From noreply at r-forge.r-project.org Fri Sep 6 21:35:15 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 6 Sep 2013 21:35:15 +0200 (CEST) Subject: [Distr-commits] r895 - in branches: distr-2.4/pkg/SweaveListingUtils distr-2.4/pkg/distr distr-2.4/pkg/distrDoc distr-2.4/pkg/distrDoc/vignettes distr-2.4/pkg/distrTEst distr-2.4/pkg/distrTeach distr-2.5/pkg/SweaveListingUtils distr-2.5/pkg/distr distr-2.5/pkg/distr/man distr-2.5/pkg/distrDoc distr-2.5/pkg/distrDoc/vignettes distr-2.5/pkg/distrEllipse distr-2.5/pkg/distrEx distr-2.5/pkg/distrEx/R distr-2.5/pkg/distrEx/man distr-2.5/pkg/distrMod distr-2.5/pkg/distrMod/R distr-2.5/pkg/distrRmetrics distr-2.5/pkg/distrRmetrics/man distr-2.5/pkg/distrSim distr-2.5/pkg/distrTEst distr-2.5/pkg/distrTeach distr-2.5/pkg/startupmsg Message-ID: <20130906193515.3ACAF1859A2@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-06 21:35:14 +0200 (Fri, 06 Sep 2013) New Revision: 895 Added: branches/distr-2.5/pkg/distrEllipse/.Rbuildignore branches/distr-2.5/pkg/distrEx/.Rbuildignore branches/distr-2.5/pkg/distrRmetrics/.Rbuildignore branches/distr-2.5/pkg/distrSim/.Rbuildignore branches/distr-2.5/pkg/distrTEst/.Rbuildignore branches/distr-2.5/pkg/distrTeach/.Rbuildignore branches/distr-2.5/pkg/startupmsg/.Rbuildignore Modified: branches/distr-2.4/pkg/SweaveListingUtils/.Rbuildignore branches/distr-2.4/pkg/SweaveListingUtils/DESCRIPTION branches/distr-2.4/pkg/distr/.Rbuildignore branches/distr-2.4/pkg/distrDoc/DESCRIPTION branches/distr-2.4/pkg/distrDoc/NAMESPACE branches/distr-2.4/pkg/distrDoc/vignettes/distr.Rnw branches/distr-2.4/pkg/distrTEst/DESCRIPTION branches/distr-2.4/pkg/distrTEst/NAMESPACE branches/distr-2.4/pkg/distrTeach/NAMESPACE branches/distr-2.5/pkg/SweaveListingUtils/.Rbuildignore branches/distr-2.5/pkg/SweaveListingUtils/DESCRIPTION branches/distr-2.5/pkg/distr/.Rbuildignore branches/distr-2.5/pkg/distr/DESCRIPTION branches/distr-2.5/pkg/distr/man/RtoDPQ.LC.Rd branches/distr-2.5/pkg/distr/man/RtoDPQ.Rd branches/distr-2.5/pkg/distr/man/plot-methods.Rd branches/distr-2.5/pkg/distrDoc/.Rbuildignore branches/distr-2.5/pkg/distrDoc/DESCRIPTION branches/distr-2.5/pkg/distrDoc/NAMESPACE branches/distr-2.5/pkg/distrDoc/vignettes/distr.Rnw branches/distr-2.5/pkg/distrEllipse/DESCRIPTION branches/distr-2.5/pkg/distrEllipse/NAMESPACE branches/distr-2.5/pkg/distrEx/DESCRIPTION branches/distr-2.5/pkg/distrEx/NAMESPACE branches/distr-2.5/pkg/distrEx/R/AllClass.R branches/distr-2.5/pkg/distrEx/R/ClippedMoments.R branches/distr-2.5/pkg/distrEx/R/ConvexContamination.R branches/distr-2.5/pkg/distrEx/R/Expectation.R branches/distr-2.5/pkg/distrEx/R/Functionals.R branches/distr-2.5/pkg/distrEx/R/Kurtosis.R branches/distr-2.5/pkg/distrEx/man/E.Rd branches/distr-2.5/pkg/distrMod/.Rbuildignore branches/distr-2.5/pkg/distrMod/DESCRIPTION branches/distr-2.5/pkg/distrMod/NAMESPACE branches/distr-2.5/pkg/distrMod/R/0distrModUtils.R branches/distr-2.5/pkg/distrRmetrics/DESCRIPTION branches/distr-2.5/pkg/distrRmetrics/NAMESPACE branches/distr-2.5/pkg/distrRmetrics/man/SNorm-class.Rd branches/distr-2.5/pkg/distrRmetrics/man/SNorm.Rd branches/distr-2.5/pkg/distrRmetrics/man/SSTd-class.Rd branches/distr-2.5/pkg/distrRmetrics/man/SSTd.Rd branches/distr-2.5/pkg/distrRmetrics/man/STd.Rd branches/distr-2.5/pkg/distrSim/DESCRIPTION branches/distr-2.5/pkg/distrTEst/DESCRIPTION branches/distr-2.5/pkg/distrTEst/NAMESPACE branches/distr-2.5/pkg/distrTeach/DESCRIPTION branches/distr-2.5/pkg/distrTeach/NAMESPACE Log: fixed issues detected with new checks in R CMD check --as-cran R-devel, version r63824 Modified: branches/distr-2.4/pkg/SweaveListingUtils/.Rbuildignore =================================================================== --- branches/distr-2.4/pkg/SweaveListingUtils/.Rbuildignore 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/SweaveListingUtils/.Rbuildignore 2013-09-06 19:35:14 UTC (rev 895) @@ -1 +1,2 @@ ^.*\.svn.+ +.*-Ex\.R \ No newline at end of file Modified: branches/distr-2.4/pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- branches/distr-2.4/pkg/SweaveListingUtils/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/SweaveListingUtils/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -4,14 +4,13 @@ Version: 0.6 Depends: R(>= 2.10.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines -Imports: stats ByteCompile: yes Author: Peter Ruckdeschel Description: provides utilities for defining R / Rd as Tex-package-listings "language" and including R / Rd source file (sniplets) copied from R-forge in its most recent version (or another url) thereby avoiding inconsistencies between vignette and documented source code Maintainer: Peter Ruckdeschel License: LGPL-3 -Date: 2013-01-10 +Date: 2013-09-06 LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} SVNRevision: 834 Modified: branches/distr-2.4/pkg/distr/.Rbuildignore =================================================================== --- branches/distr-2.4/pkg/distr/.Rbuildignore 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/distr/.Rbuildignore 2013-09-06 19:35:14 UTC (rev 895) @@ -1,2 +1,3 @@ inst/doc/Rplots.pdf ^.*\.svn.+ +.*-Ex\.R \ No newline at end of file Modified: branches/distr-2.4/pkg/distrDoc/DESCRIPTION =================================================================== --- branches/distr-2.4/pkg/distrDoc/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/distrDoc/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -1,11 +1,11 @@ Package: distrDoc -Version: 2.4 -Date: 2013-01-09 +Version: 2.4.1 +Date: 2013-09-06 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 Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Maintainer: Peter Ruckdeschel -Depends: R(>= 2.6.0), tools, startupmsg, distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0), distrTeach(>= 2.2.0), RandVar(>= 0.7), +Depends: R(>= 2.6.0), tools, 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 Suggests: Biobase, SweaveListingUtils ByteCompile: yes @@ -14,4 +14,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 834 +SVNRevision: 895 Modified: branches/distr-2.4/pkg/distrDoc/NAMESPACE =================================================================== --- branches/distr-2.4/pkg/distrDoc/NAMESPACE 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/distrDoc/NAMESPACE 2013-09-06 19:35:14 UTC (rev 895) @@ -1,10 +1,85 @@ import("methods") -import("startupmsg") import("MASS") import("distr") import("distrEx") -import("distrSim") import("RandVar") -import("distrMod") -import("distrTeach") -import("distrTEst") + +importFrom("stats4","profile") +exportClasses("MatrixorFunction", "OptionalNumericOrMatrixOrCall", + "OptionalDistrListOrCall", "OptionalNumericOrMatrix", + "ShowDetails", + "FunctionSymmetry", "NonSymmetric", "EvenSymmetric", "OddSymmetric", + "FunSymmList", + "ParamFamParameter", + "ProbFamily", "ParamFamily", "L2ParamFamily") +exportClasses("RiskType", + "asRisk", "asCov", "trAsCov", "asHampel", "asBias", "asGRisk", + "asMSE", "asUnOvShoot", + "fiRisk", "fiCov", "trFiCov", "fiHampel", "fiMSE", "fiBias", + "fiUnOvShoot") +exportClasses("BiasType", "onesidedBias", "asymmetricBias", "symmetricBias") +exportClasses("asSemivar", "asRiskwithBias") +exportClasses("L2GroupParamFamily", "L2LocationFamily", + "L2ScaleFamily", "L2LocationScaleFamily") +exportClasses("L2LocationScaleUnion") +exportClasses("L2ScaleShapeUnion", "L2ScaleUnion") +exportClasses("ParamWithScaleFamParameter", "ParamWithShapeFamParameter", + "ParamWithScaleAndShapeFamParameter") +exportClasses("BinomFamily","PoisFamily", "NormLocationFamily", + "NormScaleFamily", "ExpScaleFamily", + "LnormScaleFamily", "GammaFamily", "BetaFamily", "NormLocationScaleFamily", + "CauchyLocationScaleFamily") +exportClasses("NormType", "QFNorm", "InfoNorm", "SelfNorm") +exportClasses("Estimate", "MCEstimate") +exportClasses("Confint") +exportMethods("distrSymm") +exportMethods("distribution", "props", "props<-", "addProp<-", "main", "main<-", + "nuisance", "nuisance<-", "trafo", "trafo<-", "trafo.fct", + "fixed", "fixed<-", "modifyParam", + "dimension", "show", "print", "plot", "param", "E", "name", + "L2deriv", "L2derivSymm", "L2derivDistr", "L2derivDistrSymm", + "FisherInfo", "checkL2deriv", "fam.call") +exportMethods("completecases") +exportMethods("bound", "width") +exportMethods("nu", "name", "sign", "nu<-", "name<-", "sign<-", "biastype", "biastype<-") +exportMethods("existsPIC") +exportMethods("modifyModel") +exportMethods("norm", "QuadForm<-", "QuadForm", "fct", + "fct<-", "normtype", "normtype<-") +exportMethods("r", "d", "p", "q", + "estimate", "estimate.call", "samplesize.estimate", "call.estimate", + "name.estimate", "trafo.estimate", "nuisance.estimate", + "fixed.estimate", "Infos", "Infos<-", "addInfo<-", + "criterion", "criterion<-", "criterion.fct", "method", + "samplesize", "asvar", "asvar<-", "optimwarn", + "withPosRestr", "withPosRestr<-") +exportMethods("untransformed.estimate", "untransformed.asvar") +exportMethods("confint") +exportMethods("validParameter") +exportMethods("startPar", "makeOKPar") +exportMethods("scaleshapename", "scalename", "LogDeriv") +exportMethods("coerce", "profile", "locscalename", "scaleshapename<-") +exportMethods("mleCalc", "mceCalc") +exportMethods("qqplot") +export("distrModMASK") +export("trafoEst") +export("distrModOptions", "distrModoptions", "getdistrModOption", + "Estimator", "MCEstimator", "MLEstimator", "MDEstimator") +export("NonSymmetric", "EvenSymmetric", "OddSymmetric", "FunSymmList") +export("ParamFamParameter", "ParamFamily", "L2ParamFamily", + "BinomFamily", "PoisFamily", "NbinomFamily", "NormLocationFamily", + "NormScaleFamily", "ExpScaleFamily", + "LnormScaleFamily", "GammaFamily", "BetaFamily", "NormLocationScaleFamily", + "CauchyLocationScaleFamily", "NbinomwithSizeFamily", "NbinomMeanSizeFamily") +export("asCov", "trAsCov", "asHampel", "asBias", "asMSE", "asUnOvShoot", + "fiCov", "trFiCov", "fiHampel", "fiMSE", "fiBias", "fiUnOvShoot") +export("positiveBias", "negativeBias", "symmetricBias", + "asymmetricBias", "asSemivar") +export("isKerAinKerB") +export("L2LocationFamily", "L2ScaleFamily", "L2LocationScaleFamily") +export("EuclideanNorm", "QuadFormNorm") +export("NormType", "QFNorm", "InfoNorm", "SelfNorm") +export("NormScaleUnknownLocationFamily", "NormLocationUnknownScaleFamily") +export("L2LocationUnknownScaleFamily", "L2ScaleUnknownLocationFamily") +export("meRes", "get.criterion.fct") +export("addAlphTrsp2col") Modified: branches/distr-2.4/pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- branches/distr-2.4/pkg/distrDoc/vignettes/distr.Rnw 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/distrDoc/vignettes/distr.Rnw 2013-09-06 19:35:14 UTC (rev 895) @@ -1,5 +1,5 @@ %\VignetteIndexEntry{distr - manual} -%\VignetteDepends{startupmsg,distr} +%\VignetteDepends{distr} %\VignetteKeyword{probability distribution,simulation,estimation} %\VignettePackage{distr} % Modified: branches/distr-2.4/pkg/distrTEst/DESCRIPTION =================================================================== --- branches/distr-2.4/pkg/distrTEst/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/distrTEst/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -2,9 +2,8 @@ Version: 2.4 Date: 2013-01-10 Title: Estimation and Testing classes based on package distr -Depends: R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.2), distrSim(>= 2.2), startupmsg +Depends: R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distrSim(>= 2.2) Suggests: distrEx(>= 2.2) -Imports: stats Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Description: Evaluation (S4-)classes based on package distr for evaluating procedures (estimators/tests) at data/simulation in a unified way. Maintainer: Peter Ruckdeschel Modified: branches/distr-2.4/pkg/distrTEst/NAMESPACE =================================================================== --- branches/distr-2.4/pkg/distrTEst/NAMESPACE 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/distrTEst/NAMESPACE 2013-09-06 19:35:14 UTC (rev 895) @@ -2,6 +2,7 @@ import("startupmsg") import("distr") import("distrSim") +import("setRNG") export("EvaluationList", "distrTEstoptions", "getdistrTEstOption") exportClasses("numericorNULL", "Evaluation", "EvaluationList", Modified: branches/distr-2.4/pkg/distrTeach/NAMESPACE =================================================================== --- branches/distr-2.4/pkg/distrTeach/NAMESPACE 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.4/pkg/distrTeach/NAMESPACE 2013-09-06 19:35:14 UTC (rev 895) @@ -1,6 +1,7 @@ import("startupmsg") import("distr") import("distrEx") +import("methods") exportMethods("plotCLT") export("illustrateLLN") Modified: branches/distr-2.5/pkg/SweaveListingUtils/.Rbuildignore =================================================================== --- branches/distr-2.5/pkg/SweaveListingUtils/.Rbuildignore 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/SweaveListingUtils/.Rbuildignore 2013-09-06 19:35:14 UTC (rev 895) @@ -1 +1,2 @@ ^.*\.svn.+ +.*-Ex\.R \ No newline at end of file Modified: branches/distr-2.5/pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/SweaveListingUtils/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/SweaveListingUtils/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -4,7 +4,6 @@ Version: 0.7 Depends: R(>= 2.14.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines -Imports: stats ByteCompile: yes Author: Peter Ruckdeschel Description: provides utilities for defining R / Rd as Tex-package-listings "language" and including R / Rd source file (sniplets) copied from R-forge in its most Modified: branches/distr-2.5/pkg/distr/.Rbuildignore =================================================================== --- branches/distr-2.5/pkg/distr/.Rbuildignore 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distr/.Rbuildignore 2013-09-06 19:35:14 UTC (rev 895) @@ -1,2 +1,3 @@ inst/doc/Rplots.pdf ^.*\.svn.+ +.*-Ex\.R \ No newline at end of file Modified: branches/distr-2.5/pkg/distr/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distr/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distr/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -6,7 +6,7 @@ Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Maintainer: Peter Ruckdeschel Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils -Suggests: distrEx, SweaveListingUtils +Suggests: distrEx Imports: stats ByteCompile: yes Encoding: latin1 Modified: branches/distr-2.5/pkg/distr/man/RtoDPQ.LC.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/RtoDPQ.LC.Rd 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distr/man/RtoDPQ.LC.Rd 2013-09-06 19:35:14 UTC (rev 895) @@ -4,7 +4,8 @@ \description{ function to do get empirical density, cumulative distribution and quantile function from random numbers} \usage{ -RtoDPQ.LC(r, e = getdistrOption("RtoDPQ.e"), n = getdistrOption("DefaultNrGridPoints"), y = NULL) +RtoDPQ.LC(r, e = getdistrOption("RtoDPQ.e"), + n = getdistrOption("DefaultNrGridPoints"), y = NULL) } \arguments{ \item{r}{ the random number generator } Modified: branches/distr-2.5/pkg/distr/man/RtoDPQ.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/RtoDPQ.Rd 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distr/man/RtoDPQ.Rd 2013-09-06 19:35:14 UTC (rev 895) @@ -4,7 +4,8 @@ \description{ function to do get empirical density, cumulative distribution and quantile function from random numbers} \usage{ -RtoDPQ(r, e = getdistrOption("RtoDPQ.e"), n = getdistrOption("DefaultNrGridPoints"), y = NULL) +RtoDPQ(r, e = getdistrOption("RtoDPQ.e"), + n = getdistrOption("DefaultNrGridPoints"), y = NULL) } \arguments{ \item{r}{ the random number generator } Modified: branches/distr-2.5/pkg/distr/man/plot-methods.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/plot-methods.Rd 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distr/man/plot-methods.Rd 2013-09-06 19:35:14 UTC (rev 895) @@ -12,41 +12,41 @@ \description{plot-methods} \usage{plot(x, y, ...) \S4method{plot}{AbscontDistribution,missing}(x, width = 10, height = 5.5, - withSweave = getdistrOption("withSweave"), xlim = NULL, ylim = NULL, ngrid = 1000, - verticals = TRUE, do.points = TRUE, main = FALSE, inner = TRUE, - sub = FALSE, bmar = par("mar")[1], tmar = par("mar")[3], ..., + withSweave = getdistrOption("withSweave"), xlim = NULL, ylim = NULL, + ngrid = 1000, verticals = TRUE, do.points = TRUE, main = FALSE, + inner = TRUE, sub = FALSE, bmar = par("mar")[1], tmar = par("mar")[3], ..., cex.main = par("cex.main"), cex.inner = 1.2, cex.sub = par("cex.sub"), col.points = par("col"), col.vert = par("col"), col.main = par("col.main"), col.inner = par("col.main"), col.sub = par("col.sub"), cex.points = 2.0, pch.u = 21, pch.a = 16, mfColRow = TRUE, to.draw.arg = NULL) \S4method{plot}{DiscreteDistribution,missing}(x, width = 10, height = 5.5, - withSweave = getdistrOption("withSweave"), xlim = NULL, ylim = NULL, verticals = TRUE, - do.points = TRUE, main = FALSE, inner = TRUE, sub = FALSE, + withSweave = getdistrOption("withSweave"), xlim = NULL, ylim = NULL, + verticals = TRUE, do.points = TRUE, main = FALSE, inner = TRUE, sub = FALSE, bmar = par("mar")[1], tmar = par("mar")[3], ..., cex.main = par("cex.main"), cex.inner = 1.2, cex.sub = par("cex.sub"), col.points = par("col"), col.hor = par("col"), col.vert = par("col"), col.main = par("col.main"), col.inner = par("col.main"), - col.sub = par("col.sub"), cex.points = 2.0, pch.u = 21, pch.a = 16, mfColRow = TRUE, - to.draw.arg = NULL) + col.sub = par("col.sub"), cex.points = 2.0, pch.u = 21, pch.a = 16, + mfColRow = TRUE, to.draw.arg = NULL) \S4method{plot}{AffLinUnivarLebDecDistribution,missing}(x, width = 10, - height = 5.5, withSweave = getdistrOption("withSweave"), xlim = NULL, ylim = NULL, ngrid = 1000, - verticals = TRUE, do.points = TRUE, main = FALSE, inner = TRUE, sub = FALSE, - bmar = par("mar")[1], tmar = par("mar")[3], ..., cex.main = par("cex.main"), - cex.inner = 1.2, cex.sub = par("cex.sub"), col.points = par("col"), - col.hor = par("col"), col.vert = par("col"), col.main = par("col.main"), - col.inner = par("col.main"), col.sub = par("col.sub"), cex.points = 2.0, - pch.u = 21, pch.a = 16, mfColRow = TRUE, - to.draw.arg = NULL) + height = 5.5, withSweave = getdistrOption("withSweave"), xlim = NULL, + ylim = NULL, ngrid = 1000, verticals = TRUE, do.points = TRUE, main = FALSE, + inner = TRUE, sub = FALSE, bmar = par("mar")[1], tmar = par("mar")[3], ..., + cex.main = par("cex.main"), cex.inner = 1.2, cex.sub = par("cex.sub"), + col.points = par("col"), col.hor = par("col"), col.vert = par("col"), + col.main = par("col.main"), col.inner = par("col.main"), + col.sub = par("col.sub"), cex.points = 2.0, pch.u = 21, pch.a = 16, + mfColRow = TRUE, to.draw.arg = NULL) \S4method{plot}{UnivarLebDecDistribution,missing}(x, width = 10, - height = 14.5, withSweave = getdistrOption("withSweave"), xlim = NULL, ylim = NULL, ngrid = 1000, - verticals = TRUE, do.points = TRUE, main = FALSE, inner = TRUE, sub = FALSE, - bmar = par("mar")[1], tmar = par("mar")[3], ..., cex.main = par("cex.main"), - cex.inner = 0.9, cex.sub = par("cex.sub"), col.points = par("col"), - col.hor = par("col"), col.vert = par("col"), col.main = par("col.main"), - col.inner = par("col.main"), col.sub = par("col.sub"), cex.points = 2.0, - pch.u = 21, pch.a = 16, mfColRow = TRUE, - to.draw.arg = NULL) + height = 14.5, withSweave = getdistrOption("withSweave"), xlim = NULL, + ylim = NULL, ngrid = 1000, verticals = TRUE, do.points = TRUE, main = FALSE, + inner = TRUE, sub = FALSE, bmar = par("mar")[1], tmar = par("mar")[3], ..., + cex.main = par("cex.main"), cex.inner = 0.9, cex.sub = par("cex.sub"), + col.points = par("col"), col.hor = par("col"), col.vert = par("col"), + col.main = par("col.main"), col.inner = par("col.main"), + col.sub = par("col.sub"), cex.points = 2.0, pch.u = 21, pch.a = 16, + mfColRow = TRUE, to.draw.arg = NULL) \S4method{plot}{DistrList,missing}(x, y, ...) \S4method{plot}{CompoundDistribution,missing}(x, y, ...) } Modified: branches/distr-2.5/pkg/distrDoc/.Rbuildignore =================================================================== --- branches/distr-2.5/pkg/distrDoc/.Rbuildignore 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrDoc/.Rbuildignore 2013-09-06 19:35:14 UTC (rev 895) @@ -1,3 +1,4 @@ ^.*\.svn.+ inst/doc/Rplots.pdf inst/doc/Rplots.ps +.