]], fun=fun,...)
+ if(l==1) return(res)
+ for(i in 2:l){
+ res0 <- object at mixCoeff[i]*E(object=object at mixDistr[[i]], fun=fun, ...)
+ res <- res + res0
+ }
+ return(res)
+ })
+setMethod("var", signature(x = "MultivarMixingDistribution"),
+ function(x,...){
+ l <- length(x at mixCoeff)
+ if(l==1L) return(var(x at mixDistr[[1]],...))
+ E1 <- E2 <- 0
+ for(i in 1:l){
+ E10 <- E(x at mixDistr[[i]], ...)
+ E1 <- E1 + x at mixCoeff[i]*E10
+ E2 <- E2 + (E10%*%t(E10)+var(x at mixDistr[[i]],...)) *
+ x at mixCoeff[i]
+ }
+ return(E2-E1%*%t(E1))})
+
+
setMethod("plot", signature(x = "MultivarMixingDistribution", y = "missing"),
function(x, Nsim = getdistrEllipseOption("Nsim"), ...,
withED = getdistrEllipseOption("withED"),
@@ -177,7 +181,7 @@
function(object){
cls <- class(object)[1]
cat(showobj(object, className = cls))
- ws <- distr:::.IssueWarn(object at .withArith, object at .withSim)
+ ws <- .IssueWarn(object at .withArith, object at .withSim)
if(!is.null(ws$msgA)) warning(ws$msgA)
if(!is.null(ws$msgS)) warning(ws$msgS)
}
Modified: pkg/distrEllipse/R/MVNorm.R
===================================================================
--- pkg/distrEllipse/R/MVNorm.R 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/R/MVNorm.R 2015-11-06 17:18:16 UTC (rev 1069)
@@ -58,7 +58,7 @@
## MVNormParameter
setMethod("mean", "MVNormParameter",
- function(x) object at loc)
+ function(x) x at loc)
setMethod("sigma", "MVNormParameter",
function(object) object at scale%*%t(object at scale))
@@ -68,4 +68,4 @@
function(object) object at param@scale%*%t(object at param@scale))
setMethod("mean", "MVNormDistribution",
- function(x) object at param@loc)
+ function(x) x at param@loc)
Modified: pkg/distrEllipse/R/SphericalDistribution.R
===================================================================
--- pkg/distrEllipse/R/SphericalDistribution.R 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/R/SphericalDistribution.R 2015-11-06 17:18:16 UTC (rev 1069)
@@ -90,16 +90,16 @@
dots <- match.call(call = sys.call(sys.parent(1)),
expand.dots = FALSE)$"..."
cex <- 0.5
- if(hasArg(cex)) cex <- dots$cex
+ if(hasArg("cex")) cex <- dots$cex
col <- "black"
- if(hasArg(col)) col <- dots$col
+ if(hasArg("col")) col <- dots$col
qchs <- qchisq(.95, df = 2)^.5
col.Ed <- rep(col.Ed, length.out = 2)
X <- r(x)(2000)
- if(hasArg(panel))
+ if(hasArg("panel"))
pairs(t(X), ...)
else
pairs(t(X), ...,
Modified: pkg/distrEllipse/inst/NEWS
===================================================================
--- pkg/distrEllipse/inst/NEWS 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/inst/NEWS 2015-11-06 17:18:16 UTC (rev 1069)
@@ -8,6 +8,20 @@
information)
##############
+v 2.6
+##############
+
+user-visible CHANGES:
++ title changed to title style / capitalization
+
+under the hood:
+
++ removed ::: internal dependencies (within distr-Fam of pkgs) by copying
+ respective routines
++ fixed E and var methods for MultivarMixingDistribution
++ enhanced imports in DESCRIPTION by explicating second order imports
+
+##############
v 2.5
##############
Modified: pkg/distrEllipse/man/0distrEllipse-package.Rd
===================================================================
--- pkg/distrEllipse/man/0distrEllipse-package.Rd 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/man/0distrEllipse-package.Rd 2015-11-06 17:18:16 UTC (rev 1069)
@@ -3,7 +3,7 @@
\alias{distrEllipse}
\docType{package}
\title{
-distrEllipse -- S4 classes for elliptically contoured distributions
+distrEllipse -- S4 Classes for Elliptically Contoured Distributions
}
\description{
\pkg{distrEllipse} provides infrastructure / (S4-)classes for elliptically
@@ -12,14 +12,16 @@
\details{
\tabular{ll}{
Package: \tab distrEllipse \cr
-Version: \tab 2.5 \cr
-Date: \tab 2013-09-12 \cr
-Depends: \tab R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-1),
- distr(>= 2.2), distrEx(>= 2.2), distrSim(>= 2.2), startupmsg\cr
-LazyLoad: \tab yes \cr
+Version: \tab 2.6 \cr
+Date: \tab 2015-11-06 \cr
+Depends: \tab R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-1), distr(>= 2.2),
+ distrEx(>= 2.2), distrSim(>= 2.2)\cr
+Suggests: \tab distrMod(>= 2.2), distrTEst(>= 2.2)\cr
+Imports: \tab startupmsg, stats\cr
+ByteCompile: \tab yes \cr
License: \tab LGPL-3 \cr
URL: \tab http://distr.r-forge.r-project.org/\cr
-SVNRevision: \tab 913 \cr
+SVNRevision: \tab 1055 \cr
}
}
\section{Classes}{