*-Ex\.R \ No newline at end of file Modified: branches/distr-2.5/pkg/distrDoc/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distrDoc/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrDoc/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -7,7 +7,7 @@ distrMod, distrSim, distrTEst, distrTeach, and distrEllipse Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Maintainer: Peter Ruckdeschel -Depends: R(>= 2.14.0), tools, startupmsg, distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= +Depends: R(>= 2.14.0), tools, 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 Suggests: Biobase, SweaveListingUtils Modified: branches/distr-2.5/pkg/distrDoc/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distrDoc/NAMESPACE 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrDoc/NAMESPACE 2013-09-06 19:35:14 UTC (rev 895) @@ -1,10 +1,62 @@ import("methods") -import("startupmsg") import("MASS") import("distr") import("distrEx") import("distrSim") +import("distrTEst") +import("distrTeach") import("RandVar") -import("distrMod") -import("distrTeach") -import("distrTEst") +importMethodsFrom("distrMod", "addInfo<-","addProp<-","asvar","asvar<-", + "biastype","biastype<-","bound","call.estimate", + "checkL2deriv","coerce","completecases","confint", + "criterion","criterion.fct","criterion<-","d", + "dimension","distrSymm","E","estimate","estimate.call", + "existsPIC","fam.call","fct","fct<-","FisherInfo", + "fixed","fixed.estimate","fixed<-","Infos","Infos<-", + "L2deriv","L2derivDistr","L2derivDistrSymm","L2derivSymm", + "locscalename","LogDeriv", + "main","main<-","makeOKPar","mceCalc","method","mleCalc", + "modifyModel","modifyParam","name","name.estimate","name<-","norm", + "normtype","normtype<-","nu","nu<-","nuisance", + "nuisance.estimate","nuisance<-","optimwarn","p","param", + "plot","print","profile","props", + "props<-","q","qqplot","QuadForm","QuadForm<-","r", + "samplesize.estimate","scalename","scaleshapename", + "scaleshapename<-","show","sign", + "sign<-","startPar","trafo","trafo.estimate", + "trafo.fct","trafo<-","untransformed.asvar", + "untransformed.estimate","validParameter","width", + "withPosRestr","withPosRestr<-") +importFrom("distrMod","addAlphTrsp2col","asBias","asCov","asHampel","asMSE", + "asSemivar","asUnOvShoot","asymmetricBias","BetaFamily","BinomFamily", + "CauchyLocationScaleFamily","distrModMASK", + "distrModoptions","distrModOptions","Estimator","EuclideanNorm", + "EvenSymmetric","ExpScaleFamily","fiBias","fiCov","fiHampel","fiMSE", + "fiUnOvShoot","FunSymmList","GammaFamily","get.criterion.fct", + "getdistrModOption","InfoNorm","isKerAinKerB","L2LocationFamily", + "L2LocationScaleFamily","L2LocationUnknownScaleFamily", + "L2ParamFamily","L2ScaleFamily","L2ScaleUnknownLocationFamily", + "LnormScaleFamily","MCEstimator","MDEstimator","meRes", + "MLEstimator","NbinomFamily","NbinomMeanSizeFamily", + "NbinomwithSizeFamily","negativeBias","NonSymmetric", + "NormLocationFamily","NormLocationScaleFamily", + "NormLocationUnknownScaleFamily","NormScaleFamily", + "NormScaleUnknownLocationFamily","NormType","OddSymmetric", + "ParamFamily","ParamFamParameter","PoisFamily", + "positiveBias","QFNorm", + "QuadFormNorm","SelfNorm","symmetricBias","trafoEst") +importClassesFrom("distrMod","asBias","asCov","asGRisk","asHampel","asMSE", + "asRisk","asRiskwithBias","asSemivar","asUnOvShoot","asymmetricBias", + "BetaFamily","BiasType","BinomFamily","CauchyLocationScaleFamily", + "Confint","Estimate","EvenSymmetric","ExpScaleFamily","fiBias","fiCov", + "fiHampel","fiMSE","fiRisk","fiUnOvShoot","FunctionSymmetry","FunSymmList", + "GammaFamily","InfoNorm","L2GroupParamFamily","L2LocationFamily", + "L2LocationScaleFamily","L2LocationScaleUnion","L2ParamFamily", + "L2ScaleFamily","L2ScaleShapeUnion","L2ScaleUnion","LnormScaleFamily", + "MatrixorFunction","MCEstimate","NonSymmetric","NormLocationFamily", + "NormLocationScaleFamily","NormScaleFamily","NormType","OddSymmetric", + "onesidedBias","OptionalDistrListOrCall","OptionalNumericOrMatrix", + "OptionalNumericOrMatrixOrCall","ParamFamily","ParamFamParameter", + "ParamWithScaleAndShapeFamParameter","ParamWithScaleFamParameter", + "ParamWithShapeFamParameter","PoisFamily","ProbFamily","QFNorm", + "RiskType","SelfNorm","ShowDetails","symmetricBias","trAsCov","trFiCov") \ No newline at end of file Modified: branches/distr-2.5/pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- branches/distr-2.5/pkg/distrDoc/vignettes/distr.Rnw 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrDoc/vignettes/distr.Rnw 2013-09-06 19:35:14 UTC (rev 895) @@ -1,5 +1,5 @@ %\VignetteIndexEntry{distr - manual} -%\VignetteDepends{startupmsg,distr} +%\VignetteDepends{distr} %\VignetteKeyword{probability distribution,simulation,estimation} %\VignettePackage{distr} % Added: branches/distr-2.5/pkg/distrEllipse/.Rbuildignore =================================================================== --- branches/distr-2.5/pkg/distrEllipse/.Rbuildignore (rev 0) +++ branches/distr-2.5/pkg/distrEllipse/.Rbuildignore 2013-09-06 19:35:14 UTC (rev 895) @@ -0,0 +1,3 @@ +inst/doc/Rplots.pdf +^.*\.svn.+ +.*-Ex\.R \ No newline at end of file Modified: branches/distr-2.5/pkg/distrEllipse/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distrEllipse/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEllipse/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -3,7 +3,7 @@ Date: 2013-01-09 Title: S4 classes for elliptically contoured distributions Depends: R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-1), distr(>= 2.2), - distrEx(>= 2.2), distrSim(>= 2.2), startupmsg + 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 Modified: branches/distr-2.5/pkg/distrEllipse/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distrEllipse/NAMESPACE 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEllipse/NAMESPACE 2013-09-06 19:35:14 UTC (rev 895) @@ -1,6 +1,5 @@ import("methods") importFrom("setRNG", "setRNG") -import("startupmsg") import("mvtnorm") import("distr") import("distrEx") Added: branches/distr-2.5/pkg/distrEx/.Rbuildignore =================================================================== --- branches/distr-2.5/pkg/distrEx/.Rbuildignore (rev 0) +++ branches/distr-2.5/pkg/distrEx/.Rbuildignore 2013-09-06 19:35:14 UTC (rev 895) @@ -0,0 +1,3 @@ +inst/doc/Rplots.pdf +^.*\.svn.+ +.*-Ex\.R \ No newline at end of file Modified: branches/distr-2.5/pkg/distrEx/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distrEx/DESCRIPTION 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) @@ -3,7 +3,7 @@ Date: 2013-01-09 Title: Extensions of package distr Description: Extensions of package distr and some additional functionality -Depends: R(>= 2.6.0), methods, distr(>= 2.2), startupmsg +Depends: R(>= 2.6.0), methods, distr(>= 2.2) Suggests: tcltk Author: Matthias Kohl, Peter Ruckdeschel, Nataliya Horbenko Maintainer: Matthias Kohl Modified: branches/distr-2.5/pkg/distrEx/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distrEx/NAMESPACE 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/NAMESPACE 2013-09-06 19:35:14 UTC (rev 895) @@ -1,6 +1,5 @@ useDynLib("distrEx") -import("startupmsg") import("methods") import("distr") Modified: branches/distr-2.5/pkg/distrEx/R/AllClass.R =================================================================== --- branches/distr-2.5/pkg/distrEx/R/AllClass.R 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/R/AllClass.R 2013-09-06 19:35:14 UTC (rev 895) @@ -1,8 +1,25 @@ -.isEqual01 <- distr:::.isEqual01 ## for faster access due to local caching in package namespace +.isEqual <- function(p0, p1, tol = min( getdistrOption("TruncQuantile")/2, + .Machine$double.eps^.7 + )) + abs(p0-p1)< tol +.isEqual01 <- function(x) .isEqual(x,0)|.isEqual(x,1) +.inArgs <- function(arg, fct) + {as.character(arg) %in% names(formals(fct))} + + .onLoad <- function(lib, pkg){ # require("methods", character = TRUE, quietly = TRUE) } +.ULC.cast <- function(x){ + if( is(x,"AbscontDistribution")) + x <- as(as(x,"AbscontDistribution"), "UnivarLebDecDistribution") + if(is(x,"DiscreteDistribution")) + x <- as(as(x,"DiscreteDistribution"), "UnivarLebDecDistribution") + if(!is(x,"UnivarLebDecDistribution")) + x <- as(x,"UnivarLebDecDistribution") + return(x) +} .onAttach <- function(library, pkg) Modified: branches/distr-2.5/pkg/distrEx/R/ClippedMoments.R =================================================================== --- branches/distr-2.5/pkg/distrEx/R/ClippedMoments.R 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/R/ClippedMoments.R 2013-09-06 19:35:14 UTC (rev 895) @@ -1,8 +1,6 @@ ############################################################################### ## Clipped first and second moments ############################################################################### -.inArgs <- distr:::.inArgs - setMethod("m1df", "UnivariateDistribution", function(object, upper, ... ){ mc <- match.call() Modified: branches/distr-2.5/pkg/distrEx/R/ConvexContamination.R =================================================================== --- branches/distr-2.5/pkg/distrEx/R/ConvexContamination.R 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/R/ConvexContamination.R 2013-09-06 19:35:14 UTC (rev 895) @@ -73,7 +73,7 @@ Symmetry <- NoSymmetry() if(is(e1 at Symmetry,"SphericalSymmetry")&& is(e2 at Symmetry,"SphericalSymmetry")) - if(distr:::.isEqual(SymmCenter(e1 at Symmetry),SymmCenter(e2 at Symmetry))) + if(.isEqual(SymmCenter(e1 at Symmetry),SymmCenter(e2 at Symmetry))) Symmetry <- SphericalSymmetry(SymmCenter(e1 at Symmetry)) return(new("AbscontDistribution", r = rfun, d = dfun, p = pfun, @@ -157,7 +157,7 @@ Symmetry <- NoSymmetry() if(is(e1 at Symmetry,"SphericalSymmetry")&& is(e2 at Symmetry,"SphericalSymmetry")) - if(distr:::.isEqual(SymmCenter(e1 at Symmetry),SymmCenter(e2 at Symmetry))) + if(.isEqual(SymmCenter(e1 at Symmetry),SymmCenter(e2 at Symmetry))) Symmetry <- SphericalSymmetry(SymmCenter(e1 at Symmetry)) return(new("DiscreteDistribution", r = rfun, d = dfun, p = pfun, q = qfun, @@ -230,7 +230,7 @@ Symmetry <- NoSymmetry() if(is(e1 at Symmetry,"SphericalSymmetry")&& is(e2 at Symmetry,"SphericalSymmetry")) - if(distr:::.isEqual(SymmCenter(e1 at Symmetry),SymmCenter(e2 at Symmetry))) + if(.isEqual(SymmCenter(e1 at Symmetry),SymmCenter(e2 at Symmetry))) Symmetry <- SphericalSymmetry(SymmCenter(e1 at Symmetry)) return(new("UnivariateDistribution", img = img(e1), r = rfun, d = NULL, Modified: branches/distr-2.5/pkg/distrEx/R/Expectation.R =================================================================== --- branches/distr-2.5/pkg/distrEx/R/Expectation.R 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/R/Expectation.R 2013-09-06 19:35:14 UTC (rev 895) @@ -844,7 +844,7 @@ lowerTruncQuantile = getdistrExOption("ElowerTruncQuantile"), upperTruncQuantile = getdistrExOption("EupperTruncQuantile"), IQR.fac = getdistrExOption("IQR.fac"), ... ){ - object <- distr:::.ULC.cast(object) + object <- .ULC.cast(object) I.ac <- E(acPart(object), fun = fun, cond = cond, low = low, upp = upp, rel.tol = rel.tol, lowerTruncQuantile = lowerTruncQuantile, Modified: branches/distr-2.5/pkg/distrEx/R/Functionals.R =================================================================== --- branches/distr-2.5/pkg/distrEx/R/Functionals.R 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/R/Functionals.R 2013-09-06 19:35:14 UTC (rev 895) @@ -20,7 +20,7 @@ } LowIsUpp <- if(low == -Inf) - low == -upp else distr:::.isEqual(ztr-low,upp-ztr) + low == -upp else .isEqual(ztr-low,upp-ztr) if(LowIsUpp && missing(cond)&&missing(fun)){ if(is(Symmetry(x),"SphericalSymmetry")) Modified: branches/distr-2.5/pkg/distrEx/R/Kurtosis.R =================================================================== --- branches/distr-2.5/pkg/distrEx/R/Kurtosis.R 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/R/Kurtosis.R 2013-09-06 19:35:14 UTC (rev 895) @@ -14,7 +14,7 @@ if(hasArg(low)) low <- dots$low if(hasArg(upp)) upp <- dots$upp LowIsUpp <- if(low == -Inf) - low == -upp else distr:::.isEqual(low,upp) + low == -upp else .isEqual(low,upp) if(LowIsUpp && missing(cond)&&missing(fun)){ if(is(Symmetry(x),"SphericalSymmetry")){ Modified: branches/distr-2.5/pkg/distrEx/man/E.Rd =================================================================== --- branches/distr-2.5/pkg/distrEx/man/E.Rd 2013-04-22 16:21:50 UTC (rev 894) +++ branches/distr-2.5/pkg/distrEx/man/E.Rd 2013-09-06 19:35:14 UTC (rev 895) @@ -73,7 +73,8 @@ low = NULL, upp = NULL, Nsim = getdistrExOption("MCIterations"), ...) \S4method{E}{UnivariateDistribution,function,missing}(object, fun, [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 895 From noreply at r-forge.r-project.org Fri Sep 6 21:51:19 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 6 Sep 2013 21:51:19 +0200 (CEST) Subject: [Distr-commits] r896 - in pkg/distrDoc: . R inst man vignettes Message-ID: <20130906195119.56D46185A7C@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-06 21:51:19 +0200 (Fri, 06 Sep 2013) New Revision: 896 Modified: pkg/distrDoc/DESCRIPTION pkg/distrDoc/NAMESPACE pkg/distrDoc/R/distrDoc.R pkg/distrDoc/inst/NEWS pkg/distrDoc/man/0distrDoc-package.Rd pkg/distrDoc/vignettes/distr.Rnw Log: built new version distrDoc_2.4.1.tar.gz in trunk Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2013-09-06 19:35:14 UTC (rev 895) +++ pkg/distrDoc/DESCRIPTION 2013-09-06 19:51:19 UTC (rev 896) @@ -1,15 +1,12 @@ Package: distrDoc Version: 2.4.1 -Date: 2013-02-08 -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 +Date: 2013-09-06 +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 Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Maintainer: Peter Ruckdeschel -Depends: R(>= 2.14.0), tools, startupmsg, 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 +Depends: R(>= 2.6.0), tools, 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 Suggests: Biobase, SweaveListingUtils ByteCompile: yes Encoding: latin1 @@ -17,4 +14,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 879 +SVNRevision: 896 Modified: pkg/distrDoc/NAMESPACE =================================================================== --- pkg/distrDoc/NAMESPACE 2013-09-06 19:35:14 UTC (rev 895) +++ pkg/distrDoc/NAMESPACE 2013-09-06 19:51:19 UTC (rev 896) @@ -1,10 +1,85 @@ import("methods") -import("startupmsg") import("MASS") import("distr") import("distrEx") -import("distrSim") import("RandVar") -import("distrMod") -import("distrTeach") -import("distrTEst") + +importFrom("stats4","profile") +exportClasses("MatrixorFunction", "OptionalNumericOrMatrixOrCall", + "OptionalDistrListOrCall", "OptionalNumericOrMatrix", + "ShowDetails", + "FunctionSymmetry", "NonSymmetric", "EvenSymmetric", "OddSymmetric", + "FunSymmList", + "ParamFamParameter", + "ProbFamily", "ParamFamily", "L2ParamFamily") +exportClasses("RiskType", + "asRisk", "asCov", "trAsCov", "asHampel", "asBias", "asGRisk", + "asMSE", "asUnOvShoot", + "fiRisk", "fiCov", "trFiCov", "fiHampel", "fiMSE", "fiBias", + "fiUnOvShoot") +exportClasses("BiasType", "onesidedBias", "asymmetricBias", "symmetricBias") +exportClasses("asSemivar", "asRiskwithBias") +exportClasses("L2GroupParamFamily", "L2LocationFamily", + "L2ScaleFamily", "L2LocationScaleFamily") +exportClasses("L2LocationScaleUnion") +exportClasses("L2ScaleShapeUnion", "L2ScaleUnion") +exportClasses("ParamWithScaleFamParameter", "ParamWithShapeFamParameter", + "ParamWithScaleAndShapeFamParameter") +exportClasses("BinomFamily","PoisFamily", "NormLocationFamily", + "NormScaleFamily", "ExpScaleFamily", + "LnormScaleFamily", "GammaFamily", "BetaFamily", "NormLocationScaleFamily", + "CauchyLocationScaleFamily") +exportClasses("NormType", "QFNorm", "InfoNorm", "SelfNorm") +exportClasses("Estimate", "MCEstimate") +exportClasses("Confint") +exportMethods("distrSymm") +exportMethods("distribution", "props", "props<-", "addProp<-", "main", "main<-", + "nuisance", "nuisance<-", "trafo", "trafo<-", "trafo.fct", + "fixed", "fixed<-", "modifyParam", + "dimension", "show", "print", "plot", "param", "E", "name", + "L2deriv", "L2derivSymm", "L2derivDistr", "L2derivDistrSymm", + "FisherInfo", "checkL2deriv", "fam.call") +exportMethods("completecases") +exportMethods("bound", "width") +exportMethods("nu", "name", "sign", "nu<-", "name<-", "sign<-", "biastype", "biastype<-") +exportMethods("existsPIC") +exportMethods("modifyModel") +exportMethods("norm", "QuadForm<-", "QuadForm", "fct", + "fct<-", "normtype", "normtype<-") +exportMethods("r", "d", "p", "q", + "estimate", "estimate.call", "samplesize.estimate", "call.estimate", + "name.estimate", "trafo.estimate", "nuisance.estimate", + "fixed.estimate", "Infos", "Infos<-", "addInfo<-", + "criterion", "criterion<-", "criterion.fct", "method", + "samplesize", "asvar", "asvar<-", "optimwarn", + "withPosRestr", "withPosRestr<-") +exportMethods("untransformed.estimate", "untransformed.asvar") +exportMethods("confint") +exportMethods("validParameter") +exportMethods("startPar", "makeOKPar") +exportMethods("scaleshapename", "scalename", "LogDeriv") +exportMethods("coerce", "profile", "locscalename", "scaleshapename<-") +exportMethods("mleCalc", "mceCalc") +exportMethods("qqplot") +export("distrModMASK") +export("trafoEst") +export("distrModOptions", "distrModoptions", "getdistrModOption", + "Estimator", "MCEstimator", "MLEstimator", "MDEstimator") +export("NonSymmetric", "EvenSymmetric", "OddSymmetric", "FunSymmList") +export("ParamFamParameter", "ParamFamily", "L2ParamFamily", + "BinomFamily", "PoisFamily", "NbinomFamily", "NormLocationFamily", + "NormScaleFamily", "ExpScaleFamily", + "LnormScaleFamily", "GammaFamily", "BetaFamily", "NormLocationScaleFamily", + "CauchyLocationScaleFamily", "NbinomwithSizeFamily", "NbinomMeanSizeFamily") +export("asCov", "trAsCov", "asHampel", "asBias", "asMSE", "asUnOvShoot", + "fiCov", "trFiCov", "fiHampel", "fiMSE", "fiBias", "fiUnOvShoot") +export("positiveBias", "negativeBias", "symmetricBias", + "asymmetricBias", "asSemivar") +export("isKerAinKerB") +export("L2LocationFamily", "L2ScaleFamily", "L2LocationScaleFamily") +export("EuclideanNorm", "QuadFormNorm") +export("NormType", "QFNorm", "InfoNorm", "SelfNorm") +export("NormScaleUnknownLocationFamily", "NormLocationUnknownScaleFamily") +export("L2LocationUnknownScaleFamily", "L2ScaleUnknownLocationFamily") +export("meRes", "get.criterion.fct") +export("addAlphTrsp2col") Modified: pkg/distrDoc/R/distrDoc.R =================================================================== --- pkg/distrDoc/R/distrDoc.R 2013-09-06 19:35:14 UTC (rev 895) +++ pkg/distrDoc/R/distrDoc.R 2013-09-06 19:51:19 UTC (rev 896) @@ -1,5 +1,5 @@ .onLoad <- function(lib, pkg) { # extended 03-28-06: P.R. - # require("methods", character = TRUE, quietly = TRUE) +# require("methods", character = TRUE, quietly = TRUE) } .onAttach <- function(libname, pkgname) Modified: pkg/distrDoc/inst/NEWS =================================================================== --- pkg/distrDoc/inst/NEWS 2013-09-06 19:35:14 UTC (rev 895) +++ pkg/distrDoc/inst/NEWS 2013-09-06 19:51:19 UTC (rev 896) @@ -29,7 +29,6 @@ + shrinking inst/doc in order to prevent B. Ripley from archiving distrDoc + tried to get the imports in NAMESPACE files in the right order + For some strange reason, examle CIex in vignette threw an error; have changed seed; now it works again. -+ deleted no longer needed chm folders BUGFIXES: Modified: pkg/distrDoc/man/0distrDoc-package.Rd =================================================================== --- pkg/distrDoc/man/0distrDoc-package.Rd 2013-09-06 19:35:14 UTC (rev 895) +++ pkg/distrDoc/man/0distrDoc-package.Rd 2013-09-06 19:51:19 UTC (rev 896) @@ -14,14 +14,14 @@ \details{ \tabular{ll}{ Package: \tab distrDoc \cr -Version: \tab 2.4.1 \cr -Date: \tab 2013-02-08 \cr +Version: \tab 2.4 \cr +Date: \tab 2013-01-09 \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 License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 879 \cr +SVNRevision: \tab 834 \cr }} Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2013-09-06 19:35:14 UTC (rev 895) +++ pkg/distrDoc/vignettes/distr.Rnw 2013-09-06 19:51:19 UTC (rev 896) @@ -1,5 +1,5 @@ %\VignetteIndexEntry{distr - manual} -%\VignetteDepends{startupmsg,distr} +%\VignetteDepends{distr} %\VignetteKeyword{probability distribution,simulation,estimation} %\VignettePackage{distr} % @@ -9,8 +9,8 @@ % Version control information: \svnidlong {$HeadURL: svn+ssh://ruckdeschel at svn.r-forge.r-project.org/svnroot/distr/branches/distr-2.4/pkg/distrDoc/vignettes/distr.Rnw $} -{$LastChangedDate: 2012-05-22 14:40:14 +0200 (Di, 22 Mai 2012) $} -{$LastChangedRevision: 816 $} +{$LastChangedDate: 2013-09-06 21:35:14 +0200 (Fr, 06 Sep 2013) $} +{$LastChangedRevision: 895 $} {$LastChangedBy: ruckdeschel $} %\svnid{$Id: example_main.tex 146 2008-12-03 13:29:19Z martin $} % Don't forget to set the svn property 'svn:keywords' to @@ -170,9 +170,6 @@ \pkg{distrTeach} to embody illustrations for basic stats courses using our distribution classes. -From version 2.4 on, we have moved support for extreme value distributions, -as well as for certain scale-shape distributions to the new package -\pkg{RobExtremes}. This concerns the Gumbel, Weibull, Pareto distributions. %\noindent The latter two of them require package \pkg{setRNG} by %\href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert} %to be installed from \href{http://cran.r-project.org/mirrors.html}{\tt CRAN}. @@ -267,8 +264,7 @@ distributions as multivariate distributions, times series distributions, conditional distributions. As an exercise, the reader is encouraged to implement extrem value distributions from the package \pkg{evd}\footnote{a solution to -this ``homework'' may be found in the sources to \pkg{distrEx}, -resp.\ from version 2.4 on, in the sources to \pkg{RobExtremes}}. The largest +this ``homework'' may be found in the sources to \pkg{distrEx}}. The largest effort will in fact be the documentation\ldots\\ We also wanted to preserve naming and notation from {\sf R}-\pkg{stats} as far as possible so that any programmer used to {\tt S} could quickly @@ -571,9 +567,9 @@ \subsubsection{Classes for multivariate distributions and for conditional distributions} -In \pkg{distrEx}, %besides providing particular distribution classes -%for the Gumbel distribution (see \code{?Gumbel}) and the Pareto -%distribution (see \code{?Pareto}), -> moved to RobExtremes +In \pkg{distrEx}, besides providing particular distribution classes +for the Gumbel distribution (see \code{?Gumbel}) and the Pareto +distribution (see \code{?Pareto}), we provide the following classes for handling multivariate distributions: @@ -1733,10 +1729,8 @@ \paragraph{exact evaluation} is available for \code{X} of class \code{Arcsine}, \code{Beta} (for noncentrality $0$), \code{Binom}, \code{Cauchy}, \code{Chisq}, \code{Dirac}, \code{Exp}, \code{Fd}, -\code{Gammad}, \code{Geom}, %\code{Gumbel}, -> moved to RobExtremes -\code{Hyper}, \code{Logis}, \code{Lnorm}, -\code{Nbinom}, \code{Norm}, %\code{Pareto}, -> moved to RobExtremes -\code{Pois}, \code{Td}, \code{Unif}. % \code{Weibull} -> moved to RobExtremes +\code{Gammad}, \code{Geom}, \code{Gumbel}, \code{Hyper}, \code{Logis}, \code{Lnorm}, +\code{Nbinom}, \code{Norm}, \code{Pareto}, \code{Pois}, \code{Td}, \code{Unif}, \code{Weibull}. \paragraph{examples} $ \mbox{ }$\newline %<>= %SweaveListingOptions("inSweave"=TRUE) @@ -1848,11 +1842,8 @@ function and no condition argument is given: this is available for \code{X} of class \code{Arcsine}, \code{Beta} (for noncentrality $0$), \code{Binom}, \code{Cauchy}, \code{Chisq}, \code{Dirac}, \code{Exp}, \code{Fd}, -\code{Gammad}, \code{Geom}, %\code{Gumbel}, -> moved to RobExtremes -\code{Hyper}, \code{Logis}, \code{Lnorm}, -\code{Nbinom}, \code{Norm}, % \code{Pareto}, -> moved to RobExtremes -\code{Pois}, \code{Unif}, \code{Td}. -%, \code{Weibull}. -> moved to RobExtremes +\code{Gammad}, \code{Geom}, \code{Gumbel}, \code{Hyper}, \code{Logis}, \code{Lnorm}, +\code{Nbinom}, \code{Norm}, \code{Pareto}, \code{Pois}, \code{Unif}, \code{Td}, \code{Weibull}. \subsubsection{Further functionals} By the same techniques we provide the following functionals for univariate distributions: @@ -2739,14 +2730,13 @@ \subsection{Dependencies} In package \pkg{distr}, from version 2.0, we make use of \code{D1ss} from \href{mailto:maechler at stat.math.ethz.ch}{Martin M\"achler's} package \pkg{sfsmisc}. -In package \pkg{distrEx}, up to version 2.4, we needed +In package \pkg{distrEx}, we need \href{mailto:alec_stephenson at hotmail.com}{Alec Stephenson's} package \pkg{evd} for the extreme value distributions implemented therein, as well as \href{mailto:Vincent.Goulet at act.ulaval.ca}{Vincent Goulet}'s and Mathieu Pigeon's package \pkg{actuar} for the (single parameter) Pareto distribution (from \pkg{distrEx} version 2.1 on) which has been ported to our framework by -\href{mailto:nhorbenko at kpmg.de}{Nataliya Horbenko}. -From version 2.4 on, this infrastructure has moved to package \pkg{RobExtremes}. +\href{mailto:Nataliya.Horbenko at itwm.fraunhofer.de}{Nataliya Horbenko}. In package \pkg{distrSim}, and conseqently also in package \pkg{distrTEst} we use \href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert's} From noreply at r-forge.r-project.org Fri Sep 6 22:55:06 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 6 Sep 2013 22:55:06 +0200 (CEST) Subject: [Distr-commits] r897 - pkg/distrDoc Message-ID: <20130906205507.1637B185E3B@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-06 22:55:06 +0200 (Fri, 06 Sep 2013) New Revision: 897 Modified: pkg/distrDoc/.Rbuildignore pkg/distrDoc/DESCRIPTION pkg/distrDoc/NAMESPACE Log: distrDoc issue fixed Modified: pkg/distrDoc/.Rbuildignore =================================================================== --- pkg/distrDoc/.Rbuildignore 2013-09-06 19:51:19 UTC (rev 896) +++ pkg/distrDoc/.Rbuildignore 2013-09-06 20:55:06 UTC (rev 897) @@ -1,3 +1,4 @@ ^.*\.svn.+ inst/doc/Rplots.pdf inst/doc/Rplots.ps +.*-Ex\.R \ No newline at end of file Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2013-09-06 19:51:19 UTC (rev 896) +++ pkg/distrDoc/DESCRIPTION 2013-09-06 20:55:06 UTC (rev 897) @@ -14,4 +14,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 896 +SVNRevision: 897 Modified: pkg/distrDoc/NAMESPACE =================================================================== --- pkg/distrDoc/NAMESPACE 2013-09-06 19:51:19 UTC (rev 896) +++ pkg/distrDoc/NAMESPACE 2013-09-06 20:55:06 UTC (rev 897) @@ -2,84 +2,61 @@ import("MASS") import("distr") import("distrEx") +import("distrSim") +import("distrTEst") +import("distrTeach") import("RandVar") - -importFrom("stats4","profile") -exportClasses("MatrixorFunction", "OptionalNumericOrMatrixOrCall", - "OptionalDistrListOrCall", "OptionalNumericOrMatrix", - "ShowDetails", - "FunctionSymmetry", "NonSymmetric", "EvenSymmetric", "OddSymmetric", - "FunSymmList", - "ParamFamParameter", - "ProbFamily", "ParamFamily", "L2ParamFamily") -exportClasses("RiskType", - "asRisk", "asCov", "trAsCov", "asHampel", "asBias", "asGRisk", - "asMSE", "asUnOvShoot", - "fiRisk", "fiCov", "trFiCov", "fiHampel", "fiMSE", "fiBias", - "fiUnOvShoot") -exportClasses("BiasType", "onesidedBias", "asymmetricBias", "symmetricBias") -exportClasses("asSemivar", "asRiskwithBias") -exportClasses("L2GroupParamFamily", "L2LocationFamily", - "L2ScaleFamily", "L2LocationScaleFamily") -exportClasses("L2LocationScaleUnion") -exportClasses("L2ScaleShapeUnion", "L2ScaleUnion") -exportClasses("ParamWithScaleFamParameter", "ParamWithShapeFamParameter", - "ParamWithScaleAndShapeFamParameter") -exportClasses("BinomFamily","PoisFamily", "NormLocationFamily", - "NormScaleFamily", "ExpScaleFamily", - "LnormScaleFamily", "GammaFamily", "BetaFamily", "NormLocationScaleFamily", - "CauchyLocationScaleFamily") -exportClasses("NormType", "QFNorm", "InfoNorm", "SelfNorm") -exportClasses("Estimate", "MCEstimate") -exportClasses("Confint") -exportMethods("distrSymm") -exportMethods("distribution", "props", "props<-", "addProp<-", "main", "main<-", - "nuisance", "nuisance<-", "trafo", "trafo<-", "trafo.fct", - "fixed", "fixed<-", "modifyParam", - "dimension", "show", "print", "plot", "param", "E", "name", - "L2deriv", "L2derivSymm", "L2derivDistr", "L2derivDistrSymm", - "FisherInfo", "checkL2deriv", "fam.call") -exportMethods("completecases") -exportMethods("bound", "width") -exportMethods("nu", "name", "sign", "nu<-", "name<-", "sign<-", "biastype", "biastype<-") -exportMethods("existsPIC") -exportMethods("modifyModel") -exportMethods("norm", "QuadForm<-", "QuadForm", "fct", - "fct<-", "normtype", "normtype<-") -exportMethods("r", "d", "p", "q", - "estimate", "estimate.call", "samplesize.estimate", "call.estimate", - "name.estimate", "trafo.estimate", "nuisance.estimate", - "fixed.estimate", "Infos", "Infos<-", "addInfo<-", - "criterion", "criterion<-", "criterion.fct", "method", - "samplesize", "asvar", "asvar<-", "optimwarn", - "withPosRestr", "withPosRestr<-") -exportMethods("untransformed.estimate", "untransformed.asvar") -exportMethods("confint") -exportMethods("validParameter") -exportMethods("startPar", "makeOKPar") -exportMethods("scaleshapename", "scalename", "LogDeriv") -exportMethods("coerce", "profile", "locscalename", "scaleshapename<-") -exportMethods("mleCalc", "mceCalc") -exportMethods("qqplot") -export("distrModMASK") -export("trafoEst") -export("distrModOptions", "distrModoptions", "getdistrModOption", - "Estimator", "MCEstimator", "MLEstimator", "MDEstimator") -export("NonSymmetric", "EvenSymmetric", "OddSymmetric", "FunSymmList") -export("ParamFamParameter", "ParamFamily", "L2ParamFamily", - "BinomFamily", "PoisFamily", "NbinomFamily", "NormLocationFamily", - "NormScaleFamily", "ExpScaleFamily", - "LnormScaleFamily", "GammaFamily", "BetaFamily", "NormLocationScaleFamily", - "CauchyLocationScaleFamily", "NbinomwithSizeFamily", "NbinomMeanSizeFamily") -export("asCov", "trAsCov", "asHampel", "asBias", "asMSE", "asUnOvShoot", - "fiCov", "trFiCov", "fiHampel", "fiMSE", "fiBias", "fiUnOvShoot") -export("positiveBias", "negativeBias", "symmetricBias", - "asymmetricBias", "asSemivar") -export("isKerAinKerB") -export("L2LocationFamily", "L2ScaleFamily", "L2LocationScaleFamily") -export("EuclideanNorm", "QuadFormNorm") -export("NormType", "QFNorm", "InfoNorm", "SelfNorm") -export("NormScaleUnknownLocationFamily", "NormLocationUnknownScaleFamily") -export("L2LocationUnknownScaleFamily", "L2ScaleUnknownLocationFamily") -export("meRes", "get.criterion.fct") -export("addAlphTrsp2col") +importMethodsFrom("distrMod", "addInfo<-","addProp<-","asvar","asvar<-", + "biastype","biastype<-","bound","call.estimate", + "checkL2deriv","coerce","completecases","confint", + "criterion","criterion.fct","criterion<-","d", + "dimension","distrSymm","E","estimate","estimate.call", + "existsPIC","fam.call","fct","fct<-","FisherInfo", + "fixed","fixed.estimate","fixed<-","Infos","Infos<-", + "L2deriv","L2derivDistr","L2derivDistrSymm","L2derivSymm", + "locscalename","LogDeriv", + "main","main<-","makeOKPar","mceCalc","method","mleCalc", + "modifyModel","modifyParam","name","name.estimate","name<-","norm", + "normtype","normtype<-","nu","nu<-","nuisance", + "nuisance.estimate","nuisance<-","optimwarn","p","param", + "plot","print","profile","props", + "props<-","q","qqplot","QuadForm","QuadForm<-","r", + "samplesize.estimate","scalename","scaleshapename", + "scaleshapename<-","show","sign", + "sign<-","startPar","trafo","trafo.estimate", + "trafo.fct","trafo<-","untransformed.asvar", + "untransformed.estimate","validParameter","width", + "withPosRestr","withPosRestr<-") +importFrom("distrMod","addAlphTrsp2col","asBias","asCov","asHampel","asMSE", + "asSemivar","asUnOvShoot","asymmetricBias","BetaFamily","BinomFamily", + "CauchyLocationScaleFamily","distrModMASK", + "distrModoptions","distrModOptions","Estimator","EuclideanNorm", + "EvenSymmetric","ExpScaleFamily","fiBias","fiCov","fiHampel","fiMSE", + "fiUnOvShoot","FunSymmList","GammaFamily","get.criterion.fct", + "getdistrModOption","InfoNorm","isKerAinKerB","L2LocationFamily", + "L2LocationScaleFamily","L2LocationUnknownScaleFamily", + "L2ParamFamily","L2ScaleFamily","L2ScaleUnknownLocationFamily", + "LnormScaleFamily","MCEstimator","MDEstimator","meRes", + "MLEstimator","NbinomFamily","NbinomMeanSizeFamily", + "NbinomwithSizeFamily","negativeBias","NonSymmetric", + "NormLocationFamily","NormLocationScaleFamily", + "NormLocationUnknownScaleFamily","NormScaleFamily", + "NormScaleUnknownLocationFamily","NormType","OddSymmetric", + "ParamFamily","ParamFamParameter","PoisFamily", + "positiveBias","QFNorm", + "QuadFormNorm","SelfNorm","symmetricBias","trafoEst") +importClassesFrom("distrMod","asBias","asCov","asGRisk","asHampel","asMSE", + "asRisk","asRiskwithBias","asSemivar","asUnOvShoot","asymmetricBias", + "BetaFamily","BiasType","BinomFamily","CauchyLocationScaleFamily", + "Confint","Estimate","EvenSymmetric","ExpScaleFamily","fiBias","fiCov", + "fiHampel","fiMSE","fiRisk","fiUnOvShoot","FunctionSymmetry","FunSymmList", + "GammaFamily","InfoNorm","L2GroupParamFamily","L2LocationFamily", + "L2LocationScaleFamily","L2LocationScaleUnion","L2ParamFamily", + "L2ScaleFamily","L2ScaleShapeUnion","L2ScaleUnion","LnormScaleFamily", + "MatrixorFunction","MCEstimate","NonSymmetric","NormLocationFamily", + "NormLocationScaleFamily","NormScaleFamily","NormType","OddSymmetric", + "onesidedBias","OptionalDistrListOrCall","OptionalNumericOrMatrix", + "OptionalNumericOrMatrixOrCall","ParamFamily","ParamFamParameter", + "ParamWithScaleAndShapeFamParameter","ParamWithScaleFamParameter", + "ParamWithShapeFamParameter","PoisFamily","ProbFamily","QFNorm", + "RiskType","SelfNorm","ShowDetails","symmetricBias","trAsCov","trFiCov") \ No newline at end of file From noreply at r-forge.r-project.org Sat Sep 7 01:02:11 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 7 Sep 2013 01:02:11 +0200 (CEST) Subject: [Distr-commits] r898 - in branches/distr-2.5/pkg: distr distrEx/R distrMod distrMod/R Message-ID: <20130906230211.48430185912@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-07 01:02:10 +0200 (Sat, 07 Sep 2013) New Revision: 898 Modified: branches/distr-2.5/pkg/distr/NAMESPACE branches/distr-2.5/pkg/distrEx/R/AllClass.R branches/distr-2.5/pkg/distrMod/NAMESPACE branches/distr-2.5/pkg/distrMod/R/0distrModUtils.R Log: exported some utilities from distr and distrMod Modified: branches/distr-2.5/pkg/distr/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-06 20:55:06 UTC (rev 897) +++ branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-06 23:02:10 UTC (rev 898) @@ -3,6 +3,7 @@ importFrom("graphics", "plot") importFrom("sfsmisc", "D1ss") import("startupmsg") +import("SweaveListingUtils") export("Beta", "Binom", "Cauchy", "Chisq", "Dirac","Exp", "DExp", "Fd", "Gammad", @@ -93,3 +94,5 @@ "DistrSymmList") export("qqbounds","igamma") exportMethods("qqplot") +export(".isEqual",".isEqual01", ".inArgs", ".fillList", + ".presubs", ".makeLenAndOrder", ".DistrCollapse") \ No newline at end of file Modified: branches/distr-2.5/pkg/distrEx/R/AllClass.R =================================================================== --- branches/distr-2.5/pkg/distrEx/R/AllClass.R 2013-09-06 20:55:06 UTC (rev 897) +++ branches/distr-2.5/pkg/distrEx/R/AllClass.R 2013-09-06 23:02:10 UTC (rev 898) @@ -1,13 +1,3 @@ -.isEqual <- function(p0, p1, tol = min( getdistrOption("TruncQuantile")/2, - .Machine$double.eps^.7 - )) - abs(p0-p1)< tol -.isEqual01 <- function(x) .isEqual(x,0)|.isEqual(x,1) -.inArgs <- function(arg, fct) - {as.character(arg) %in% names(formals(fct))} - - - .onLoad <- function(lib, pkg){ # require("methods", character = TRUE, quietly = TRUE) } Modified: branches/distr-2.5/pkg/distrMod/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distrMod/NAMESPACE 2013-09-06 20:55:06 UTC (rev 897) +++ branches/distr-2.5/pkg/distrMod/NAMESPACE 2013-09-06 23:02:10 UTC (rev 898) @@ -83,3 +83,4 @@ export("L2LocationUnknownScaleFamily", "L2ScaleUnknownLocationFamily") export("meRes", "get.criterion.fct") export("addAlphTrsp2col") +export(".deleteDim",".isUnitMatrix") \ No newline at end of file Modified: branches/distr-2.5/pkg/distrMod/R/0distrModUtils.R =================================================================== --- branches/distr-2.5/pkg/distrMod/R/0distrModUtils.R 2013-09-06 20:55:06 UTC (rev 897) +++ branches/distr-2.5/pkg/distrMod/R/0distrModUtils.R 2013-09-06 23:02:10 UTC (rev 898) @@ -1,3 +1,9 @@ +.isUnitMatrix <- function(m){ +### checks whether m is unit matrix + m.row <- nrow(m) + isTRUE(all.equal(m, diag(m.row), check.attributes = FALSE)) + } + .deleteDim <- function(x){ attribs <- attributes(x) attribs$dim <- NULL @@ -64,12 +70,6 @@ ### end of borrowed code -.isUnitMatrix <- function(m){ -### checks whether m is unit matrix - m.row <- nrow(m) - isTRUE(all.equal(m, diag(m.row), check.attributes = FALSE)) - } - .validTrafo <- function(trafo, dimension, dimensionwithN){ ##checks whether trafo is valid ret <- FALSE From noreply at r-forge.r-project.org Sat Sep 7 20:30:08 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 7 Sep 2013 20:30:08 +0200 (CEST) Subject: [Distr-commits] r899 - pkg/distrDoc Message-ID: <20130907183009.10B6C18532E@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-07 20:30:08 +0200 (Sat, 07 Sep 2013) New Revision: 899 Modified: pkg/distrDoc/DESCRIPTION pkg/distrDoc/NAMESPACE Log: distrDoc: CRAN version (With classes "OptionalDistrListOrCall", "OptionalNumericOrMatrixOrCall" not yet in the imports...) Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2013-09-06 23:02:10 UTC (rev 898) +++ pkg/distrDoc/DESCRIPTION 2013-09-07 18:30:08 UTC (rev 899) @@ -5,9 +5,10 @@ Description: provides documentation in form of a common vignette to packages distr, distrEx, distrMod, distrSim, distrTEst, distrTeach, and distrEllipse Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Maintainer: Peter Ruckdeschel -Depends: R(>= 2.6.0), tools, 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 -Suggests: Biobase, SweaveListingUtils +Depends: R(>= 2.6.0) +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, startupmsg, SweaveListingUtils +Suggests: Biobase ByteCompile: yes Encoding: latin1 License: LGPL-3 Modified: pkg/distrDoc/NAMESPACE =================================================================== --- pkg/distrDoc/NAMESPACE 2013-09-06 23:02:10 UTC (rev 898) +++ pkg/distrDoc/NAMESPACE 2013-09-07 18:30:08 UTC (rev 899) @@ -1,4 +1,6 @@ import("methods") +import("SweaveListingUtils") +importFrom("startupmsg","buildStartupMessage") import("MASS") import("distr") import("distrEx") @@ -55,8 +57,8 @@ "L2ScaleFamily","L2ScaleShapeUnion","L2ScaleUnion","LnormScaleFamily", "MatrixorFunction","MCEstimate","NonSymmetric","NormLocationFamily", "NormLocationScaleFamily","NormScaleFamily","NormType","OddSymmetric", - "onesidedBias","OptionalDistrListOrCall","OptionalNumericOrMatrix", - "OptionalNumericOrMatrixOrCall","ParamFamily","ParamFamParameter", + "onesidedBias","OptionalNumericOrMatrix", + "ParamFamily","ParamFamParameter", "ParamWithScaleAndShapeFamParameter","ParamWithScaleFamParameter", "ParamWithShapeFamParameter","PoisFamily","ProbFamily","QFNorm", "RiskType","SelfNorm","ShowDetails","symmetricBias","trAsCov","trFiCov") \ No newline at end of file From noreply at r-forge.r-project.org Sat Sep 7 20:30:57 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 7 Sep 2013 20:30:57 +0200 (CEST) Subject: [Distr-commits] r900 - branches/distr-2.5/pkg/distrDoc Message-ID: <20130907183057.598ED185E50@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-07 20:30:57 +0200 (Sat, 07 Sep 2013) New Revision: 900 Modified: branches/distr-2.5/pkg/distrDoc/DESCRIPTION branches/distr-2.5/pkg/distrDoc/NAMESPACE Log: distrDoc: and the respective update of the devel version Modified: branches/distr-2.5/pkg/distrDoc/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distrDoc/DESCRIPTION 2013-09-07 18:30:08 UTC (rev 899) +++ branches/distr-2.5/pkg/distrDoc/DESCRIPTION 2013-09-07 18:30:57 UTC (rev 900) @@ -7,10 +7,11 @@ distrMod, distrSim, distrTEst, distrTeach, and distrEllipse Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Maintainer: Peter Ruckdeschel -Depends: R(>= 2.14.0), tools, distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= +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 -Suggests: Biobase, SweaveListingUtils + MASS, methods, SweaveListingUtils, startupmsg +Suggests: Biobase ByteCompile: yes Encoding: latin1 License: LGPL-3 Modified: branches/distr-2.5/pkg/distrDoc/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distrDoc/NAMESPACE 2013-09-07 18:30:08 UTC (rev 899) +++ branches/distr-2.5/pkg/distrDoc/NAMESPACE 2013-09-07 18:30:57 UTC (rev 900) @@ -1,4 +1,6 @@ import("methods") +import("SweaveListingUtils") +importFrom("startupmsg","buildStartupMessage") import("MASS") import("distr") import("distrEx") From noreply at r-forge.r-project.org Tue Sep 10 12:12:54 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 10 Sep 2013 12:12:54 +0200 (CEST) Subject: [Distr-commits] r901 - in branches/distr-2.5/pkg: distr distr/R distr/man distrDoc distrMod/R distrSim distrSim/R Message-ID: <20130910101254.515A2180954@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-10 12:12:54 +0200 (Tue, 10 Sep 2013) New Revision: 901 Added: branches/distr-2.5/pkg/distr/man/internalGenerics.Rd Modified: branches/distr-2.5/pkg/distr/NAMESPACE branches/distr-2.5/pkg/distr/R/AllGenerics.R branches/distr-2.5/pkg/distr/man/operators-methods.Rd branches/distr-2.5/pkg/distr/man/qqplot.Rd branches/distr-2.5/pkg/distrDoc/NAMESPACE branches/distr-2.5/pkg/distrMod/R/AllGeneric.R branches/distr-2.5/pkg/distrSim/NAMESPACE branches/distr-2.5/pkg/distrSim/R/AllGenerics.R Log: [devel-branch] moved the generics of 'distribution' and 'samplesize' from pkgs distrSim and distrMod to pkg distr in order to avoid conflicts in import; in pkg distr inserted some \dontrun{.}'s in examples of qqplot and operators-methods Modified: branches/distr-2.5/pkg/distr/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-10 10:12:54 UTC (rev 901) @@ -95,4 +95,5 @@ export("qqbounds","igamma") exportMethods("qqplot") export(".isEqual",".isEqual01", ".inArgs", ".fillList", - ".presubs", ".makeLenAndOrder", ".DistrCollapse") \ No newline at end of file + ".presubs", ".makeLenAndOrder", ".DistrCollapse") +export("samplesize", "distribution") \ No newline at end of file Modified: branches/distr-2.5/pkg/distr/R/AllGenerics.R =================================================================== --- branches/distr-2.5/pkg/distr/R/AllGenerics.R 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distr/R/AllGenerics.R 2013-09-10 10:12:54 UTC (rev 901) @@ -443,4 +443,10 @@ } if(!isGeneric("Symmetry")){ setGeneric("Symmetry", function(object) standardGeneric("Symmetry")) -} \ No newline at end of file +} +if(!isGeneric("distribution")){ + setGeneric("distribution", function(object) standardGeneric("distribution")) +} +if(!isGeneric("samplesize")){ + setGeneric("samplesize", function(object, ...) standardGeneric("samplesize")) +} Added: branches/distr-2.5/pkg/distr/man/internalGenerics.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/internalGenerics.Rd (rev 0) +++ branches/distr-2.5/pkg/distr/man/internalGenerics.Rd 2013-09-10 10:12:54 UTC (rev 901) @@ -0,0 +1,23 @@ +\name{internalGenerics} +\alias{internalGenerics} +\alias{distribution} +\alias{samplesize} +\title{Internal: Common Generics 'distribution' and 'samplesize'} +\description{ + In order to be able to use packages \pkg{distrSim} and \pkg{distrMod} independently, + it is necessary to import the respective generic from a prior package, i.e., + \pkg{distr}. + } +\usage{ +distribution(object) +samplesize(object, ...) +} +\arguments{ + \item{object}{ the first argument to dispatch on in the actual methods. } + \item{\dots}{ additional arguments for function \code{samplesize}. } +} + +\author{ + Peter Ruckdeschel \email{Peter.Ruckdeschel at itwm.fraunhofer.de}} + +\keyword{internal} Modified: branches/distr-2.5/pkg/distr/man/operators-methods.