Modified: pkg/distrEllipse/man/EllipticalDistribution-class.Rd
===================================================================
--- pkg/distrEllipse/man/EllipticalDistribution-class.Rd 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/man/EllipticalDistribution-class.Rd 2015-11-06 17:18:16 UTC (rev 1069)
@@ -6,6 +6,7 @@
\alias{scale<-,EllipticalDistribution-method}
\alias{location<-,EllipticalDistribution-method}
\alias{E,EllipticalDistribution,missing,missing-method}
+\alias{E,EllipticalDistribution,function,missing-method}
\alias{var,EllipticalDistribution-method}
\alias{+,EllipticalDistribution,numeric-method}
\alias{*,EllipticalDistribution,numeric-method}
@@ -84,6 +85,9 @@
\item{E}{\code{signature(object = "EllipticalDistribution", fun = "missing", cond = "missing")}:
expectation of an elliptically symmetric distribution; exact.
}
+ \item{E}{\code{signature(object = "EllipticalDistribution", fun = "function", cond = "missing")}:
+ expectation of an elliptically symmetric distribution; by simulation.
+ }
\item{var}{\code{signature(x = "EllipticalDistribution")}:
expectation of an elliptically symmetric distribution; exact.
}
Modified: pkg/distrEllipse/man/MultivarDistrList-class.Rd
===================================================================
--- pkg/distrEllipse/man/MultivarDistrList-class.Rd 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/man/MultivarDistrList-class.Rd 2015-11-06 17:18:16 UTC (rev 1069)
@@ -52,7 +52,6 @@
(DL2 <- MultivarDistrList(MVNorm(),
EllipticalDistribution(radDistr=Exp(), loc=c(1,2),
scale=diag(c(3,1))),MVt()))
-
}
\keyword{distribution}
\keyword{list}
Modified: pkg/distrEllipse/man/MultivarMixingDistribution-class.Rd
===================================================================
--- pkg/distrEllipse/man/MultivarMixingDistribution-class.Rd 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/man/MultivarMixingDistribution-class.Rd 2015-11-06 17:18:16 UTC (rev 1069)
@@ -20,7 +20,9 @@
\alias{Symmetry,MultivarMixingDistribution-method}
\alias{dimension,MultivarMixingDistribution-method}
\alias{dim,MultivarMixingDistribution-method}
-\alias{E,MultivarMixingDistribution,ANY,ANY-method}
+\alias{E,MultivarMixingDistribution,missing,missing-method}
+\alias{E,MultivarMixingDistribution,function,missing-method}
+\alias{var,MultivarMixingDistribution-method}
\alias{show,MultivarMixingDistribution-method}
\alias{showobj,MultivarMixingDistribution-method}
@@ -120,6 +122,8 @@
mylist2
p(mylist)(0.3)
mixDistr(mylist2)
+E(mylist)
+var(mylist)
##multivariate
E1 <- diag(1,2)\%*\%EllipticalDistribution(radDistr=Gammad())+c(1,2)
@@ -130,6 +134,8 @@
mylistD2
p(mylistD)
mixDistr(mylistD2)
+E(mylistD2)
+var(mylistD2)
}
\keyword{distribution}
\concept{discrete distribution}
Modified: pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save
===================================================================
--- pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2015-11-06 17:17:45 UTC (rev 1068)
+++ pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2015-11-06 17:18:16 UTC (rev 1069)
@@ -1,7 +1,7 @@
-R version 3.0.1 Patched (2013-09-02 r63805) -- "Good Sport"
-Copyright (C) 2013 The R Foundation for Statistical Computing
-Platform: i386-w64-mingw32/i386 (32-bit)
+R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences"
+Copyright (C) 2015 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -20,33 +20,21 @@
> pkgname <- "distrEllipse"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
-> options(pager = "console")
-> base::assign(".ExTimings", "distrEllipse-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('distrEllipse')
Loading required package: mvtnorm
Loading required package: setRNG
Loading required package: distr
Loading required package: startupmsg
-:startupmsg> Utilities for start-up messages (version 0.9)
+:startupmsg> Utilities for Start-Up Messages (version 0.9.1)
:startupmsg>
:startupmsg> For more information see ?"startupmsg",
:startupmsg> NEWS("startupmsg")
Loading required package: sfsmisc
Loading required package: SweaveListingUtils
-:SweaveListingUtils> Utilities for Sweave together with
-:SweaveListingUtils> TeX listings package (version 0.7)
+:SweaveListingUtils> Utilities for Sweave Together with
+:SweaveListingUtils> TeX 'listings' Package (version
+:SweaveListingUtils> 0.7)
:SweaveListingUtils>
:SweaveListingUtils> NOTE: Support for this package
:SweaveListingUtils> will stop soon.