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/operators-methods.Rd 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distr/man/operators-methods.Rd 2013-09-10 10:12:54 UTC (rev 901) @@ -328,7 +328,10 @@ N / a + sin( a * P - N) N * P N / N +\dontrun{ +## takes a little time N ^ P +} 1.2 ^ N abs(N) ^ 1.3 } Modified: branches/distr-2.5/pkg/distr/man/qqplot.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/qqplot.Rd 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distr/man/qqplot.Rd 2013-09-10 10:12:54 UTC (rev 901) @@ -133,6 +133,8 @@ mylist2 <- mylist+0.1 qqplot(mylist,mylist2) qqplot(mylist,mylist2,exact.pCI=FALSE,exact.sCI=FALSE) +\dontrun{ +## takes time qqplot(mylist,mylist2,nosym.pCI=TRUE) ## some ac. distribution with a gap mylist3 <- UnivarMixingDistribution(Unif(0,0.3),Unif(0.6,1),mixCoeff=c(0.8,0.2)) @@ -141,5 +143,6 @@ qqplot(mylist3,mylist4) qqplot(mylist3,mylist4,nosym.pCI=TRUE) } +} \keyword{hplot} \keyword{distribution} Modified: branches/distr-2.5/pkg/distrDoc/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distrDoc/NAMESPACE 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distrDoc/NAMESPACE 2013-09-10 10:12:54 UTC (rev 901) @@ -8,57 +8,4 @@ import("distrTEst") import("distrTeach") import("RandVar") -importMethodsFrom("distrMod", "addInfo<-","addProp<-","asvar","asvar<-", - "biastype","biastype<-","bound","call.estimate", - "checkL2deriv","coerce","completecases","confint", - "criterion","criterion.fct","criterion<-","d", - "dimension","distrSymm","E","estimate","estimate.call", - "existsPIC","fam.call","fct","fct<-","FisherInfo", - "fixed","fixed.estimate","fixed<-","Infos","Infos<-", - "L2deriv","L2derivDistr","L2derivDistrSymm","L2derivSymm", - "locscalename","LogDeriv", - "main","main<-","makeOKPar","mceCalc","method","mleCalc", - "modifyModel","modifyParam","name","name.estimate","name<-","norm", - "normtype","normtype<-","nu","nu<-","nuisance", - "nuisance.estimate","nuisance<-","optimwarn","p","param", - "plot","print","profile","props", - "props<-","q","qqplot","QuadForm","QuadForm<-","r", - "samplesize.estimate","scalename","scaleshapename", - "scaleshapename<-","show","sign", - "sign<-","startPar","trafo","trafo.estimate", - "trafo.fct","trafo<-","untransformed.asvar", - "untransformed.estimate","validParameter","width", - "withPosRestr","withPosRestr<-") -importFrom("distrMod","addAlphTrsp2col","asBias","asCov","asHampel","asMSE", - "asSemivar","asUnOvShoot","asymmetricBias","BetaFamily","BinomFamily", - "CauchyLocationScaleFamily","distrModMASK", - "distrModoptions","distrModOptions","Estimator","EuclideanNorm", - "EvenSymmetric","ExpScaleFamily","fiBias","fiCov","fiHampel","fiMSE", - "fiUnOvShoot","FunSymmList","GammaFamily","get.criterion.fct", - "getdistrModOption","InfoNorm","isKerAinKerB","L2LocationFamily", - "L2LocationScaleFamily","L2LocationUnknownScaleFamily", - "L2ParamFamily","L2ScaleFamily","L2ScaleUnknownLocationFamily", - "LnormScaleFamily","MCEstimator","MDEstimator","meRes", - "MLEstimator","NbinomFamily","NbinomMeanSizeFamily", - "NbinomwithSizeFamily","negativeBias","NonSymmetric", - "NormLocationFamily","NormLocationScaleFamily", - "NormLocationUnknownScaleFamily","NormScaleFamily", - "NormScaleUnknownLocationFamily","NormType","OddSymmetric", - "ParamFamily","ParamFamParameter","PoisFamily", - "positiveBias","QFNorm", - "QuadFormNorm","SelfNorm","symmetricBias","trafoEst") -importClassesFrom("distrMod","asBias","asCov","asGRisk","asHampel","asMSE", - "asRisk","asRiskwithBias","asSemivar","asUnOvShoot","asymmetricBias", - "BetaFamily","BiasType","BinomFamily","CauchyLocationScaleFamily", - "Confint","Estimate","EvenSymmetric","ExpScaleFamily","fiBias","fiCov", - "fiHampel","fiMSE","fiRisk","fiUnOvShoot","FunctionSymmetry","FunSymmList", - "GammaFamily","InfoNorm","L2GroupParamFamily","L2LocationFamily", - "L2LocationScaleFamily","L2LocationScaleUnion","L2ParamFamily", - "L2ScaleFamily","L2ScaleShapeUnion","L2ScaleUnion","LnormScaleFamily", - "MatrixorFunction","MCEstimate","NonSymmetric","NormLocationFamily", - "NormLocationScaleFamily","NormScaleFamily","NormType","OddSymmetric", - "onesidedBias","OptionalDistrListOrCall","OptionalNumericOrMatrix", - "OptionalNumericOrMatrixOrCall","ParamFamily","ParamFamParameter", - "ParamWithScaleAndShapeFamParameter","ParamWithScaleFamParameter", - "ParamWithShapeFamParameter","PoisFamily","ProbFamily","QFNorm", - "RiskType","SelfNorm","ShowDetails","symmetricBias","trAsCov","trFiCov") \ No newline at end of file +import("distrMod") Modified: branches/distr-2.5/pkg/distrMod/R/AllGeneric.R =================================================================== --- branches/distr-2.5/pkg/distrMod/R/AllGeneric.R 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distrMod/R/AllGeneric.R 2013-09-10 10:12:54 UTC (rev 901) @@ -31,9 +31,6 @@ if(!isGeneric("distrSymm")){ setGeneric("distrSymm", function(object) standardGeneric("distrSymm")) } -if(!isGeneric("distribution")){ - setGeneric("distribution", function(object) standardGeneric("distribution")) -} if(!isGeneric("props")){ setGeneric("props", function(object) standardGeneric("props")) } @@ -202,9 +199,6 @@ if(!isGeneric("completecases")){ setGeneric("completecases", function(object) standardGeneric("completecases")) } -if(!isGeneric("samplesize")){ - setGeneric("samplesize", function(object, ...) standardGeneric("samplesize")) -} if(!isGeneric("asvar")){ setGeneric("asvar", function(object) standardGeneric("asvar")) } Modified: branches/distr-2.5/pkg/distrSim/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distrSim/NAMESPACE 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distrSim/NAMESPACE 2013-09-10 10:12:54 UTC (rev 901) @@ -1,5 +1,4 @@ import("methods") -import("startupmsg") importFrom("stats", "simulate") importFrom("setRNG", "setRNG") import("distr") Modified: branches/distr-2.5/pkg/distrSim/R/AllGenerics.R =================================================================== --- branches/distr-2.5/pkg/distrSim/R/AllGenerics.R 2013-09-07 18:30:57 UTC (rev 900) +++ branches/distr-2.5/pkg/distrSim/R/AllGenerics.R 2013-09-10 10:12:54 UTC (rev 901) @@ -12,9 +12,7 @@ setGeneric("Data", function(object) standardGeneric("Data")) if(!isGeneric("runs")) setGeneric("runs", function(object) standardGeneric("runs")) -if(!isGeneric("samplesize")) - setGeneric("samplesize", function(object) standardGeneric("samplesize")) -if(!isGeneric("obsDim")) +if(!isGeneric("obsDim")) setGeneric("obsDim", function(object) standardGeneric("obsDim")) ### new v.1.8 if(!isGeneric("name")) @@ -95,8 +93,6 @@ ## Access Methods if(!isGeneric("seed")) setGeneric("seed", function(object) standardGeneric("seed")) -if(!isGeneric("distribution")) - setGeneric("distribution", function(object) standardGeneric("distribution")) ## Replace Methoden if(!isGeneric("seed<-")) From noreply at r-forge.r-project.org Wed Sep 11 03:21:14 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Sep 2013 03:21:14 +0200 (CEST) Subject: [Distr-commits] r902 - pkg/setRNG Message-ID: <20130911012114.E5BB6185D82@r-forge.r-project.org> Author: pgilbert Date: 2013-09-11 03:21:10 +0200 (Wed, 11 Sep 2013) New Revision: 902 Modified: pkg/setRNG/.Rbuildignore pkg/setRNG/DESCRIPTION pkg/setRNG/NEWS Log: adjusted .Rbuildignore to exclude S/ directory. Modified: pkg/setRNG/.Rbuildignore =================================================================== --- pkg/setRNG/.Rbuildignore 2013-09-10 10:12:54 UTC (rev 901) +++ pkg/setRNG/.Rbuildignore 2013-09-11 01:21:10 UTC (rev 902) @@ -15,3 +15,4 @@ inst/doc/(^|.*)\.stdout$ .Rd2dvi(^|.*) (^|.*)\.ps$ +^S$ Modified: pkg/setRNG/DESCRIPTION =================================================================== --- pkg/setRNG/DESCRIPTION 2013-09-10 10:12:54 UTC (rev 901) +++ pkg/setRNG/DESCRIPTION 2013-09-11 01:21:10 UTC (rev 902) @@ -7,7 +7,7 @@ necessary information for reproducibility. See the vignette and reference manual for examples. Depends: R (>= 2.5.0) -Version: 2011.11-2 +Version: 2013.9-1 LazyLoad: yes License: GPL-2 | file LICENSE Author: Paul Gilbert Modified: pkg/setRNG/NEWS =================================================================== --- pkg/setRNG/NEWS 2013-09-10 10:12:54 UTC (rev 901) +++ pkg/setRNG/NEWS 2013-09-11 01:21:10 UTC (rev 902) @@ -1,3 +1,7 @@ +Changes in setRNG version 2013.9-1 + + o adjusted .Rbuildignore to exclude S/ directory. + Changes in setRNG version 2011.11-1 o updated maintainer email address. From noreply at r-forge.r-project.org Wed Sep 11 10:31:51 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Sep 2013 10:31:51 +0200 (CEST) Subject: [Distr-commits] r903 - in branches/distr-2.5/pkg: SweaveListingUtils/inst distr/inst distrDoc/inst distrEllipse/inst distrEx/inst distrMod/inst distrRmetrics/inst distrSim/inst distrTEst/inst distrTeach/inst startupmsg/inst Message-ID: <20130911083152.0D890184D0D@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-11 10:31:51 +0200 (Wed, 11 Sep 2013) New Revision: 903 Modified: branches/distr-2.5/pkg/SweaveListingUtils/inst/NEWS branches/distr-2.5/pkg/distr/inst/NEWS branches/distr-2.5/pkg/distrDoc/inst/NEWS branches/distr-2.5/pkg/distrEllipse/inst/NEWS branches/distr-2.5/pkg/distrEx/inst/NEWS branches/distr-2.5/pkg/distrMod/inst/NEWS branches/distr-2.5/pkg/distrMod/inst/TOBEDONE branches/distr-2.5/pkg/distrRmetrics/inst/NEWS branches/distr-2.5/pkg/distrSim/inst/NEWS branches/distr-2.5/pkg/distrTEst/inst/NEWS branches/distr-2.5/pkg/distrTeach/inst/NEWS branches/distr-2.5/pkg/startupmsg/inst/NEWS Log: updated NEWS entries and, for distrMod, the TOBEDONE entry Modified: branches/distr-2.5/pkg/SweaveListingUtils/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/SweaveListingUtils/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/SweaveListingUtils/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -9,8 +9,10 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends under the hood: ++ added .Rbuildignore BUGFIXES: Modified: branches/distr-2.5/pkg/distr/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distr/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distr/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -14,11 +14,17 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends under the hood: ++ added .Rbuildignore ++ exported some routines which had been internal so far to + avoid calls by ::: BUGFIXES: + fixed .makedotsPt -issue discovered by Gerald --> thx ++ moved generics to "distribution" and "samplesize" to pkg distr to avoid + conflict with pkg distrMod ############## Modified: branches/distr-2.5/pkg/distrDoc/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrDoc/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrDoc/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -14,8 +14,11 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: +cleaned DESCRIPTION file +except for R itself moved all Depends to Imports in DESCRIPTION file under the hood: +added .Rbuildignore BUGFIXES: Modified: branches/distr-2.5/pkg/distrEllipse/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrEllipse/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrEllipse/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -11,7 +11,21 @@ v 2.5 ############## +user-visible CHANGES: +GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends + +under the hood: + ++ added .Rbuildignore ++ used some recently exported routines which had been internal so far to + avoid calls by ::: + +BUGFIXES ++ fixed some links in html-man pages + + ############## v 2.4 ############## Modified: branches/distr-2.5/pkg/distrEx/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrEx/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrEx/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -14,8 +14,12 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends under the hood: ++ use some newly exmported routines which had been internal so far to + avoid calls by ::: ++ added .Rbuildignore BUGFIXES: Modified: branches/distr-2.5/pkg/distrMod/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrMod/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrMod/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -14,6 +14,7 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends under the hood: + For speeding up things, we now have an option withL2derivDistr = TRUE which @@ -46,9 +47,15 @@ cases we do neither want to produce a call nor an evaluated call to imageDistr... ++ added .Rbuildignore -BUGFIXES: ++ exported some routines which had been internal so far to + avoid calls by ::: + BUGFIXES: ++ moved generics to "distribution" and "samplesize" to pkg distr to avoid + conflict with pkg distrSim + ############## v 2.4 ############## Modified: branches/distr-2.5/pkg/distrMod/inst/TOBEDONE =================================================================== --- branches/distr-2.5/pkg/distrMod/inst/TOBEDONE 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrMod/inst/TOBEDONE 2013-09-11 08:31:51 UTC (rev 903) @@ -18,6 +18,8 @@ + model classes for multivariate location and scale based on distrEllipse -+ integration of GParetoFamily (not so soon) ++ generic functions to quantify model fit quality like AIC, BIC -+ generic functions to quantify model fit quality like AIC, BIC \ No newline at end of file ++ enhance class ParamFamParameter by some slot metric for the + parameter space -> to be used for clipping with non-standard norms + (compare d_beta norms GEV, GPareto) \ No newline at end of file Modified: branches/distr-2.5/pkg/distrRmetrics/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrRmetrics/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrRmetrics/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -6,7 +6,23 @@ package-individual development, but rather are chosen for the distrXXX family as a whole in order to ease updating "depends" information) + +############## +v 2.5 +############## +user-visible CHANGES: + +GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends + +under the hood: + ++ added .Rbuildignore + +BUGFIXES ++ fixed some links in html-man pages + ############## v 2.4 ############## Modified: branches/distr-2.5/pkg/distrSim/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrSim/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrSim/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -14,10 +14,14 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends under the hood: ++ added .Rbuildignore BUGFIXES: ++ moved generics to "distribution" and "samplesize" to pkg distr to avoid + conflict with pkg distrMod ############## v 2.4 Modified: branches/distr-2.5/pkg/distrTEst/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrTEst/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrTEst/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -9,8 +9,10 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends under the hood: +added .Rbuildignore BUGFIXES: Modified: branches/distr-2.5/pkg/distrTeach/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distrTeach/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/distrTeach/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -14,10 +14,13 @@ user-visible CHANGES: GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends under the hood: -BUGFIXES: ++ added .Rbuildignore + +BUGFIXES ############## v 2.4 Modified: branches/distr-2.5/pkg/startupmsg/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/startupmsg/inst/NEWS 2013-09-11 01:21:10 UTC (rev 902) +++ branches/distr-2.5/pkg/startupmsg/inst/NEWS 2013-09-11 08:31:51 UTC (rev 903) @@ -11,6 +11,7 @@ GENERAL ENHANCEMENTS: under the hood: +added .Rbuildignore BUGFIXES: From noreply at r-forge.r-project.org Wed Sep 11 14:57:39 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Sep 2013 14:57:39 +0200 (CEST) Subject: [Distr-commits] r904 - in branches/distr-2.5/pkg/distr: . man tests/Examples Message-ID: <20130911125739.BF7CD183B91@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-11 14:57:39 +0200 (Wed, 11 Sep 2013) New Revision: 904 Modified: branches/distr-2.5/pkg/distr/.Rbuildignore branches/distr-2.5/pkg/distr/man/qqplot.Rd branches/distr-2.5/pkg/distr/tests/Examples/distr-Ex.Rout.save Log: [devel] distr-2.5 prepared for release Modified: branches/distr-2.5/pkg/distr/.Rbuildignore =================================================================== --- branches/distr-2.5/pkg/distr/.Rbuildignore 2013-09-11 08:31:51 UTC (rev 903) +++ branches/distr-2.5/pkg/distr/.Rbuildignore 2013-09-11 12:57:39 UTC (rev 904) @@ -1,3 +1,4 @@ inst/doc/Rplots.pdf ^.*\.svn.+ -.*-Ex\.R \ No newline at end of file +.*-Ex\.R +build \ No newline at end of file Modified: branches/distr-2.5/pkg/distr/man/qqplot.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/qqplot.Rd 2013-09-11 08:31:51 UTC (rev 903) +++ branches/distr-2.5/pkg/distr/man/qqplot.Rd 2013-09-11 12:57:39 UTC (rev 904) @@ -126,7 +126,10 @@ P <- Pois(5) B <- Binom(size=2000,prob=5/2000) qqplot(B,P) +\dontrun{ +## takes too much time for R CMD check --as-cran qqplot(B,P, nosym.pCI=TRUE) +} ## some Lebesgue-Decomposed distributions: mylist <- UnivarLebDecDistribution(discretePart=Binom(3,.3), acPart=Norm(2,2), acWeight=11/20) @@ -134,7 +137,7 @@ qqplot(mylist,mylist2) qqplot(mylist,mylist2,exact.pCI=FALSE,exact.sCI=FALSE) \dontrun{ -## takes time +## takes too much time for R CMD check --as-cran qqplot(mylist,mylist2,nosym.pCI=TRUE) ## some ac. distribution with a gap mylist3 <- UnivarMixingDistribution(Unif(0,0.3),Unif(0.6,1),mixCoeff=c(0.8,0.2)) Modified: branches/distr-2.5/pkg/distr/tests/Examples/distr-Ex.Rout.save =================================================================== --- branches/distr-2.5/pkg/distr/tests/Examples/distr-Ex.Rout.save 2013-09-11 08:31:51 UTC (rev 903) +++ branches/distr-2.5/pkg/distr/tests/Examples/distr-Ex.Rout.save 2013-09-11 12:57:39 UTC (rev 904) @@ -1,2811 +1,3078 @@ - -R version 2.15.0 Patched (2012-05-26 r59450) -- "Easter Beagle" -Copyright (C) 2012 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 -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. -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 <- "distr" -> source(file.path(R.home("share"), "R", "examples-header.R")) -> options(warn = 1) -> library('distr') -Loading required package: startupmsg -:startupmsg> Utilities for start-up messages (version 0.8) -: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 0.6) -:SweaveListingUtils> -:SweaveListingUtils> Some functions from package 'base' -:SweaveListingUtils> are intentionally masked ---see -:SweaveListingUtils> SweaveListingMASK(). -:SweaveListingUtils> -:SweaveListingUtils> Note that global options are -:SweaveListingUtils> controlled by -:SweaveListingUtils> SweaveListingoptions() ---c.f. -:SweaveListingUtils> ?"SweaveListingoptions". -:SweaveListingUtils> -:SweaveListingUtils> For more information see -:SweaveListingUtils> ?"SweaveListingUtils", -:SweaveListingUtils> NEWS("SweaveListingUtils") -:SweaveListingUtils> There is a vignette to this -:SweaveListingUtils> package; try -:SweaveListingUtils> vignette("ExampleSweaveListingUtils"). - - -Attaching package: ?SweaveListingUtils? - -The following object(s) are masked from ?package:base?: - - library, require - -:distr> Object oriented implementation of distributions (version -:distr> 2.4) -:distr> -:distr> Attention: Arithmetics on distribution objects are -:distr> understood as operations on corresponding random variables -:distr> (r.v.s); see distrARITH(). -:distr> -:distr> Some functions from package 'stats' are intentionally masked -:distr> ---see distrMASK(). -:distr> -:distr> Note that global options are controlled by distroptions() -:distr> ---c.f. ?"distroptions". -:distr> -:distr> For more information see ?"distr", NEWS("distr"), as well as -:distr> http://distr.r-forge.r-project.org/ -:distr> Package "distrDoc" provides a vignette to this package as -:distr> well as to several extension packages; try -:distr> vignette("distr"). - - -Attaching package: ?distr? - -The following object(s) are masked from ?package:stats?: - - df, qqplot, sd - -> -> assign(".oldSearch", search(), pos = 'CheckExEnv') -> cleanEx() -> nameEx("0distr-package") -> ### * 0distr-package -> -> flush(stderr()); flush(stdout()) -> -> ### Name: distr-package -> ### Title: distr - object orientated implementation of distributions -> ### Aliases: distr-package distr -> ### Keywords: package distribution -> -> ### ** Examples -> -> X <- Unif(2,3) -> Y <- Pois(lambda = 3) -> Z <- X+Y # generates Law of corresponding independent variables -Warning in .makeDNew(x, dpn, h = 1, standM = "int") : - 'integrate()' threw an error ---result may be inaccurate. -> p(Z)(0.2) -[1] 0 -> r(Z)(1000) - [1] 6.579102 4.779275 3.372658 4.632594 3.217653 2.833188 5.836883 - [8] 4.328749 6.265813 2.547148 6.076999 8.133506 3.549124 7.967771 - [15] 4.282188 5.334846 5.539449 5.441803 3.869821 6.553436 6.532861 - [22] 8.883538 5.557134 7.066122 5.258768 2.550905 6.796403 3.145013 - [29] 3.486209 5.707381 6.944007 3.826960 6.383630 8.323171 8.907333 - [36] 7.056447 2.114501 4.904405 6.198231 5.835608 2.628063 6.578858 - [43] 3.072209 7.283379 4.889372 5.162274 4.432173 5.755494 4.371829 - [50] 4.179435 3.676957 3.343576 3.335259 5.945975 5.712469 4.512781 - [57] 3.670003 6.359885 6.723871 5.154257 4.752679 3.084680 6.164728 - [64] 5.980637 5.935260 5.065854 2.531672 4.055380 4.378224 5.166891 - [71] 6.558560 6.743660 6.059266 7.432974 7.402949 4.851098 6.300433 - [78] 8.925874 3.993535 4.602505 4.957766 2.634655 7.653118 3.972603 - [85] 5.345732 3.754893 5.776172 8.286398 8.446992 7.560786 6.635046 - [92] 8.711620 4.107038 4.367655 8.993393 4.432253 10.929256 4.073590 - [99] 5.577728 7.706458 7.484063 6.119480 3.191338 3.039565 3.491861 - [106] 5.339283 4.443054 3.735495 3.518061 6.380735 9.683830 4.579353 - [113] 6.700189 6.147659 3.976503 5.340870 9.642431 4.107585 4.609351 - [120] 4.178274 5.338655 5.502983 5.574192 3.938589 5.164298 9.568823 - [127] 6.277261 7.587950 3.822969 3.486584 5.308142 6.057207 3.523045 - [134] 5.481863 4.357590 3.278691 5.547702 4.912094 2.255964 4.017637 - [141] 5.827255 6.049479 7.595250 3.981267 6.569439 6.727461 4.151836 - [148] 5.318238 6.699690 4.854844 4.378279 5.275432 8.988444 2.134025 - [155] 5.977953 2.642202 5.600517 4.162107 7.143829 3.762430 5.781959 - [162] 4.217105 4.714697 4.293084 7.271073 5.903164 3.934551 6.452999 - [169] 3.329169 5.398796 4.169447 6.209014 5.827562 6.347140 5.599187 - [176] 6.452403 5.093153 7.896114 6.262903 2.711165 4.249534 5.896619 - [183] 9.174417 5.468117 2.795493 2.341466 3.478540 3.260784 6.985835 - [190] 4.438382 5.730667 5.680872 5.907649 4.760867 6.853652 8.254687 - [197] 4.453843 4.784929 4.591713 2.988044 5.927597 5.885563 4.569294 - [204] 6.919895 6.290173 4.256231 3.720954 7.162789 3.482136 4.980341 - [211] 7.714786 7.603208 2.756598 7.042582 3.892577 7.766692 5.472288 - [218] 5.897596 5.407148 2.767171 5.941631 8.765190 6.650673 3.923338 - [225] 4.270002 5.960052 6.441325 4.262422 3.362592 8.902643 9.294795 - [232] 3.214329 7.052151 7.936144 7.840518 6.612929 6.048513 4.269719 - [239] 7.760647 7.917457 6.042595 4.623126 6.025792 7.996861 2.177719 - [246] 6.654859 4.661239 3.820550 7.876687 6.082439 5.830691 4.417018 - [253] 5.066648 3.104336 6.731124 4.594065 5.534583 6.048505 4.615337 - [260] 9.738851 3.117800 10.366602 2.135035 5.297118 5.908073 2.112919 - [267] 6.564549 6.008583 4.787502 11.807161 6.509220 8.478424 6.403077 - [274] 5.543653 6.007867 5.173895 2.896862 5.519487 4.973214 5.805484 - [281] 5.949032 6.285357 5.619059 5.795161 6.935567 4.526653 5.831893 - [288] 4.800116 6.658077 4.995597 4.845622 4.879891 6.482920 4.094898 - [295] 5.028267 6.009440 4.823092 7.043040 10.823171 4.091859 4.864138 - [302] 4.022668 10.050640 2.949141 6.228148 4.626769 5.439620 4.599773 - [309] 6.968634 4.994205 3.273534 4.287168 9.199977 10.196245 9.991003 - [316] 6.955347 5.506245 4.236431 3.517317 5.577783 3.218334 7.222556 - [323] 4.825124 4.363241 4.924039 3.320962 5.120049 5.210499 4.559181 - [330] 3.403327 2.789545 6.471046 3.873281 7.176098 4.305160 5.395722 - [337] 7.004994 4.898506 4.424281 4.020754 3.632583 4.253636 7.789985 - [344] 5.114602 7.069107 4.200499 3.293541 9.391404 5.353941 4.003051 - [351] 2.304293 3.531214 6.863910 8.259209 2.093975 4.083890 4.257744 - [358] 2.086540 6.117788 3.186305 3.069495 5.338623 6.860354 7.781543 - [365] 6.277202 4.723161 4.633321 6.156335 5.152739 4.158852 6.895088 - [372] 8.289939 4.018619 2.049620 5.593186 3.241354 3.304142 4.794494 - [379] 5.750661 6.589345 3.136211 4.627482 5.864843 2.597692 4.197970 - [386] 4.982050 3.131675 8.181336 8.788943 5.236139 5.860343 6.419425 - [393] 8.651857 3.579700 5.323007 6.431335 3.417773 4.522973 4.432197 - [400] 8.182775 5.070290 5.964844 9.542852 4.748663 4.554676 9.680594 - [407] 7.250223 10.284465 4.126663 5.693831 7.880095 7.968802 3.317698 - [414] 4.045398 6.949944 5.400209 5.371284 3.324154 3.560770 6.091314 - [421] 7.774884 5.413062 4.823627 4.365933 3.883124 3.245356 3.594525 - [428] 4.365887 9.745536 6.011345 8.925059 4.869513 5.638617 8.295089 - [435] 8.935575 3.663063 5.618220 8.561209 3.176157 5.520921 6.711753 - [442] 7.925893 4.067052 7.236690 7.695405 4.332264 4.113306 4.939782 - [449] 7.372087 5.706058 7.751002 6.403756 4.227362 4.273287 6.072921 - [456] 4.910409 2.459842 7.600472 4.275654 6.973216 6.873162 9.751179 - [463] 4.136125 6.655204 2.080379 6.265311 4.223805 3.498867 4.924211 - [470] 5.800581 4.806109 6.664286 2.229823 3.286322 6.061472 3.949581 - [477] 7.649938 5.617929 6.072907 7.494375 6.440831 8.013917 7.248682 - [484] 7.171046 5.345439 7.456406 6.654902 6.953591 5.726936 5.247356 - [491] 3.613288 5.128787 5.052366 4.567321 5.740011 5.750754 9.352847 - [498] 7.125697 4.866561 4.069580 6.650475 4.244731 4.329885 3.274329 - [505] 4.979835 7.913374 4.674176 6.326536 7.148619 6.579086 5.477506 - [512] 7.960702 3.157628 4.002058 6.086027 5.238919 5.590526 4.435348 - [519] 5.597217 8.762081 5.789205 9.470844 5.934225 8.645870 4.665628 - [526] 6.270418 6.502792 8.638165 3.534610 7.806940 7.806592 4.497164 - [533] 4.166165 8.547377 5.185010 5.847412 7.154381 5.697753 3.821394 - [540] 8.387257 5.753594 7.799001 6.051941 4.888510 6.764761 7.341601 - [547] 4.123064 4.173528 3.565936 4.346350 6.853956 4.203341 3.216346 - [554] 5.590785 5.713518 4.339589 5.375326 9.243176 5.887737 2.112778 - [561] 5.742362 4.044285 5.720649 3.863230 5.039876 5.721132 6.326835 - [568] 3.726445 3.032174 4.372235 6.415886 4.121232 7.407248 4.424386 - [575] 4.357479 6.830058 5.365814 6.293699 2.374506 3.719549 2.100653 - [582] 6.691715 8.235638 4.779743 6.282059 3.706763 6.619718 6.544563 - [589] 7.924641 3.531242 4.271171 3.905814 8.020223 6.779150 7.364992 - [596] 5.307303 4.160868 3.176943 5.693852 2.621652 6.468918 5.869892 - [603] 3.693521 4.506954 5.913281 4.812330 6.404537 6.794142 4.017008 - [610] 5.548779 6.254126 6.253319 4.624762 4.090745 6.460816 2.913422 - [617] 4.485198 3.388693 4.171777 3.677474 3.292837 6.075759 5.719630 - [624] 7.132900 2.991177 8.098001 5.837644 4.548980 4.983142 5.703874 - [631] 4.281914 6.253390 3.177424 6.002899 5.454130 6.992385 7.816874 - [638] 8.066406 4.898936 4.829592 3.024088 3.472519 7.272335 7.336495 - [645] 3.057295 5.205245 5.869878 5.940514 4.960493 4.123543 6.881292 - [652] 5.565367 5.532138 4.599130 7.057423 3.152381 7.322148 5.617132 - [659] 6.080236 4.957499 4.928580 5.950919 7.106630 4.557867 5.742990 - [666] 4.342305 5.370324 5.661521 5.077816 4.189266 7.408123 4.212645 - [673] 9.980272 5.455587 6.955461 5.027057 4.040872 6.516094 5.102335 - [680] 4.762621 5.161881 5.168592 7.857960 4.060331 4.329365 5.821864 - [687] 5.446692 4.958970 4.770069 6.251505 5.219794 4.975353 6.647226 - [694] 8.646266 2.638373 4.096875 7.459760 5.963888 4.921418 3.200894 - [701] 4.305496 6.087948 3.489525 6.390110 5.178165 8.226200 7.341701 - [708] 3.126380 7.065164 4.277436 2.600411 6.273144 4.941489 4.799276 - [715] 4.089915 4.392771 6.174850 3.456753 7.481765 5.142862 4.034420 - [722] 4.202052 6.264259 4.744758 3.353447 5.877194 4.135481 5.570409 - [729] 8.412244 4.225636 4.797575 6.398676 2.591563 6.906964 5.384810 - [736] 6.371892 5.374292 6.182153 3.041935 6.261203 10.304963 2.178528 - [743] 5.558146 7.371060 4.642810 5.924116 3.259350 6.239350 3.848965 - [750] 4.699012 6.884430 7.209243 4.528550 5.228070 8.102115 4.102062 - [757] 3.150018 2.116710 5.626661 5.515649 2.670773 6.861331 4.636687 - [764] 9.570007 7.894844 8.275016 4.490435 7.946827 6.142462 5.174121 - [771] 7.886910 3.507694 6.190410 5.562037 4.547680 3.893744 6.704781 - [778] 5.561152 7.447658 6.105691 4.658082 7.168129 5.486573 5.167835 - [785] 3.129796 6.416057 5.255846 4.693766 5.249084 5.958214 8.764405 - [792] 3.841370 5.875610 2.009616 7.036117 3.285925 6.080532 4.968795 - [799] 8.564562 6.984705 5.836639 6.880194 3.244425 7.732067 4.498606 - [806] 6.503376 4.568116 4.652677 8.064712 11.676612 4.735372 3.111300 - [813] 3.046655 6.130910 4.880956 6.839725 2.868143 3.033383 6.107907 - [820] 6.549297 8.109318 6.722591 7.725010 4.789522 9.617478 3.503007 - [827] 4.456149 3.034666 6.209639 5.342787 3.545595 7.769484 4.428765 - [834] 3.686462 5.521869 5.796536 3.903052 6.432457 6.331940 6.917115 - [841] 5.209280 5.812735 4.300713 7.572182 5.386782 8.279482 5.260043 - [848] 5.959384 5.634133 8.081877 3.926206 5.890943 5.912085 5.718499 - [855] 3.682528 5.555186 6.401709 5.863838 2.074414 5.283284 11.162637 - [862] 2.763897 5.116376 3.167472 3.475884 4.005788 5.974413 2.114148 - [869] 2.080774 5.322919 5.118785 9.985772 2.404148 6.241782 4.354879 - [876] 4.153240 5.287548 6.256672 4.157690 7.029772 4.811628 6.579173 - [883] 6.576732 2.701487 6.063766 3.502483 3.383950 5.426416 5.544390 - [890] 6.643638 3.791192 3.846853 4.072626 7.860111 6.956165 5.926419 - [897] 3.053964 5.246409 6.487370 6.100063 4.195159 6.213572 5.207682 - [904] 6.028771 8.234566 3.107185 5.277316 2.696022 4.266257 4.660477 - [911] 7.212417 5.005266 4.102903 6.287400 8.444156 6.692993 7.020884 - [918] 6.955752 6.804111 5.911740 5.309467 7.323928 4.138360 6.957561 - [925] 2.232669 5.023715 7.052112 4.932720 5.038752 6.807114 4.696882 - [932] 4.388051 4.390583 5.982333 3.216765 8.566960 5.980336 6.574558 - [939] 4.632867 7.782993 2.856876 5.041593 5.895225 4.188517 2.387342 - [946] 7.494502 4.370316 6.693625 3.733155 4.308550 6.972442 5.243334 - [953] 5.835028 7.390576 8.908864 6.607566 5.607495 6.894327 2.975288 - [960] 7.676351 5.091139 3.777949 7.517544 6.652370 5.339298 5.292120 - [967] 6.783712 2.319966 5.489278 5.134142 5.653294 4.783924 6.921809 - [974] 8.258464 4.513233 5.858583 3.151414 5.641468 3.825477 7.972295 - [981] 4.173126 4.710022 6.110715 7.416779 9.284621 4.341155 5.168895 - [988] 3.547097 3.797206 6.858631 6.332270 3.515725 3.371685 4.436701 - [995] 5.742429 10.011101 6.046900 4.371818 6.658157 7.529650 -> plot(Z+sin(Norm())) -> -> -> cleanEx() -> nameEx("AbscontDistribution-class") -> ### * AbscontDistribution-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: AbscontDistribution-class -> ### Title: Class "AbscontDistribution" -> ### Aliases: AbscontDistribution-class AffLinDistribution-class -> ### AffLinAbscontDistribution-class sqrt,AbscontDistribution-method -> ### initialize,AbscontDistribution-method -> ### initialize,AffLinAbscontDistribution-method -> ### sqrt,AbscontDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> N <- Norm() # N is a normal distribution with mean=0 and sd=1. -> E <- Exp() # E is an exponential distribution with rate=1. -> A1 <- E+1 # a new absolutely continuous distributions with exact slots d, p, q -> A2 <- A1*3 # a new absolutely continuous distributions with exact slots d, p, q -> A3 <- N*0.9 + E*0.1 # a new absolutely continuous distribution with approximated slots d, p, q -> r(A3)(1) # one random number generated from this distribution, e.g. -0.7150937 -[1] -0.5492378 -> d(A3)(0) # The (approximated) density for x=0 is 0.4379882. -[1] 0.4379965 -> p(A3)(0) # The (approximated) probability that x <= 0 is 0.4562021. -[1] 0.4561991 -> q(A3)(.1) # The (approximated) 10 percent quantile is 0.1. -[1] -1.060145 -> -> -> -> cleanEx() -> nameEx("AbscontDistribution") -> ### * AbscontDistribution -> -> flush(stderr()); flush(stdout()) -> -> ### Name: AbscontDistribution -> ### Title: Generating function "AbscontDistribution" -> ### Aliases: AbscontDistribution -> ### Keywords: distribution -> -> ### ** Examples -> -> plot(Norm()) -> plot(AbscontDistribution(r = rnorm)) -> plot(AbscontDistribution(d = dnorm)) -> plot(AbscontDistribution(p = pnorm)) -> plot(AbscontDistribution(q = qnorm)) -> plot(Ac <- AbscontDistribution(d = function(x, log = FALSE){ -+ d <- exp(-abs(x^3)) -+ ## unstandardized!! -+ if(log) d <- log(d) -+ return(d)}, -+ withStand = TRUE)) -> -> -> -> cleanEx() -> nameEx("Arcsine-class") -> ### * Arcsine-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Arcsine-class -> ### Title: Class "Arcsine" -> ### Aliases: Arcsine-class Arcsine initialize,Arcsine-method -> ### Keywords: distribution -> -> ### ** Examples -> -> A <- Arcsine() -> # A is a Arcsine distribution with shape1 = 1 and shape2 = 1. -> r(A)(3) # three random number generated from this distribution, e.g. 0.6979795 -[1] -0.6718297 -0.3910154 0.2268826 -> d(A)(c(-2,-1,-0.2,0,0.2,1,2)) # Density at x=c(-1,-0.2,0,0.2,1). -[1] 0.0000000 Inf 0.3248737 0.3183099 0.3248737 Inf 0.0000000 -> p(A)(c(-2,-1,-0.2,0,0.2,1,2)) # cdf at q=c(-1,-0.2,0,0.2,1). -[1] 0.0000000 0.0000000 0.4359058 0.5000000 0.5640942 1.0000000 1.0000000 -> q(A)(c(0,0.2,1,2)) # quantile function at at x=c(0,0.2,1). -[1] -1.000000 -0.809017 1.000000 NA -> -> -> -> cleanEx() -> nameEx("Beta-class") -> ### * Beta-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Beta-class -> ### Title: Class "Beta" -> ### Aliases: Beta-class Beta initialize,Beta-method -> ### Keywords: distribution -> -> ### ** Examples -> -> B <- Beta(shape1 = 1, shape2 = 1) -> # B is a beta distribution with shape1 = 1 and shape2 = 1. -> r(B)(1) # one random number generated from this distribution, e.g. 0.6979795 -[1] 0.7344913 -> d(B)(1) # Density of this distribution is 1 for x=1. -[1] 1 -> p(B)(1) # Probability that x < 1 is 1. -[1] 1 -> q(B)(.1) # Probability that x < 0.1 is 0.1. -[1] 0.1 -> shape1(B) # shape1 of this distribution is 1. -[1] 1 -> shape1(B) <- 2 # shape1 of this distribution is now 2. -> Bn <- Beta(shape1 = 1, shape2 = 3, ncp = 5) -> # Bn is a beta distribution with shape1 = 1 and shape2 = 3 and ncp = 5. -> B0 <- Bn; ncp(B0) <- 0; -> # B0 is just the same beta distribution as Bn but with ncp = 0 -> q(B0)(0.1) ## -[1] 0.03451062 -> q(Bn)(0.1) ## => from R 2.3.0 on ncp no longer ignored... -[1] 0.2047932 -> -> -> -> cleanEx() -> nameEx("BetaParameter-class") -> ### * BetaParameter-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: BetaParameter-class -> ### Title: Class "BetaParameter" -> ### Aliases: BetaParameter-class initialize,BetaParameter-method -> ### Keywords: distribution -> -> ### ** Examples -> -> W <- new("BetaParameter", shape1 = 1, shape2 = 1, ncp = 0) -> shape2(W) # shape2 of this distribution is 1. -[1] 1 -> shape2(W) <- 2 # shape2 of this distribution is now 2. -> -> -> -> cleanEx() -> nameEx("Binom-class") -> ### * Binom-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Binom-class -> ### Title: Class "Binom" -> ### Aliases: Binom-class Binom initialize,Binom-method -> ### Keywords: distribution -> -> ### ** Examples -> -> B <- Binom(prob=0.5,size=1) # B is a binomial distribution with prob=0.5 and size=1. -> r(B)(1) # # one random number generated from this distribution, e.g. 1 -[1] 0 -> d(B)(1) # Density of this distribution is 0.5 for x=1. -[1] 0.5 -> p(B)(0.4) # Probability that x<0.4 is 0.5. -[1] 0.5 -> q(B)(.1) # x=0 is the smallest value x such that p(B)(x)>=0.1. -[1] 0 -> size(B) # size of this distribution is 1. -[1] 1 -> size(B) <- 2 # size of this distribution is now 2. -> C <- Binom(prob = 0.5, size = 1) # C is a binomial distribution with prob=0.5 and size=1. -> D <- Binom(prob = 0.6, size = 1) # D is a binomial distribution with prob=0.6 and size=1. -> E <- B + C # E is a binomial distribution with prob=0.5 and size=3. -> F <- B + D # F is an object of class LatticeDistribution. -> G <- B + as(D,"DiscreteDistribution") ## DiscreteDistribution -> -> -> -> cleanEx() -> nameEx("BinomParameter-class") -> ### * BinomParameter-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: BinomParameter-class -> ### Title: Class "BinomParameter" -> ### Aliases: BinomParameter-class initialize,BinomParameter-method -> ### Keywords: distribution -> -> ### ** Examples -> -> W <- new("BinomParameter",prob=0.5,size=1) -> size(W) # size of this distribution is 1. -[1] 1 -> size(W) <- 2 # size of this distribution is now 2. -> -> -> -> cleanEx() -> nameEx("Cauchy-class") -> ### * Cauchy-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Cauchy-class -> ### Title: Class "Cauchy" -> ### Aliases: Cauchy-class Cauchy initialize,Cauchy-method -> ### Keywords: distribution -> -> ### ** Examples -> -> C <- Cauchy(location = 1, scale = 1) # C is a Cauchy distribution with location=1 and scale=1. -> r(C)(1) # one random number generated from this distribution, e.g. 4.104603 -[1] 2.10252 -> d(C)(1) # Density of this distribution is 0.3183099 for x=1. -[1] 0.3183099 -> p(C)(1) # Probability that x<1 is 0.5. -[1] 0.5 -> q(C)(.1) # Probability that x<-2.077684 is 0.1. -[1] -2.077684 -> location(C) # location of this distribution is 1. -[1] 1 -> location(C) <- 2 # location of this distribution is now 2. -> is(C,"Td") # no -[1] FALSE -> C0 <- Cauchy() # standard, i.e. location = 0, scale = 1 -> is(C0,"Td") # yes -[1] TRUE -> as(C0,"Td") -Distribution Object of Class: Td - df: 1 - ncp: 0 -> -> -> -> cleanEx() -> nameEx("CauchyParameter-class") -> ### * CauchyParameter-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: CauchyParameter-class -> ### Title: Class "CauchyParameter" -> ### Aliases: CauchyParameter-class initialize,CauchyParameter-method -> ### Keywords: distribution -> -> ### ** Examples -> -> W <- new("CauchyParameter",location=1,scale=1) -> location(W) # location of this distribution is 1. -[1] 1 -> location(W) <- 2 # location of this distribution is now 2. -> -> -> -> cleanEx() -> nameEx("Chisq-class") -> ### * Chisq-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Chisq-class -> ### Title: Class "Chisq" -> ### Aliases: Chisq-class Chisq initialize,Chisq-method -> ### Keywords: distribution -> -> ### ** Examples -> -> C <- Chisq(df = 1, ncp = 1) # C is a chi-squared distribution with df=1 and ncp=1. -> r(C)(1) # one random number generated from this distribution, e.g. 0.2557184 -[1] 3.052466 -> d(C)(1) # Density of this distribution is 0.2264666 for x = 1. -[1] 0.2264666 -> p(C)(1) # Probability that x < 1 is 0.4772499. -[1] 0.4772499 -> q(C)(.1) # Probability that x < 0.04270125 is 0.1. -[1] 0.04270125 -> df(C) # df of this distribution is 1. -[1] 1 -> df(C) <- 2 # df of this distribution is now 2. -> is(C, "Gammad") # no -[1] FALSE -> C0 <- Chisq() # default: Chisq(df=1,ncp=0) -> is(C0, "Gammad") # yes -[1] TRUE -> as(C0,"Gammad") -Distribution Object of Class: Gammad - shape: 0.5 - scale: 2 -> -> -> -> cleanEx() -> nameEx("ChisqParameter-class") -> ### * ChisqParameter-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: ChisqParameter-class -> ### Title: Class "ChisqParameter" -> ### Aliases: ChisqParameter-class initialize,ChisqParameter-method -> ### Keywords: distribution -> -> ### ** Examples -> -> W <- new("ChisqParameter",df=1,ncp=1) -> ncp(W) # ncp of this distribution is 1. -[1] 1 -> ncp(W) <- 2 # ncp of this distribution is now 2. -> -> -> -> cleanEx() -> nameEx("CompoundDistribution-class") -> ### * CompoundDistribution-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: CompoundDistribution-class -> ### Title: Class "CompoundDistribution" -> ### Aliases: CompoundDistribution-class NumbOfSummandsDistr SummandsDistr -> ### NumbOfSummandsDistr-methods SummandsDistr-methods -> ### NumbOfSummandsDistr,CompoundDistribution-method -> ### SummandsDistr,CompoundDistribution-method -> ### coerce,CompoundDistribution,UnivarLebDecDistribution-method -> ### UnivDistrListOrDistribution-class -> ### Keywords: distribution -> -> ### ** Examples -> -> CP <- CompoundDistribution(Pois(),Norm()) -> CP -An object of class "CompoundDistribution" - - The frequency distribution is: -Distribution Object of Class: Pois -lambda: 1 - The summands distribution is/are: -Distribution Object of Class: Norm -mean: 0 -sd: 1 - -This Distribution is: -An object of class "UnivarLebDecDistribution" ---- a Lebesgue decomposed distribution: - - Its discrete part (with weight 0.368000) is a -Distribution Object of Class: Dirac -location: 0 -This part is accessible with 'discretePart()'. - - Its absolutely continuous part (with weight 0.632000) is a -Distribution Object of Class: AbscontDistribution -This part is accessible with 'acPart()'. -Warning in function (object) : - arithmetics on distributions are understood as operations on r.v.'s -see 'distrARITH()'; for switching off this warning see '?distroptions' -> p(CP)(0.3) -[1] 0.7436411 -> plot(CP) -> -> -> -> cleanEx() -> nameEx("CompoundDistribution") -> ### * CompoundDistribution -> -> flush(stderr()); flush(stdout()) -> -> ### Name: CompoundDistribution -> ### Title: Generating function for Class "CompoundDistribution" -> ### Aliases: CompoundDistribution -> ### Keywords: distribution list -> -> ### ** Examples -> -> CP0 <- CompoundDistribution(Pois(), Norm()) -> CP0 -An object of class "CompoundDistribution" - - The frequency distribution is: -Distribution Object of Class: Pois -lambda: 1 - The summands distribution is/are: -Distribution Object of Class: Norm -mean: 0 -sd: 1 - -This Distribution is: -An object of class "UnivarLebDecDistribution" ---- a Lebesgue decomposed distribution: - - Its discrete part (with weight 0.368000) is a -Distribution Object of Class: Dirac -location: 0 -This part is accessible with 'discretePart()'. - - Its absolutely continuous part (with weight 0.632000) is a -Distribution Object of Class: AbscontDistribution -This part is accessible with 'acPart()'. -Warning in function (object) : - arithmetics on distributions are understood as operations on r.v.'s -see 'distrARITH()'; for switching off this warning see '?distroptions' -> CP1 <- CompoundDistribution(DiscreteDistribution(supp = c(1,5,9,11), -+ prob = dbinom(0:3, size = 3,prob = 0.3)),Norm()) -> CP1 -An object of class "CompoundDistribution" - - The frequency distribution is: -Distribution Object of Class: DiscreteDistribution - The summands distribution is/are: -Distribution Object of Class: Norm -mean: 0 -sd: 1 - -This Distribution is: -Distribution Object of Class: AbscontDistribution -Warning in function (object) : - arithmetics on distributions are understood as operations on r.v.'s -see 'distrARITH()'; for switching off this warning see '?distroptions' -> UL <- UnivarDistrList(Norm(), Binom(10,0.3), Chisq(df=4), Norm(), -+ Binom(10,0.3), Chisq(df=4), Norm(), Binom(10,0.3), -+ Chisq(df=4), Td(5), Td(10)) -> CP2 <- CompoundDistribution(DiscreteDistribution(supp = c(1,5,9,11), -+ prob = dbinom(0:3, size = 3, prob = 