@@ -72,14 +60,14 @@
:SweaveListingUtils> vignette("ExampleSweaveListingUtils").
-Attaching package: 'SweaveListingUtils'
+Attaching package: ‘SweaveListingUtils’
-The following objects are masked from 'package:base':
+The following objects are masked from ‘package:base’:
library, require
-:distr> Object oriented implementation of distributions (version
-:distr> 2.5.2)
+:distr> Object Oriented Implementation of Distributions (version
+:distr> 2.6)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
@@ -98,14 +86,14 @@
:distr> vignette("distr").
-Attaching package: 'distr'
+Attaching package: ‘distr’
-The following objects are masked from 'package:stats':
+The following objects are masked from ‘package:stats’:
df, qqplot, sd
Loading required package: distrEx
-:distrEx> Extensions of package distr (version 2.5)
+:distrEx> Extensions of Package 'distr' (version 2.6)
:distrEx>
:distrEx> Note: Packages "e1071", "moments", "fBasics" should be
:distrEx> attached /before/ package "distrEx". See
@@ -122,15 +110,15 @@
:distrEx> vignette("distr").
-Attaching package: 'distrEx'
+Attaching package: ‘distrEx’
-The following objects are masked from 'package:stats':
+The following objects are masked from ‘package:stats’:
IQR, mad, median, var
Loading required package: distrSim
-:distrSim> Simulation classes based on package distr (version
-:distrSim> 2.5.2)
+:distrSim> Simulation Classes Based on Package 'distr' (version
+:distrSim> 2.6)
:distrSim>
:distrSim> Some functions from package 'stats' are intentionally
:distrSim> masked ---see distrSimMASK().
@@ -144,18 +132,18 @@
:distrSim> vignette("distr").
-Attaching package: 'distrSim'
+Attaching package: ‘distrSim’
-The following object is masked from 'package:stats':
+The following object is masked from ‘package:stats’:
simulate
-The following object is masked from 'package:base':
+The following object is masked from ‘package:base’:
rbind
-:distrEllipse> S4 classes for elliptically contoured
-:distrEllipse> distributions (version 2.5)
+:distrEllipse> S4 Classes for Elliptically Contoured
+:distrEllipse> Distributions (version 2.6)
:distrEllipse>
:distrEllipse> Some functions from package 'stats' are
:distrEllipse> intentionally masked ---see
@@ -177,7 +165,6 @@
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EllipticalDistribution-class
> ### Title: Elliptical distribution class
> ### Aliases: EllipticalDistribution-class
@@ -186,6 +173,7 @@
> ### scale<-,EllipticalDistribution-method
> ### location<-,EllipticalDistribution-method
> ### E,EllipticalDistribution,missing,missing-method
+> ### E,EllipticalDistribution,function,missing-method
> ### var,EllipticalDistribution-method
> ### +,EllipticalDistribution,numeric-method
> ### *,EllipticalDistribution,numeric-method
@@ -209,15 +197,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("EllipticalDistribution-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("EllipticalDistribution")
> ### * EllipticalDistribution
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EllipticalDistribution
> ### Title: Generating function for EllipticalDistribution-class
> ### Aliases: EllipticalDistribution
@@ -238,15 +223,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("EllipticalDistribution", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("EllipticalParameter-class")
> ### * EllipticalParameter-class
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EllipticalParameter-class
> ### Title: Paramter of an Elliptical distributions
> ### Aliases: EllipticalParameter-class location
@@ -274,15 +256,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("EllipticalParameter-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("MVnormDistribution-class")
> ### * MVnormDistribution-class
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MVNormDistribution-class
> ### Title: MVNorm distribution class
> ### Aliases: MVNormDistribution-class sigma,MVNormDistribution-method
@@ -304,15 +283,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("MVnormDistribution-class", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("MVnormDistribution")
> ### * MVnormDistribution
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MVNormDistribution
> ### Title: Generating function for MVNormDistribution-class
> ### Aliases: MVNormDistribution MVNorm
@@ -333,15 +309,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("MVnormDistribution", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("MVnormParameter-class")
> ### * MVnormParameter-class
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MVNormParameter-class
> ### Title: Paramter of a multivariate normal distribution
> ### Aliases: MVNormParameter-class mean mean,MVNormParameter-method sigma
@@ -366,15 +339,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/distr -r 1069
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