0.3)),UL) -> plot(CP2) -> -> -> -> cleanEx() -> nameEx("ConvPow") -> ### * ConvPow -> -> flush(stderr()); flush(stdout()) -> -> ### Name: convpow-methods -> ### Title: Distribution of the sum of univariate i.i.d r.v's -> ### Aliases: convpow convpow-methods convpow,AcDcLcDistribution-method -> ### convpow,AbscontDistribution-method convpow,LatticeDistribution-method -> ### convpow,DiscreteDistribution-method convpow,AcDcLcDistribution-method -> ### convpow,Norm-method convpow,Binom-method convpow,Nbinom-method -> ### convpow,ExpOrGammaOrChisq-method convpow,Cauchy-method -> ### convpow,Pois-method convpow,Dirac-method -> ### Keywords: distribution -> -> ### ** Examples -> -> convpow(Exp()+Pois(),4) -Distribution Object of Class: AbscontDistribution -Warning in function (object) : - arithmetics on distributions are understood as operations on r.v.'s -see 'distrARITH()'; for switching off this warning see '?distroptions' -> -> -> -> cleanEx() -> nameEx("DExp-class") -> ### * DExp-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: DExp-class -> ### Title: Class "DExp" -> ### Aliases: DExp-class DExp Laplace DoubleExponential -> ### initialize,DExp-method -> ### Keywords: distribution -> -> ### ** Examples -> -> D <- DExp(rate = 1) # D is a Laplace distribution with rate = 1. -> r(D)(1) # one random number generated from this distribution, e.g. 0.4190765 -[1] -1.181643 -> d(D)(1) # Density of this distribution is 0.1839397 for x = 1. -[1] 0.1839397 -> p(D)(1) # Probability that x < 1 is 0.8160603. -[1] 0.8160603 -> q(D)(.1) # Probability that x < -1.609438 is 0.1. -[1] -1.609438 -> rate(D) # rate of this distribution is 1. -[1] 1 -> rate(D) <- 2 # rate of this distribution is now 2. -> 3*D ### still a DExp -distribution -Distribution Object of Class: DExp - rate: 0.666666666666667 -Warning in function (object) : - arithmetics on distributions are understood as operations on r.v.'s -see 'distrARITH()'; for switching off this warning see '?distroptions' -> -> -> -> cleanEx() -> nameEx("Dirac-class") -> ### * Dirac-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Dirac-class -> ### Title: Class "Dirac" -> ### Aliases: Dirac-class Dirac initialize,Dirac-method log,Dirac-method -> ### Math,Dirac-method -> ### Keywords: distribution -> -> ### ** Examples -> -> D <- Dirac(location = 0) # D is a Dirac distribution with location=0. -> r(D)(1) -[1] 0 -> # r(D)(1) generates a pseudo-random-number according to a Dirac -> # distribution with location = 0, -> # which of course will take 0 as value almost surely. -> d(D)(0) # Density of this distribution is 1 for x = 0. -[1] 1 -> p(D)(1) # Probability that x < 1 is 1. -[1] 1 -> q(D)(.1) # q(D)(x) is always 0 (= location). -[1] 0 -> location(D) # location of this distribution is 0. -[1] 0 -> location(D) <- 2 # location of this distribution is now 2. -> -> -> -> cleanEx() -> nameEx("DiracParameter-class") -> ### * DiracParameter-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: DiracParameter-class -> ### Title: Class "DiracParameter" -> ### Aliases: DiracParameter-class initialize,DiracParameter-method -> ### Keywords: distribution -> -> ### ** Examples -> -> W <- new("DiracParameter",location=1) -> location(W) # location of this distribution is 1. -[1] 1 -> location(W) <- 2 # location of this distribution is now 2. -> -> -> -> cleanEx() -> nameEx("DiscreteDistribution-class") -> ### * DiscreteDistribution-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: DiscreteDistribution-class -> ### Title: Class "DiscreteDistribution" -> ### Aliases: DiscreteDistribution-class AffLinDiscreteDistribution-class -> ### initialize,DiscreteDistribution-method -> ### initialize,AffLinDiscreteDistribution-method -> ### sqrt,DiscreteDistribution-method -> ### coerce,DiscreteDistribution,LatticeDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> # Dirac-measure at 0 -> D1 <- DiscreteDistribution(supp = 0) -> support(D1) -[1] 0 -> -> # simple discrete distribution -> D2 <- DiscreteDistribution(supp = c(1:5), prob = c(0.1, 0.2, 0.3, 0.2, 0.2)) -> plot(D2) -> (pp <- p(D2)(support(D2))) [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 904 From noreply at r-forge.r-project.org Wed Sep 11 15:26:22 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Sep 2013 15:26:22 +0200 (CEST) Subject: [Distr-commits] r905 - branches/distr-2.5/pkg/distr branches/distr-2.5/pkg/distrMod branches/distr-2.5/pkg/distrMod/tests/Examples branches/distr-2.5/pkg/distrSim pkg/distr pkg/distr/R pkg/distr/inst pkg/distr/man pkg/distr/tests/Examples pkg/distrMod pkg/distrMod/R pkg/distrMod/inst pkg/distrMod/man pkg/distrMod/tests/Examples pkg/distrSim pkg/distrSim/R pkg/distrSim/inst pkg/distrSim/man pkg/distrSim/tests/Examples Message-ID: <20130911132622.5B113183D8F@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-11 15:26:21 +0200 (Wed, 11 Sep 2013) New Revision: 905 Added: pkg/distr/R/makedots.R pkg/distr/man/internalGenerics.Rd pkg/distrSim/.Rbuildignore pkg/distrSim/distrSim-Ex.R Modified: branches/distr-2.5/pkg/distr/DESCRIPTION branches/distr-2.5/pkg/distrMod/DESCRIPTION branches/distr-2.5/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save branches/distr-2.5/pkg/distrSim/DESCRIPTION pkg/distr/.Rbuildignore pkg/distr/DESCRIPTION pkg/distr/NAMESPACE pkg/distr/R/AllGenerics.R pkg/distr/R/plot-methods.R pkg/distr/R/plot-methods_LebDec.R pkg/distr/inst/NEWS pkg/distr/man/0distr-package.Rd pkg/distr/man/RtoDPQ.LC.Rd pkg/distr/man/RtoDPQ.Rd pkg/distr/man/operators-methods.Rd pkg/distr/man/plot-methods.Rd pkg/distr/man/qqplot.Rd pkg/distr/tests/Examples/distr-Ex.Rout.save pkg/distrMod/.Rbuildignore pkg/distrMod/DESCRIPTION pkg/distrMod/NAMESPACE pkg/distrMod/R/0distrModUtils.R pkg/distrMod/R/AllClass.R pkg/distrMod/R/AllGeneric.R pkg/distrMod/R/AllShow.R pkg/distrMod/R/Estimate.R pkg/distrMod/R/Estimator.R pkg/distrMod/R/L2GroupFamilies.R pkg/distrMod/R/L2ParamFamily.R pkg/distrMod/R/MCEstimator.R pkg/distrMod/R/MDEstimator.R pkg/distrMod/R/MLEstimator.R pkg/distrMod/R/SimpleL2ParamFamilies.R pkg/distrMod/R/confint.R pkg/distrMod/R/internalMleCalc.R pkg/distrMod/R/modifyModel.R pkg/distrMod/inst/NEWS pkg/distrMod/inst/TOBEDONE pkg/distrMod/man/0distrMod-package.Rd pkg/distrMod/man/BetaFamily.Rd pkg/distrMod/man/Estimator.Rd pkg/distrMod/man/GammaFamily.Rd pkg/distrMod/man/L2ParamFamily-class.Rd pkg/distrMod/man/L2ParamFamily.Rd pkg/distrMod/man/MCEstimator.Rd pkg/distrMod/man/MDEstimator.Rd pkg/distrMod/man/MLEstimator.Rd pkg/distrMod/man/NBinomFamily.Rd pkg/distrMod/man/ParamFamily-class.Rd pkg/distrMod/man/internalClassUnions-class.Rd pkg/distrMod/man/internalmleHelpers.Rd pkg/distrMod/man/modifyModel-methods.Rd pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save pkg/distrSim/DESCRIPTION pkg/distrSim/NAMESPACE pkg/distrSim/R/AllGenerics.R pkg/distrSim/inst/NEWS pkg/distrSim/man/0distrSim-package.Rd pkg/distrSim/tests/Examples/distrSim-Ex.Rout.save Log: prepared distr-distrMod-distrSim-2.5-versions for submission Modified: branches/distr-2.5/pkg/distr/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distr/DESCRIPTION 2013-09-11 12:57:39 UTC (rev 904) +++ branches/distr-2.5/pkg/distr/DESCRIPTION 2013-09-11 13:26:21 UTC (rev 905) @@ -1,5 +1,5 @@ Package: distr -Version: 2.5 +Version: 2.5.1 Date: 2013-01-09 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions Modified: branches/distr-2.5/pkg/distrMod/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distrMod/DESCRIPTION 2013-09-11 12:57:39 UTC (rev 904) +++ branches/distr-2.5/pkg/distrMod/DESCRIPTION 2013-09-11 13:26:21 UTC (rev 905) @@ -1,5 +1,5 @@ Package: distrMod -Version: 2.5 +Version: 2.5.1 Date: 2013-01-09 Title: Object oriented implementation of probability models Description: Object oriented implementation of probability models based on packages 'distr' and Modified: branches/distr-2.5/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save =================================================================== --- branches/distr-2.5/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2013-09-11 12:57:39 UTC (rev 904) +++ branches/distr-2.5/pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2013-09-11 13:26:21 UTC (rev 905) @@ -1,3060 +1,3372 @@ - -R version 2.15.0 Patched (2012-05-26 r59450) -- "Easter Beagle" -Copyright (C) 2012 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 -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. -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 <- "distrMod" -> source(file.path(R.home("share"), "R", "examples-header.R")) -> options(warn = 1) -> library('distrMod') -Loading required package: startupmsg -:startupmsg> Utilities for start-up messages (version 0.8) -:startupmsg> -:startupmsg> For more information see ?"startupmsg", -:startupmsg> NEWS("startupmsg") - -Loading required package: distr -Loading required package: sfsmisc -Loading required package: SweaveListingUtils -:SweaveListingUtils> Utilities for Sweave together with -:SweaveListingUtils> TeX listings package (version 0.6) -:SweaveListingUtils> -:SweaveListingUtils> Some functions from package 'base' -:SweaveListingUtils> are intentionally masked ---see -:SweaveListingUtils> SweaveListingMASK(). -:SweaveListingUtils> -:SweaveListingUtils> Note that global options are -:SweaveListingUtils> controlled by -:SweaveListingUtils> SweaveListingoptions() ---c.f. -:SweaveListingUtils> ?"SweaveListingoptions". -:SweaveListingUtils> -:SweaveListingUtils> For more information see -:SweaveListingUtils> ?"SweaveListingUtils", -:SweaveListingUtils> NEWS("SweaveListingUtils") -:SweaveListingUtils> There is a vignette to this -:SweaveListingUtils> package; try -:SweaveListingUtils> vignette("ExampleSweaveListingUtils"). - - -Attaching package: ?SweaveListingUtils? - -The following object(s) are masked from ?package:base?: - - library, require - -:distr> Object oriented implementation of distributions (version -:distr> 2.4) -:distr> -:distr> Attention: Arithmetics on distribution objects are -:distr> understood as operations on corresponding random variables -:distr> (r.v.s); see distrARITH(). -:distr> -:distr> Some functions from package 'stats' are intentionally masked -:distr> ---see distrMASK(). -:distr> -:distr> Note that global options are controlled by distroptions() -:distr> ---c.f. ?"distroptions". -:distr> -:distr> For more information see ?"distr", NEWS("distr"), as well as -:distr> http://distr.r-forge.r-project.org/ -:distr> Package "distrDoc" provides a vignette to this package as -:distr> well as to several extension packages; try -:distr> vignette("distr"). - - -Attaching package: ?distr? - -The following object(s) are masked from ?package:stats?: - - df, qqplot, sd - -Loading required package: distrEx -:distrEx> Extensions of package distr (version 2.4) -:distrEx> -:distrEx> Note: Packages "e1071", "moments", "fBasics" should be -:distrEx> attached /before/ package "distrEx". See -:distrEx> distrExMASK().Note: Extreme value distribution -:distrEx> functionality has been moved to -:distrEx> -:distrEx> package "RobExtremes". See distrExMOVED(). -:distrEx> -:distrEx> For more information see ?"distrEx", NEWS("distrEx"), as -:distrEx> well as -:distrEx> http://distr.r-forge.r-project.org/ -:distrEx> Package "distrDoc" provides a vignette to this package -:distrEx> as well as to several related packages; try -:distrEx> vignette("distr"). - - -Attaching package: ?distrEx? - -The following object(s) are masked from ?package:stats?: - - IQR, mad, median, var - -Loading required package: RandVar -:RandVar> Implementation of random variables (version 0.8.1) -:RandVar> -:RandVar> For more information see ?"RandVar", NEWS("RandVar"), as -:RandVar> well as -:RandVar> http://robast.r-forge.r-project.org/ -:RandVar> This package also includes a vignette; try -:RandVar> vignette("RandVar"). - -Loading required package: MASS -Loading required package: stats4 -:distrMod> Object oriented implementation of probability models -:distrMod> (version 2.4) -:distrMod> -:distrMod> Some functions from pkg's 'base' and 'stats' are -:distrMod> intentionally masked ---see distrModMASK(). -:distrMod> -:distrMod> Note that global options are controlled by -:distrMod> distrModoptions() ---c.f. ?"distrModoptions". -:distrMod> -:distrMod> For more information see ?"distrMod", -:distrMod> NEWS("distrMod"), as well as -:distrMod> http://distr.r-forge.r-project.org/ -:distrMod> There is a vignette to this package; try -:distrMod> vignette("distrMod"). -:distrMod> Package "distrDoc" provides a vignette to the other -:distrMod> distrXXX packages, -:distrMod> as well as to several related packages; try -:distrMod> vignette("distr"). - - -Attaching package: ?distrMod? - -The following object(s) are masked from ?package:stats4?: - - confint - -The following object(s) are masked from ?package:stats?: - - confint - -The following object(s) are masked from ?package:base?: - - norm - -> -> assign(".oldSearch", search(), pos = 'CheckExEnv') -> cleanEx() -> nameEx("BetaFamily") -> ### * BetaFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: BetaFamily -> ### Title: Generating function for Beta families -> ### Aliases: BetaFamily -> ### Keywords: models -> -> ### ** Examples -> -> (B1 <- BetaFamily()) -An object of class "BetaFamily" -### name: Beta family - -### distribution: Distribution Object of Class: Beta - shape1: 1 - shape2: 1 - ncp: 0 - -### param: An object of class "ParamFamParameter" -name: shape1 and shape2 -shape1: 1 -shape2: 1 -trafo: - shape1 shape2 -shape1 1 0 -shape2 0 1 - -### props: -[1] "The Beta family is invariant in the following sense" -[2] "if (x_i)~Beta(s1,s2) then (1-x_i)~Beta(s2,s1)" -> FisherInfo(B1) -An object of class "PosSemDefSymmMatrix" - shape1 shape2 -shape1 1.0000000 -0.6449341 -shape2 -0.6449341 1.0000000 -> checkL2deriv(B1) -precision of centering: 3.96327e-05 3.963591e-05 -precision of Fisher information: - shape1 shape2 -shape1 -1.851068e-05 1.648326e-06 -shape2 1.648326e-06 -1.851068e-05 -$maximum.deviation -[1] 3.963591e-05 - -> -> -> -> cleanEx() -> nameEx("BiasType-class") -> ### * BiasType-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: BiasType-class -> ### Title: Bias Type -> ### Aliases: BiasType-class name,BiasType-method name<-,BiasType-method -> ### Keywords: classes -> -> ### ** Examples -> -> aB <- positiveBias() -> name(aB) -[1] "positive Bias" -> -> -> -> cleanEx() -> nameEx("BinomFamily") -> ### * BinomFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: BinomFamily -> ### Title: Generating function for Binomial families -> ### Aliases: BinomFamily -> ### Keywords: models -> -> ### ** Examples -> -> (B1 <- BinomFamily(size = 25, prob = 0.25)) -An object of class "BinomFamily" -### name: Binomial family - -### distribution: Distribution Object of Class: Binom - size: 25 - prob: 0.25 - -### param: An object of class "ParamFamParameter" -name: probability of success -prob: 0.25 -fixed part of param.: - size: 25 -trafo: - prob -prob 1 - -### props: -[1] "The Binomial family is symmetric with respect to prob = 0.5;" -[2] "i.e., d(Binom(size, prob))(k)=d(Binom(size,1-prob))(size-k)" -> plot(B1) -> FisherInfo(B1) -An object of class "PosSemDefSymmMatrix" - prob -prob 133.3333 -> checkL2deriv(B1) -precision of centering: -6.965857e-16 -precision of Fisher information: - prob -prob 2.842171e-14 -$maximum.deviation -[1] 2.842171e-14 - -> -> -> -> cleanEx() -> nameEx("CauchyLocationScaleFamily") -> ### * CauchyLocationScaleFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: CauchyLocationScaleFamily -> ### Title: Generating function for Cauchy location and scale families -> ### Aliases: CauchyLocationScaleFamily -> ### Keywords: models -> -> ### ** Examples -> -> (C1 <- CauchyLocationScaleFamily()) -An object of class "CauchyLocationScaleFamily" -### name: Cauchy Location and scale family - -### distribution: Distribution Object of Class: Cauchy - location: 0 - scale: 1 - -### param: An object of class "ParamWithScaleFamParameter" -name: location and scale -loc: 0 -scale: 1 -trafo: - loc scale -loc 1 0 -scale 0 1 - -### props: -[1] "The Cauchy Location and scale family is invariant under" -[2] "the group of transformations 'g(x) = scale*x + loc'" -[3] "with location parameter 'loc' and scale parameter 'scale'" -> plot(C1) -> FisherInfo(C1) -An object of class "PosDefSymmMatrix" - loc scale -loc 0.5 0.0 -scale 0.0 0.5 -> ### need smaller integration range: -> distrExoptions("ElowerTruncQuantile"=1e-4,"EupperTruncQuantile"=1e-4) -> checkL2deriv(C1) -precision of centering: 0 -0.02119711 -precision of Fisher information: - loc scale -loc -3.137524e-05 0.00000000 -scale 0.000000e+00 -0.02118143 -$maximum.deviation -[1] 0.02119711 - -> distrExoptions("ElowerTruncQuantile"=1e-7,"EupperTruncQuantile"=1e-7) -> -> -> -> cleanEx() -> nameEx("Confint-class") -> ### * Confint-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Confint-class -> ### Title: Confint-class -> ### Aliases: Confint-class type,Confint-method call.estimate -> ### call.estimate,Confint-method confint,Confint,missing-method -> ### name.estimate name.estimate,Confint-method trafo.estimate -> ### trafo.estimate,Confint-method samplesize.estimate -> ### samplesize.estimate,Confint-method completecases.estimate -> ### completecases.estimate,Confint-method nuisance.estimate -> ### nuisance.estimate,Confint-method fixed.estimate -> ### fixed.estimate,Confint-method show,Confint-method -> ### print,Confint-method -> ### Keywords: classes -> -> ### ** Examples -> -> ## some transformation -> mtrafo <- function(x){ -+ nms0 <- c("scale","shape") -+ nms <- c("shape","rate") -+ fval0 <- c(x[2], 1/x[1]) -+ names(fval0) <- nms -+ mat0 <- matrix( c(0, -1/x[1]^2, 1, 0), nrow = 2, ncol = 2, -+ dimnames = list(nms,nms0)) -+ list(fval = fval0, mat = mat0)} -> -> x <- rgamma(50, scale = 0.5, shape = 3) -> -> ## parametric family of probability measures -> G <- GammaFamily(scale = 1, shape = 2, trafo = mtrafo) -> ## MLE -> res <- MLEstimator(x = x, ParamFamily = G) -> ci <- confint(res) -> print(ci, digits = 4, show.details="maximal") -A[n] asymptotic (CLT-based) confidence interval: - 2.5 % 97.5 % -shape 2.530 5.591 -rate 1.751 4.097 -Type of estimator: Maximum likelihood estimate -samplesize: 50 -Call by which estimate was produced: -MLEstimator(x = x, ParamFamily = G) -Transformation of main parameter by which estimate was produced: -function (x) -{ - nms0 <- c("scale", "shape") - nms <- c("shape", "rate") - fval0 <- c(x[2], 1/x[1]) - names(fval0) <- nms - mat0 <- matrix(c(0, -1/x[1]^2, 1, 0), nrow = 2, ncol = 2, - dimnames = list(nms, nms0)) - list(fval = fval0, mat = mat0) -} -Trafo / derivative matrix at which estimate was produced: - scale shape -shape 0.000 1 -rate -8.549 0 -> print(ci, digits = 4, show.details="medium") -A[n] asymptotic (CLT-based) confidence interval: - 2.5 % 97.5 % -shape 2.530 5.591 -rate 1.751 4.097 -Type of estimator: Maximum likelihood estimate -samplesize: 50 -Call by which estimate was produced: -MLEstimator(x = x, ParamFamily = G) -> print(ci, digits = 4, show.details="minimal") -A[n] asymptotic (CLT-based) confidence interval: - 2.5 % 97.5 % -shape 2.530 5.591 -rate 1.751 4.097 -> -> -> -> cleanEx() -> nameEx("Estimate-class") -> ### * Estimate-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Estimate-class -> ### Title: Estimate-class. -> ### Aliases: Estimate-class name,Estimate-method name<-,Estimate-method -> ### estimate estimate,Estimate-method estimate.call -> ### estimate.call,Estimate-method Infos Infos,Estimate-method samplesize -> ### samplesize,Estimate-method completecases -> ### completecases,Estimate-method asvar asvar,Estimate-method -> ### fixed,Estimate-method asvar<- asvar<-,Estimate-method -> ### nuisance,Estimate-method main,Estimate-method Infos<- -> ### Infos<-,Estimate-method addInfo<- addInfo<-,Estimate-method -> ### show,Estimate-method print,Estimate-method untransformed.estimate -> ### untransformed.estimate,Estimate-method untransformed.asvar -> ### untransformed.asvar,Estimate-method -> ### Keywords: classes -> -> ### ** Examples -> -> x <- rnorm(100) -> Estimator(x, estimator = mean, name = "mean") -Evaluations of mean: --------------------- -An object of class ?Estimate? -generated by call - Estimator(x = x, estimator = mean, name = "mean") -samplesize: 100 -estimate: - mean1 -0.1088874 -> -> x1 <- x; x1[sample(1:100,10)] <- NA -> myEst1 <- Estimator(x1, estimator = mean, name = "mean") -> samplesize(myEst1) -[1] 90 -> samplesize(myEst1, onlycomplete = FALSE) -[1] 100 -> -> -> -> cleanEx() -> nameEx("Estimator") -> ### * Estimator -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Estimator -> ### Title: Function to compute estimates -> ### Aliases: Estimator -> ### Keywords: univar -> -> ### ** Examples -> -> x <- rnorm(100) -> Estimator(x, estimator = mean, name = "mean") -Evaluations of mean: --------------------- -An object of class ?Estimate? -generated by call - Estimator(x = x, estimator = mean, name = "mean") -samplesize: 100 -estimate: - mean1 -0.1088874 -> -> X <- matrix(rnorm(1000), nrow = 10) -> Estimator(X, estimator = rowMeans, name = "mean") -Evaluations of mean: --------------------- -An object of class ?Estimate? -generated by call - Estimator(x = X, estimator = rowMeans, name = "mean") -samplesize: 100 -estimate: - rowMeans1 rowMeans2 rowMeans3 rowMeans4 rowMeans5 rowMeans6 --0.10612810 0.22309674 -0.01146361 -0.20224815 0.08660978 -0.13837167 - rowMeans7 rowMeans8 rowMeans9 rowMeans10 --0.03214991 -0.02971528 -0.13027892 0.10496336 -> -> -> -> cleanEx() -> nameEx("EvenSymmetric-class") -> ### * EvenSymmetric-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: EvenSymmetric-class -> ### Title: Class for Even Functions -> ### Aliases: EvenSymmetric-class -> ### Keywords: classes -> -> ### ** Examples -> -> new("EvenSymmetric") -type of symmetry: even function -center of symmetry: -numeric(0) -> -> -> -> cleanEx() -> nameEx("EvenSymmetric") -> ### * EvenSymmetric -> -> flush(stderr()); flush(stdout()) -> -> ### Name: EvenSymmetric -> ### Title: Generating function for EvenSymmetric-class -> ### Aliases: EvenSymmetric -> ### Keywords: math -> -> ### ** Examples -> -> EvenSymmetric() -type of symmetry: even function -center of symmetry: -[1] 0 -> -> ## The function is currently defined as -> function(SymmCenter = 0){ -+ new("EvenSymmetric", SymmCenter = SymmCenter) -+ } -function (SymmCenter = 0) -{ - new("EvenSymmetric", SymmCenter = SymmCenter) -} -> -> -> -> cleanEx() -> nameEx("ExpScaleFamily") -> ### * ExpScaleFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: ExpScaleFamily -> ### Title: Generating function for exponential scale families -> ### Aliases: ExpScaleFamily -> ### Keywords: models -> -> ### ** Examples -> -> (E1 <- ExpScaleFamily()) -An object of class "ExpScaleFamily" -### name: Exponential scale family - -### distribution: Distribution Object of Class: Exp - rate: 1 -Warning in show(x) : - arithmetics on distributions are understood as operations on r.v.'s -see 'distrARITH()'; for switching off this warning see '?distroptions' - -### param: An object of class "ParamWithScaleFamParameter" -name: scale -scale: 1 -trafo: - scale -scale 1 - -### props: -[1] "The Exponential scale family is invariant under" -[2] "the group of transformations 'g(y) = scale*y'" -[3] "with scale parameter 'scale'" -> plot(E1) -> Map(L2deriv(E1)[[1]]) -[[1]] -function (x) -{ - ((x - 0)/1 * LogDeriv((x - 0)/1) - 1)/1 -} - - -> checkL2deriv(E1) -precision of centering: -1.51181e-06 -precision of Fisher information: - scale -scale -2.61793e-05 -$maximum.deviation -[1] 2.61793e-05 - -> -> -> -> cleanEx() -> nameEx("FunSymmList-class") -> ### * FunSymmList-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: FunSymmList-class -> ### Title: List of Symmetries for a List of Functions -> ### Aliases: FunSymmList-class -> ### Keywords: classes -> -> ### ** Examples -> -> new("FunSymmList", list(NonSymmetric(), EvenSymmetric(SymmCenter = 1), -+ OddSymmetric(SymmCenter = 2))) -An object of class "FunSymmList" -[[1]] -type of symmetry: non-symmetric function -NULL - -[[2]] -type of symmetry: even function -center of symmetry: -[1] 1 - -[[3]] -type of symmetry: odd function -center of symmetry: -[1] 2 - -> -> -> -> cleanEx() -> nameEx("FunSymmList") -> ### * FunSymmList -> -> flush(stderr()); flush(stdout()) -> -> ### Name: FunSymmList -> ### Title: Generating function for FunSymmList-class -> ### Aliases: FunSymmList -> ### Keywords: math -> -> ### ** Examples -> -> FunSymmList(NonSymmetric(), EvenSymmetric(SymmCenter = 1), -+ OddSymmetric(SymmCenter = 2)) -An object of class "FunSymmList" -[[1]] -type of symmetry: non-symmetric function -NULL - -[[2]] -type of symmetry: even function -center of symmetry: -[1] 1 - -[[3]] -type of symmetry: odd function -center of symmetry: -[1] 2 - -> -> ## The function is currently defined as -> function (...){ -+ new("FunSymmList", list(...)) -+ } -function (...) -{ - new("FunSymmList", list(...)) -} -> -> -> -> cleanEx() -> nameEx("GammaFamily") -> ### * GammaFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: GammaFamily -> ### Title: Generating function for Gamma families -> ### Aliases: GammaFamily -> ### Keywords: models -> -> ### ** Examples -> -> (G1 <- GammaFamily()) -An object of class "GammaFamily" -### name: Gamma family - -### distribution: Distribution Object of Class: Gammad - shape: 1 - scale: 1 - -### param: An object of class "ParamFamParameter" -name: scale and shape -scale: 1 -shape: 1 -trafo: - scale shape -scale 1 0 -shape 0 1 -Shape parameter must not be negative. - -### props: -[1] "The Gamma family is scale invariant via the parametrization" -[2] "'(nu,shape)=(log(scale),shape)'" -> FisherInfo(G1) -An object of class "PosDefSymmMatrix" - scale shape -scale 1 1.000000 -shape 1 1.644934 -> checkL2deriv(G1) -precision of centering: -1.51181e-06 1.312514e-06 -precision of Fisher information: - scale shape -scale -2.617930e-05 -7.165188e-06 -shape -7.165188e-06 -2.862712e-05 -$maximum.deviation -[1] 2.862712e-05 - -> -> -> -> cleanEx() -> nameEx("InfoNorm") -> ### * InfoNorm -> -> flush(stderr()); flush(stdout()) -> -> ### Name: InfoNorm -> ### Title: Generating function for InfoNorm-class -> ### Aliases: InfoNorm -> ### Keywords: robust -> -> ### ** Examples -> -> InfoNorm() -An object of class "InfoNorm" -Slot "QuadForm": -An object of class "PosSemDefSymmMatrix" - [,1] -[1,] 1 - -Slot "name": -[1] "Information matrix Norm" - -Slot "fct": -function (x) -QuadFormNorm(x, A = A) - - - -> -> ## The function is currently defined as -> function(){ new("InfoNorm") } -function () -{ - new("InfoNorm") -} -> -> -> -> cleanEx() -> nameEx("L2GroupFamily-class") -> ### * L2GroupFamily-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2GroupParamFamily-class -> ### Title: L2 differentiable parametric group family -> ### Aliases: L2GroupParamFamily-class LogDeriv -> ### LogDeriv,L2GroupParamFamily-method LogDeriv<- -> ### LogDeriv<-,L2GroupParamFamily-method -> ### Keywords: classes models -> -> ### ** Examples -> -> F1 <- new("L2GroupParamFamily") -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2LocationFamily-class") -> ### * L2LocationFamily-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2LocationFamily-class -> ### Title: L2 differentiable parametric group family -> ### Aliases: L2LocationFamily-class -> ### Keywords: classes models -> -> ### ** Examples -> -> F1 <- new("L2LocationFamily") -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2LocationFamily") -> ### * L2LocationFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2LocationFamily -> ### Title: Generating function for L2LocationFamily-class -> ### Aliases: L2LocationFamily -> ### Keywords: models -> -> ### ** Examples -> -> F1 <- L2LocationFamily() -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2LocationScaleFamily-class") -> ### * L2LocationScaleFamily-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2LocationScaleFamily-class -> ### Title: L2 differentiable parametric group family -> ### Aliases: L2LocationScaleFamily-class -> ### Keywords: classes models -> -> ### ** Examples -> -> F1 <- new("L2LocationScaleFamily") -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2LocationScaleFamily") -> ### * L2LocationScaleFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2LocationScaleFamily -> ### Title: Generating function for L2LocationScaleFamily-class -> ### Aliases: L2LocationScaleFamily -> ### Keywords: models -> -> ### ** Examples -> -> F1 <- L2LocationScaleFamily() -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2LocationUnknownScaleFamily") -> ### * L2LocationUnknownScaleFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2LocationUnknownScaleFamily -> ### Title: Generating function for L2LocationScaleFamily-class in nuisance -> ### situation -> ### Aliases: L2LocationUnknownScaleFamily -> ### Keywords: models -> -> ### ** Examples -> -> F1 <- L2LocationUnknownScaleFamily() -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2ParamFamily-class") -> ### * L2ParamFamily-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2ParamFamily-class -> ### Title: L2 differentiable parametric family -> ### Aliases: plot plot-methods L2ParamFamily-class FisherInfo -> ### FisherInfo,L2ParamFamily,missing-method -> ### FisherInfo,L2ParamFamily,ParamFamParameter-method L2deriv -> ### L2deriv,L2ParamFamily,missing-method -> ### L2deriv,L2ParamFamily,ParamFamParameter-method L2derivSymm -> ### L2derivSymm,L2ParamFamily-method L2derivDistr -> ### L2derivDistr,L2ParamFamily-method L2derivDistrSymm -> ### L2derivDistrSymm,L2ParamFamily-method -> ### checkL2deriv,L2ParamFamily-method -> ### E,L2ParamFamily,EuclRandVariable,missing-method -> ### E,L2ParamFamily,EuclRandMatrix,missing-method -> ### E,L2ParamFamily,EuclRandVarList,missing-method -> ### plot,L2ParamFamily,missing-method -> ### Keywords: classes models -> -> ### ** Examples -> -> F1 <- new("L2ParamFamily") -> plot(F1) -> -> ## selection of subpanels for plotting -> F2 <- L2LocationScaleFamily() -> layout(matrix(c(1,2,3,3), nrow=2, byrow=TRUE)) -> plot(F2,mfColRow = FALSE, -+ to.draw.arg=c("p","q","loc")) -> plot(F2,mfColRow = FALSE, inner=list("empirical cdf","pseudo-inverse", -+ "L2-deriv, loc.part"), to.draw.arg=c("p","q","loc")) -> -> -> -> cleanEx() -> nameEx("L2ParamFamily") -> ### * L2ParamFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2ParamFamily -> ### Title: Generating function for L2ParamFamily-class -> ### Aliases: L2ParamFamily -> ### Keywords: models -> -> ### ** Examples -> -> F1 <- L2ParamFamily() -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2ScaleFamily-class") -> ### * L2ScaleFamily-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2ScaleFamily-class -> ### Title: L2 differentiable parametric group family -> ### Aliases: L2ScaleFamily-class -> ### Keywords: classes models -> -> ### ** Examples -> -> F1 <- new("L2ScaleFamily") -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2ScaleFamily") -> ### * L2ScaleFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2ScaleFamily -> ### Title: Generating function for L2ScaleFamily-class -> ### Aliases: L2ScaleFamily -> ### Keywords: models -> -> ### ** Examples -> -> F1 <- L2ScaleFamily() -> plot(F1) -> -> -> -> cleanEx() -> nameEx("L2ScaleUnknownLocationFamily") -> ### * L2ScaleUnknownLocationFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: L2ScaleUnknownLocationFamily -> ### Title: Generating function for L2LocationScaleFamily-class in nuisance -> ### situation -> ### Aliases: L2ScaleUnknownLocationFamily -> ### Keywords: models -> -> ### ** Examples -> -> F1 <- L2ScaleUnknownLocationFamily() -> plot(F1) -> -> -> -> cleanEx() -> nameEx("LnormScaleFamily") -> ### * LnormScaleFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: LnormScaleFamily -> ### Title: Generating function for lognormal scale families -> ### Aliases: LnormScaleFamily -> ### Keywords: models -> -> ### ** Examples -> -> (L1 <- LnormScaleFamily()) -An object of class "LnormScaleFamily" -### name: lognormal scale family - -### distribution: Distribution Object of Class: Lnorm - meanlog: 0 - sdlog: 1 -Warning in show(x) : - arithmetics on distributions are understood as operations on r.v.'s -see 'distrARITH()'; for switching off this warning see '?distroptions' - -### param: An object of class "ParamWithScaleFamParameter" -name: scale -meanlog: 1 -fixed part of param.: - : 0 -trafo: - scale -scale 1 - -### props: -[1] "The lognormal scale family is invariant under" -[2] "the group of transformations 'g(y) = scale*y'" -[3] "with scale parameter 'scale'" -> plot(L1) -> Map(L2deriv(L1)[[1]]) -[[1]] -function (x) -{ - ((x - 0)/1 * LogDeriv((x - 0)/1) - 1)/1 -} - - -> checkL2deriv(L1) -precision of centering: -0.003003394 -precision of Fisher information: - meanlog -meanlog -0.01027919 -$maximum.deviation -[1] 0.01027919 - -> -> -> -> cleanEx() -> nameEx("MCEstimate-class") -> ### * MCEstimate-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: MCEstimate-class -> ### Title: MCEstimate-class. -> ### Aliases: MCEstimate-class criterion criterion,MCEstimate-method -> ### criterion.fct criterion.fct,MCEstimate-method -> ### startPar,MCEstimate-method method method,MCEstimate-method optimwarn -> ### optimwarn,MCEstimate-method criterion<- criterion<-,MCEstimate-method -> ### coerce,MCEstimate,mle-method show,MCEstimate-method -> ### profile,MCEstimate-method -> ### Keywords: classes -> -> ### ** Examples -> -> ## (empirical) Data -> x <- rgamma(50, scale = 0.5, shape = 3) -> -> ## parametric family of probability measures -> G <- GammaFamily(scale = 1, shape = 2) -> -> MDEstimator(x, G) -Evaluations of Minimum Kolmogorov distance estimate: ----------------------------------------------------- -An object of class ?Estimate? -generated by call - MDEstimator(x = x, ParamFamily = G) -samplesize: 50 -estimate: - scale shape -0.3398645 4.2654569 -Criterion: -Kolmogorov distance - 0.06350364 -> (m <- MLEstimator(x, G)) -Evaluations of Maximum likelihood estimate: -------------------------------------------- -An object of class ?Estimate? -generated by call - MLEstimator(x = x, ParamFamily = G) -samplesize: 50 -estimate: - scale shape - 0.34200800 4.06028564 - (0.07002713) (0.78099026) -asymptotic (co)variance (multiplied with samplesize): - scale shape -scale 0.2451899 -2.568863 -shape -2.5688629 30.497289 -Criterion: -negative log-likelihood - 47.9651 -> m.mle <- as(m,"mle") -> par(mfrow=c(1,2)) -> profileM <- profile(m) -> ## plot-profile throws an error -> -> -> -> graphics::par(get("par.postscript", pos = 'CheckExEnv')) -> cleanEx() -> nameEx("MCEstimator") -> ### * MCEstimator -> -> flush(stderr()); flush(stdout()) -> -> ### Name: MCEstimator -> ### Title: Function to compute minimum criterion estimates -> ### Aliases: MCEstimator -> ### Keywords: univar -> -> ### ** Examples -> -> ## (empirical) Data -> x <- rgamma(50, scale = 0.5, shape = 3) -> -> ## parametric family of probability measures -> G <- GammaFamily(scale = 1, shape = 2) -> -> ## Maximum Likelihood estimator -> ## Note: you can directly use function MLEstimator! -> negLoglikelihood <- function(x, Distribution){ -+ res <- -sum(log(Distribution at d(x))) -+ names(res) <- "Negative Log-Likelihood" -+ return(res) -+ } -> MCEstimator(x = x, ParamFamily = G, criterion = negLoglikelihood) -Evaluations of Minimum criterion estimate: ------------------------------------------- -An object of class ?Estimate? -generated by call - MCEstimator(x = x, ParamFamily = G, criterion = negLoglikelihood) -samplesize: 50 -estimate: - scale shape - 0.34200800 4.06028564 - (0.07002713) (0.78099026) -asymptotic (co)variance (multiplied with samplesize): - scale shape -scale 0.2451899 -2.568863 -shape -2.5688629 30.497289 -Criterion: - -47.9651 -> -> ## Kolmogorov(-Smirnov) minimum distance estimator -> ## Note: you can also use function MDEstimator! -> MCEstimator(x = x, ParamFamily = G, criterion = KolmogorovDist, -+ crit.name = "Kolmogorov distance") -Evaluations of Minimum Kolmogorov distance estimate: ----------------------------------------------------- -An object of class ?Estimate? -generated by call - MCEstimator(x = x, ParamFamily = G, criterion = KolmogorovDist, - crit.name = "Kolmogorov distance") -samplesize: 50 -estimate: - scale shape - 0.33986453 4.26545692 - (0.06950044) (0.82190816) -asymptotic (co)variance (multiplied with samplesize): - scale shape -scale 0.2415156 -2.691268 -shape -2.6912675 33.776651 -Criterion: -Kolmogorov distance - 0.06350364 -> -> ## Total variation minimum distance estimator -> ## Note: you can also use function MDEstimator! -> ## discretize Gamma distribution -> MCEstimator(x = x, ParamFamily = G, criterion = TotalVarDist, -+ crit.name = "Total variation distance") -Evaluations of Minimum Total variation distance estimate: ---------------------------------------------------------- -An object of class ?Estimate? -generated by call - MCEstimator(x = x, ParamFamily = G, criterion = TotalVarDist, - crit.name = "Total variation distance") -samplesize: 50 -estimate: - scale shape - 0.28296871 5.01973059 - (0.05765312) (0.97241994) -asymptotic (co)variance (multiplied with samplesize): - scale shape -scale 0.1661941 -2.665236 -shape -2.6652363 47.280027 -Criterion: -Total variation distance - 0.4866141 -> -> ## or smooth empirical distribution (takes some time!) -> #MCEstimator(x = x, ParamFamily = G, criterion = TotalVarDist, -> # asis.smooth.discretize = "smooth", crit.name = "Total variation distance") -> -> ## Hellinger minimum distance estimator -> ## Note: you can also use function MDEstimator! -> ## discretize Gamma distribution -> distroptions(DistrResolution = 1e-8) -> MCEstimator(x = x, ParamFamily = G, criterion = HellingerDist, -+ crit.name = "Hellinger Distance", startPar = c(1,2)) -Evaluations of Minimum Hellinger Distance estimate: ---------------------------------------------------- -An object of class ?Estimate? -generated by call - MCEstimator(x = x, ParamFamily = G, criterion = HellingerDist, - crit.name = "Hellinger Distance", startPar = c(1, 2)) -samplesize: 50 -estimate: - scale shape - 1.0574423 1.6836445 - (0.2257873) (0.3091343) -asymptotic (co)variance (multiplied with samplesize): - scale shape -scale 2.548996 -3.001032 -shape -3.001032 4.778201 -Criterion: -Hellinger Distance - 0.3782642 -> distroptions(DistrResolution = 1e-6) -> -> ## or smooth empirical distribution (takes some time!) -> #MCEstimator(x = x, ParamFamily = G, criterion = HellingerDist, -> # asis.smooth.discretize = "smooth", crit.name = "Hellinger distance") -> -> -> -> cleanEx() -> nameEx("MDEstimator") -> ### * MDEstimator -> -> flush(stderr()); flush(stdout()) -> [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 905 From noreply at r-forge.r-project.org Wed Sep 11 18:32:15 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Sep 2013 18:32:15 +0200 (CEST) Subject: [Distr-commits] r906 - in pkg/distr: . R inst src Message-ID: <20130911163215.B5D0F1813BB@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-11 18:32:15 +0200 (Wed, 11 Sep 2013) New Revision: 906 Added: pkg/distr/src/ pkg/distr/src/ks.c Modified: pkg/distr/NAMESPACE pkg/distr/R/internals-qqplot.R pkg/distr/inst/NEWS Log: + in order to avoid calls to non-exported C-Code from pkg stats (for Kolmogorov-distribution) we integrated R-Core's C-code from /src/library/stats/src/ks.c rev60573 (with small changes to make it self-contained) to src folder of this pkg; in addition, we now use the shakier .C - interface again... Modified: pkg/distr/NAMESPACE =================================================================== --- pkg/distr/NAMESPACE 2013-09-11 13:26:21 UTC (rev 905) +++ pkg/distr/NAMESPACE 2013-09-11 16:32:15 UTC (rev 906) @@ -1,3 +1,4 @@ +useDynLib("distr") import("methods") import("stats") importFrom("graphics", "plot") Modified: pkg/distr/R/internals-qqplot.R =================================================================== --- pkg/distr/R/internals-qqplot.R 2013-09-11 13:26:21 UTC (rev 905) +++ pkg/distr/R/internals-qqplot.R 2013-09-11 16:32:15 UTC (rev 906) @@ -86,13 +86,17 @@ .C("pkolmogorov2x", p = as.double(p0), as.integer(n), PACKAGE = "stats")$p }else function(p0,n){ - .Call(stats:::C_pKolmogorov2x, p0, n) #, PACKAGE = "stats") +# .Call(stats:::C_pKolmogorov2x, p0, n) #, PACKAGE = "stats") + .C("pkolmogorov2x", p = as.double(p0), + as.integer(n))$p } .pks2 <- if(getRversion()<"2.16.0") function(x, tol){ .C("pkstwo", as.integer(1), p = as.double(x), as.double(tol), PACKAGE = "stats")$p }else function(x, tol){ - .Call(stats:::C_pKS2, p = x, tol) #, PACKAGE = "stats") +# .Call(stats:::C_pKS2, p = x, tol) #, PACKAGE = "stats") + .C("pkstwo", as.integer(1), + p = as.double(x), as.double(tol))$p } Modified: pkg/distr/inst/NEWS =================================================================== --- pkg/distr/inst/NEWS 2013-09-11 13:26:21 UTC (rev 905) +++ pkg/distr/inst/NEWS 2013-09-11 16:32:15 UTC (rev 906) @@ -20,7 +20,11 @@ + added .Rbuildignore + exported some routines which had been internal so far to avoid calls by ::: - ++ in order to avoid calls to non-exported C-Code from pkg stats + (for Kolmogorov-distribution) we integrated R-Core's C-code from + /src/library/stats/src/ks.c rev60573 + (with small changes to make it self-contained) to src folder of this pkg; + in addition, we now use the shakier .C - interface again... BUGFIXES: + fixed .makedotsPt -issue discovered by Gerald --> thx + moved generics to "distribution" and "samplesize" to pkg distr to avoid Added: pkg/distr/src/ks.c =================================================================== --- pkg/distr/src/ks.c (rev 0) +++ pkg/distr/src/ks.c 2013-09-11 16:32:15 UTC (rev 906) @@ -0,0 +1,261 @@ +/* + * taken from R Core: /src/library/stats/src/ks.c rev60573 + */ +/* + * R : A Computer Language for Statistical Data Analysis + * Copyright (C) 1999-2012 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, a copy is available at + * http://www.r-project.org/Licenses/ + */ + +/* ks.c + Compute the asymptotic distribution of the one- and two-sample + two-sided Kolmogorov-Smirnov statistics, and the exact distributions + in the two-sided one-sample and two-sample cases. +*/ + +#include +#include +#define PI 3.141592653589793 +#ifndef M_1_SQRT_2PI +#define M_1_SQRT_2PI 0.398942280401432677939946059934 /* 1/sqrt(2pi) */ +#endif +#ifndef M_PI_2 +#define M_PI_2 1.570796326794896619231321691640 /* pi/2 */ +#endif + +#ifndef M_PI_4 +#define M_PI_4 0.785398163397448309615660845820 /* pi/4 */ +#endif + +/* + * taken from R Core: /src/include/R_ext/RS.h rev60573 + */ +extern void *R_chk_calloc(size_t, size_t); +extern void *R_chk_realloc(void *, size_t); +extern void R_chk_free(void *); + +/* + * taken from R Core: /src/main/memory.c rev60573 + */ +void *R_chk_calloc(size_t nelem, size_t elsize) +{ + void *p; + p = calloc(nelem, elsize); + return(p); +} + +void *R_chk_realloc(void *ptr, size_t size) +{ + void *p; + /* Protect against broken realloc */ + if(ptr) p = realloc(ptr, size); else p = malloc(size); + return(p); +} + +void R_chk_free(void *ptr) +{ + /* S-PLUS warns here, but there seems no reason to do so */ + /* if(!ptr) warning("attempt to free NULL pointer by Free"); */ + if(ptr) free(ptr); /* ANSI C says free has no effect on NULL, but + better to be safe here */ +} + +#define Calloc(n, t) (t *) R_chk_calloc( (size_t) (n), sizeof(t) ) +#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) ) +#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) + +/*static void pkolmogorov2x(double *x, int *n); +static void pkstwo(int n, double *x, double tol); +*/ +static double K(int n, double d); +static void m_multiply(double *A, double *B, double *C, int m); +static void m_power(double *A, int eA, double *V, int *eV, int m, int n); + +/* Two-sample two-sided asymptotic distribution */ +void +pkstwo(int *n, double *x, double *tol) +{ +/* x[1:n] is input and output + * + * Compute + * \sum_{k=-\infty}^\infty (-1)^k e^{-2 k^2 x^2} + * = 1 + 2 \sum_{k=1}^\infty (-1)^k e^{-2 k^2 x^2} + * = \frac{\sqrt{2\pi}}{x} \sum_{k=1}^\infty \exp(-(2k-1)^2\pi^2/(8x^2)) + * + * See e.g. J. Durbin (1973), Distribution Theory for Tests Based on the + * Sample Distribution Function. SIAM. + * + * The 'standard' series expansion obviously cannot be used close to 0; + * we use the alternative series for x < 1, and a rather crude estimate + * of the series remainder term in this case, in particular using that + * ue^(-lu^2) \le e^(-lu^2 + u) \le e^(-(l-1)u^2 - u^2+u) \le e^(-(l-1)) + * provided that u and l are >= 1. + * + * (But note that for reasonable tolerances, one could simply take 0 as + * the value for x < 0.2, and use the standard expansion otherwise.) + * + */ + double new, old, s, w, z; + int i, k, k_max; + + k_max = (int) sqrt(2 - log(*tol)); + + for(i = 0; i < *n; i++) { + if(x[i] < 1) { + z = - (M_PI_2 * M_PI_4) / (x[i] * x[i]); + w = log(x[i]); + s = 0; + for(k = 1; k < k_max; k += 2) { + s += exp(k * k * z - w); + } + x[i] = s / M_1_SQRT_2PI; + } + else { + z = -2 * x[i] * x[i]; + s = -1; + k = 1; + old = 0; + new = 1; + while(fabs(old - new) > *tol) { + old = new; + new += 2 * s * exp(z * k * k); + s *= -1; + k++; + } + x[i] = new; + } + } +} + +static double +K(int n, double d) +{ + /* Compute Kolmogorov's distribution. + Code published in + George Marsaglia and Wai Wan Tsang and Jingbo Wang (2003), + "Evaluating Kolmogorov's distribution". + Journal of Statistical Software, Volume 8, 2003, Issue 18. + URL: http://www.jstatsoft.org/v08/i18/. + */ + + int k, m, i, j, g, eH, eQ; + double h, s, *H, *Q; + + /* + The faster right-tail approximation is omitted here. + s = d*d*n; + if(s > 7.24 || (s > 3.76 && n > 99)) + return 1-2*exp(-(2.000071+.331/sqrt(n)+1.409/n)*s); + */ + k = (int) (n * d) + 1; + m = 2 * k - 1; + h = k - n * d; + H = (double*) Calloc(m * m, double); + Q = (double*) Calloc(m * m, double); + for(i = 0; i < m; i++) + for(j = 0; j < m; j++) + if(i - j + 1 < 0) + H[i * m + j] = 0; + else + H[i * m + j] = 1; + for(i = 0; i < m; i++) { + H[i * m] -= pow(h, i + 1); + H[(m - 1) * m + i] -= pow(h, (m - i)); + } + H[(m - 1) * m] += ((2 * h - 1 > 0) ? pow(2 * h - 1, m) : 0); + for(i = 0; i < m; i++) + for(j=0; j < m; j++) + if(i - j + 1 > 0) + for(g = 1; g <= i - j + 1; g++) + H[i * m + j] /= g; + eH = 0; + m_power(H, eH, Q, &eQ, m, n); + s = Q[(k - 1) * m + k - 1]; + for(i = 1; i <= n; i++) { + s = s * i / n; + if(s < 1e-140) { + s *= 1e140; + eQ -= 140; + } + } + s *= pow(10., eQ); + Free(H); + Free(Q); + return(s); +} + +static void +m_multiply(double *A, double *B, double *C, int m) +{ + /* Auxiliary routine used by K(). + Matrix multiplication. + */ + int i, j, k; + double s; + for(i = 0; i < m; i++) + for(j = 0; j < m; j++) { + s = 0.; + for(k = 0; k < m; k++) + s+= A[i * m + k] * B[k * m + j]; + C[i * m + j] = s; + } +} + +static void +m_power(double *A, int eA, double *V, int *eV, int m, int n) +{ + /* Auxiliary routine used by K(). + Matrix power. + */ + double *B; + int eB , i; + + if(n == 1) { + for(i = 0; i < m * m; i++) + V[i] = A[i]; + *eV = eA; + return; + } + m_power(A, eA, V, eV, m, n / 2); + B = (double*) Calloc(m * m, double); + m_multiply(V, V, B, m); + eB = 2 * (*eV); + if((n % 2) == 0) { + for(i = 0; i < m * m; i++) + V[i] = B[i]; + *eV = eB; + } + else { + m_multiply(A, B, V, m); + *eV = eA + eB; + } + if(V[(m / 2) * m + (m / 2)] > 1e140) { + for(i = 0; i < m * m; i++) + V[i] = V[i] * 1e-140; + *eV += 140; + } + Free(B); +} +/* + * taken from R Core: /src/library/stats/src/ks.c rev56090 +*/ +void pkolmogorov2x(double *x, int *n) +{ + /* x is input and output. */ + + *x = K(*n, *x); +} + From noreply at r-forge.r-project.org Wed Sep 11 18:47:08 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Sep 2013 18:47:08 +0200 (CEST) Subject: [Distr-commits] r907 - in branches/distr-2.5/pkg/distr: . inst src Message-ID: <20130911164708.3BE3F185D82@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-11 18:47:07 +0200 (Wed, 11 Sep 2013) New Revision: 907 Added: branches/distr-2.5/pkg/distr/src/ branches/distr-2.5/pkg/distr/src/ks.c Modified: branches/distr-2.5/pkg/distr/NAMESPACE branches/distr-2.5/pkg/distr/inst/NEWS Log: [distr] backported changes in trunc to devel Modified: branches/distr-2.5/pkg/distr/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-11 16:32:15 UTC (rev 906) +++ branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-11 16:47:07 UTC (rev 907) @@ -1,3 +1,4 @@ +useDynLib("distr") import("methods") import("stats") importFrom("graphics", "plot") Modified: branches/distr-2.5/pkg/distr/inst/NEWS =================================================================== --- branches/distr-2.5/pkg/distr/inst/NEWS 2013-09-11 16:32:15 UTC (rev 906) +++ branches/distr-2.5/pkg/distr/inst/NEWS 2013-09-11 16:47:07 UTC (rev 907) @@ -20,7 +20,11 @@ + added .Rbuildignore + exported some routines which had been internal so far to avoid calls by ::: - ++ in order to avoid calls to non-exported C-Code from pkg stats + (for Kolmogorov-distribution) we integrated R-Core's C-code from + /src/library/stats/src/ks.c rev60573 + (with small changes to make it self-contained) to src folder of this pkg; + in addition, we now use the shakier .C - interface again... BUGFIXES: + fixed .makedotsPt -issue discovered by Gerald --> thx + moved generics to "distribution" and "samplesize" to pkg distr to avoid Added: branches/distr-2.5/pkg/distr/src/ks.c =================================================================== --- branches/distr-2.5/pkg/distr/src/ks.c (rev 0) +++ branches/distr-2.5/pkg/distr/src/ks.c 2013-09-11 16:47:07 UTC (rev 907) @@ -0,0 +1,261 @@ +/* + * taken from R Core: /src/library/stats/src/ks.c rev60573 + */ +/* + * R : A Computer Language for Statistical Data Analysis + * Copyright (C) 1999-2012 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, a copy is available at + * http://www.r-project.org/Licenses/ + */ + +/* ks.c + Compute the asymptotic distribution of the one- and two-sample + two-sided Kolmogorov-Smirnov statistics, and the exact distributions + in the two-sided one-sample and two-sample cases. +*/ + +#include +#include +#define PI 3.141592653589793 +#ifndef M_1_SQRT_2PI +#define M_1_SQRT_2PI 0.398942280401432677939946059934 /* 1/sqrt(2pi) */ +#endif +#ifndef M_PI_2 +#define M_PI_2 1.570796326794896619231321691640 /* pi/2 */ +#endif + +#ifndef M_PI_4 +#define M_PI_4 0.785398163397448309615660845820 /* pi/4 */ +#endif + +/* + * taken from R Core: /src/include/R_ext/RS.h rev60573 + */ +extern void *R_chk_calloc(size_t, size_t); +extern void *R_chk_realloc(void *, size_t); +extern void R_chk_free(void *); + +/* + * taken from R Core: /src/main/memory.c rev60573 + */ +void *R_chk_calloc(size_t nelem, size_t elsize) +{ + void *p; + p = calloc(nelem, elsize); + return(p); +} + +void *R_chk_realloc(void *ptr, size_t size) +{ + void *p; + /* Protect against broken realloc */ + if(ptr) p = realloc(ptr, size); else p = malloc(size); + return(p); +} + +void R_chk_free(void *ptr) +{ + /* S-PLUS warns here, but there seems no reason to do so */ + /* if(!ptr) warning("attempt to free NULL pointer by Free"); */ + if(ptr) free(ptr); /* ANSI C says free has no effect on NULL, but + better to be safe here */ +} + +#define Calloc(n, t) (t *) R_chk_calloc( (size_t) (n), sizeof(t) ) +#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) ) +#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) + +/*static void pkolmogorov2x(double *x, int *n); +static void pkstwo(int n, double *x, double tol); +*/ +static double K(int n, double d); +static void m_multiply(double *A, double *B, double *C, int m); +static void m_power(double *A, int eA, double *V, int *eV, int m, int n); + +/* Two-sample two-sided asymptotic distribution */ +void +pkstwo(int *n, double *x, double *tol) +{ +/* x[1:n] is input and output + * + * Compute + * \sum_{k=-\infty}^\infty (-1)^k e^{-2 k^2 x^2} + * = 1 + 2 \sum_{k=1}^\infty (-1)^k e^{-2 k^2 x^2} + * = \frac{\sqrt{2\pi}}{x} \sum_{k=1}^\infty \exp(-(2k-1)^2\pi^2/(8x^2)) + * + * See e.g. J. Durbin (1973), Distribution Theory for Tests Based on the + * Sample Distribution Function. SIAM. + * + * The 'standard' series expansion obviously cannot be used close to 0; + * we use the alternative series for x < 1, and a rather crude estimate + * of the series remainder term in this case, in particular using that + * ue^(-lu^2) \le e^(-lu^2 + u) \le e^(-(l-1)u^2 - u^2+u) \le e^(-(l-1)) + * provided that u and l are >= 1. + * + * (But note that for reasonable tolerances, one could simply take 0 as + * the value for x < 0.2, and use the standard expansion otherwise.) + * + */ + double new, old, s, w, z; + int i, k, k_max; + + k_max = (int) sqrt(2 - log(*tol)); + + for(i = 0; i < *n; i++) { + if(x[i] < 1) { + z = - (M_PI_2 * M_PI_4) / (x[i] * x[i]); + w = log(x[i]); + s = 0; + for(k = 1; k < k_max; k += 2) { + s += exp(k * k * z - w); + } + x[i] = s / M_1_SQRT_2PI; + } + else { + z = -2 * x[i] * x[i]; + s = -1; + k = 1; + old = 0; + new = 1; + while(fabs(old - new) > *tol) { + old = new; + new += 2 * s * exp(z * k * k); + s *= -1; + k++; + } + x[i] = new; + } + } +} + +static double +K(int n, double d) +{ + /* Compute Kolmogorov's distribution. + Code published in + George Marsaglia and Wai Wan Tsang and Jingbo Wang (2003), + "Evaluating Kolmogorov's distribution". + Journal of Statistical Software, Volume 8, 2003, Issue 18. + URL: http://www.jstatsoft.org/v08/i18/. + */ + + int k, m, i, j, g, eH, eQ; + double h, s, *H, *Q; + + /* + The faster right-tail approximation is omitted here. + s = d*d*n; + if(s > 7.24 || (s > 3.76 && n > 99)) + return 1-2*exp(-(2.000071+.331/sqrt(n)+1.409/n)*s); + */ + k = (int) (n * d) + 1; + m = 2 * k - 1; + h = k - n * d; + H = (double*) Calloc(m * m, double); + Q = (double*) Calloc(m * m, double); + for(i = 0; i < m; i++) + for(j = 0; j < m; j++) + if(i - j + 1 < 0) + H[i * m + j] = 0; + else + H[i * m + j] = 1; + for(i = 0; i < m; i++) { + H[i * m] -= pow(h, i + 1); + H[(m - 1) * m + i] -= pow(h, (m - i)); + } + H[(m - 1) * m] += ((2 * h - 1 > 0) ? pow(2 * h - 1, m) : 0); + for(i = 0; i < m; i++) + for(j=0; j < m; j++) + if(i - j + 1 > 0) + for(g = 1; g <= i - j + 1; g++) + H[i * m + j] /= g; + eH = 0; + m_power(H, eH, Q, &eQ, m, n); + s = Q[(k - 1) * m + k - 1]; + for(i = 1; i <= n; i++) { + s = s * i / n; + if(s < 1e-140) { + s *= 1e140; + eQ -= 140; + } + } + s *= pow(10., eQ); + Free(H); + Free(Q); + return(s); +} + +static void +m_multiply(double *A, double *B, double *C, int m) +{ + /* Auxiliary routine used by K(). + Matrix multiplication. + */ + int i, j, k; + double s; + for(i = 0; i < m; i++) + for(j = 0; j < m; j++) { + s = 0.; + for(k = 0; k < m; k++) + s+= A[i * m + k] * B[k * m + j]; + C[i * m + j] = s; + } +} + +static void +m_power(double *A, int eA, double *V, int *eV, int m, int n) +{ + /* Auxiliary routine used by K(). + Matrix power. + */ + double *B; + int eB , i; + + if(n == 1) { + for(i = 0; i < m * m; i++) + V[i] = A[i]; + *eV = eA; + return; + } + m_power(A, eA, V, eV, m, n / 2); + B = (double*) Calloc(m * m, double); + m_multiply(V, V, B, m); + eB = 2 * (*eV); + if((n % 2) == 0) { + for(i = 0; i < m * m; i++) + V[i] = B[i]; + *eV = eB; + } + else { + m_multiply(A, B, V, m); + *eV = eA + eB; + } + if(V[(m / 2) * m + (m / 2)] > 1e140) { + for(i = 0; i < m * m; i++) + V[i] = V[i] * 1e-140; + *eV += 140; + } + Free(B); +} +/* + * taken from R Core: /src/library/stats/src/ks.c rev56090 +*/ +void pkolmogorov2x(double *x, int *n) +{ + /* x is input and output. */ + + *x = K(*n, *x); +} + From noreply at r-forge.r-project.org Thu Sep 12 10:04:46 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Sep 2013 10:04:46 +0200 (CEST) Subject: [Distr-commits] r908 - branches branches/distr-2.5/pkg/distr branches/distr-2.5/pkg/distr/R branches/distr-2.5/pkg/distr/man branches/distr-2.5/pkg/distrMod branches/distr-2.5/pkg/distrSim branches/distr-2.5/pkg/utils pkg/distr pkg/distr/R pkg/distr/inst pkg/distr/man pkg/distr/src pkg/distrMod pkg/distrSim Message-ID: <20130912080446.F3C8C1811FD@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-12 10:04:46 +0200 (Thu, 12 Sep 2013) New Revision: 908 Added: branches/distr-2.6/ Modified: branches/distr-2.5/pkg/distr/DESCRIPTION branches/distr-2.5/pkg/distr/NAMESPACE branches/distr-2.5/pkg/distr/R/AllGenerics.R branches/distr-2.5/pkg/distr/man/internalGenerics.Rd branches/distr-2.5/pkg/distrMod/DESCRIPTION branches/distr-2.5/pkg/distrSim/DESCRIPTION branches/distr-2.5/pkg/utils/DESCRIPTIONutils.R pkg/distr/DESCRIPTION pkg/distr/R/AllGenerics.R pkg/distr/R/internals-qqplot.R pkg/distr/inst/NEWS pkg/distr/man/internalGenerics.Rd pkg/distr/src/ks.c pkg/distrMod/DESCRIPTION pkg/distrSim/DESCRIPTION Log: distr: reverted the changes in /src/library/stats/src/ks.c: including R.h etc is easier than thought... Modified: branches/distr-2.5/pkg/distr/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distr/DESCRIPTION 2013-09-11 16:47:07 UTC (rev 907) +++ branches/distr-2.5/pkg/distr/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) @@ -1,9 +1,13 @@ Package: distr -Version: 2.5.1 -Date: 2013-01-09 +Version: 2.5.2 +Date: 2013-09-12 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions -Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla +Authors at R: c(person("Florian", "Camphausen", role=c("cre")), + person("Matthias", "Kohl", role=c("aut", "cph")), + person("Peter", "Ruckdeschel", role=c("aut", "cph")), + person("Thomas", "Stabla", role=c("aut", "cph")), + person("R Core Team", role = c("ctb", "cph"))) Maintainer: Peter Ruckdeschel Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils Suggests: distrEx Modified: branches/distr-2.5/pkg/distr/NAMESPACE =================================================================== --- branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-11 16:47:07 UTC (rev 907) +++ branches/distr-2.5/pkg/distr/NAMESPACE 2013-09-12 08:04:46 UTC (rev 908) @@ -97,4 +97,4 @@ exportMethods("qqplot") export(".isEqual",".isEqual01", ".inArgs", ".fillList", ".presubs", ".makeLenAndOrder", ".DistrCollapse") -export("samplesize", "distribution") \ No newline at end of file +export("samplesize", "samplesize<-", "distribution") \ No newline at end of file Modified: branches/distr-2.5/pkg/distr/R/AllGenerics.R =================================================================== --- branches/distr-2.5/pkg/distr/R/AllGenerics.R 2013-09-11 16:47:07 UTC (rev 907) +++ branches/distr-2.5/pkg/distr/R/AllGenerics.R 2013-09-12 08:04:46 UTC (rev 908) @@ -450,3 +450,7 @@ if(!isGeneric("samplesize")){ setGeneric("samplesize", function(object, ...) standardGeneric("samplesize")) } +if(!isGeneric("samplesize<-")){ + setGeneric("samplesize<-", + function(object, value) standardGeneric("samplesize<-")) +} Modified: branches/distr-2.5/pkg/distr/man/internalGenerics.Rd =================================================================== --- branches/distr-2.5/pkg/distr/man/internalGenerics.Rd 2013-09-11 16:47:07 UTC (rev 907) +++ branches/distr-2.5/pkg/distr/man/internalGenerics.Rd 2013-09-12 08:04:46 UTC (rev 908) @@ -2,18 +2,22 @@ \alias{internalGenerics} \alias{distribution} \alias{samplesize} -\title{Internal: Common Generics 'distribution' and 'samplesize'} +\alias{samplesize<-} +\title{Internal: Common Generics 'distribution' and 'samplesize', 'samplesize<-'} \description{ - In order to be able to use packages \pkg{distrSim} and \pkg{distrMod} independently, + In order to be able to use packages \pkg{distrSim} and \pkg{distrMod} + resp. \pkg{RobAStBase} independently, it is necessary to import the respective generic from a prior package, i.e., \pkg{distr}. } \usage{ distribution(object) samplesize(object, ...) +x <- samplesize(object, value) } \arguments{ \item{object}{ the first argument to dispatch on in the actual methods. } + \item{value}{ the value to be assigned. } \item{\dots}{ additional arguments for function \code{samplesize}. } } Modified: branches/distr-2.5/pkg/distrMod/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distrMod/DESCRIPTION 2013-09-11 16:47:07 UTC (rev 907) +++ branches/distr-2.5/pkg/distrMod/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) @@ -1,12 +1,12 @@ Package: distrMod -Version: 2.5.1 +Version: 2.5.2 Date: 2013-01-09 Title: Object oriented implementation of probability models Description: Object oriented implementation of probability models based on packages 'distr' and 'distrEx' Author: Matthias Kohl, Peter Ruckdeschel Maintainer: Peter Ruckdeschel -Depends: R(>= 2.14.0), distr(>= 2.2), distrEx(>= 2.4), RandVar(>= 0.6.3), +Depends: R(>= 2.14.0), distr(>= 2.5.2), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, methods ByteCompile: yes License: LGPL-3 Modified: branches/distr-2.5/pkg/distrSim/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distrSim/DESCRIPTION 2013-09-11 16:47:07 UTC (rev 907) +++ branches/distr-2.5/pkg/distrSim/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) @@ -1,8 +1,8 @@ Package: distrSim -Version: 2.5.1 +Version: 2.5.2 Date: 2013-11-09 Title: Simulation classes based on package distr -Depends: R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.2) +Depends: R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.5.1) Suggests: distrEx(>= 2.2) Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Description: Simulation (S4-)classes based on package distr Modified: branches/distr-2.5/pkg/utils/DESCRIPTIONutils.R =================================================================== --- branches/distr-2.5/pkg/utils/DESCRIPTIONutils.R 2013-09-11 16:47:07 UTC (rev 907) +++ branches/distr-2.5/pkg/utils/DESCRIPTIONutils.R 2013-09-12 08:04:46 UTC (rev 908) @@ -153,6 +153,18 @@ changeDescription(startDir = "C:/rtest/robast",names=Names, pkgs=Pkgs, values=Values) } + +if(FALSE){ +Pkgs <- c("RandVar", "RobAStBase", "RobAStRDA", "ROptEst", "RobExtremes") +Names <- c("Version", "License") +Values <- matrix(c(c("0.9.2","LGPL-3"),rep(c("0.9","LGPL-3"),4)),2,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/robast/",names=Names, + pkgs=Pkgs, values=Values) +} + +} ############################################################################## Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distr/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) @@ -1,9 +1,13 @@ Package: distr -Version: 2.5 -Date: 2013-09-11 +Version: 2.5.1 +Date: 2013-01-09 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions -Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla +Author: person("Florian", "Camphausen", role=c("cre")), + person("Matthias", "Kohl", role=c("aut", "cph")), + person("Peter", "Ruckdeschel", role=c("aut", "cph"), + person("Thomas", "Stabla", role=c("aut", "cph")), + person("R Core Team", role = c("ctb", "cph")) Maintainer: Peter Ruckdeschel Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils Suggests: distrEx Modified: pkg/distr/R/AllGenerics.R =================================================================== --- pkg/distr/R/AllGenerics.R 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distr/R/AllGenerics.R 2013-09-12 08:04:46 UTC (rev 908) @@ -450,3 +450,7 @@ if(!isGeneric("samplesize")){ setGeneric("samplesize", function(object, ...) standardGeneric("samplesize")) } +if(!isGeneric("samplesize<-")){ + setGeneric("samplesize<-", + function(object, value) standardGeneric("samplesize<-")) +} Modified: pkg/distr/R/internals-qqplot.R =================================================================== --- pkg/distr/R/internals-qqplot.R 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distr/R/internals-qqplot.R 2013-09-12 08:04:46 UTC (rev 908) @@ -87,16 +87,18 @@ as.integer(n), PACKAGE = "stats")$p }else function(p0,n){ # .Call(stats:::C_pKolmogorov2x, p0, n) #, PACKAGE = "stats") - .C("pkolmogorov2x", p = as.double(p0), - as.integer(n))$p +# .C("pkolmogorov2x", p = as.double(p0), +# as.integer(n))$p + .Call("pKolmogorov2x", p0, n) #, PACKAGE = "stats") } .pks2 <- if(getRversion()<"2.16.0") function(x, tol){ .C("pkstwo", as.integer(1), p = as.double(x), as.double(tol), PACKAGE = "stats")$p }else function(x, tol){ # .Call(stats:::C_pKS2, p = x, tol) #, PACKAGE = "stats") - .C("pkstwo", as.integer(1), - p = as.double(x), as.double(tol))$p +# .C("pkstwo", as.integer(1), +# p = as.double(x), as.double(tol))$p + .Call("pKS2", p = x, tol) #, PACKAGE = "stats") } Modified: pkg/distr/inst/NEWS =================================================================== --- pkg/distr/inst/NEWS 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distr/inst/NEWS 2013-09-12 08:04:46 UTC (rev 908) @@ -25,12 +25,16 @@ /src/library/stats/src/ks.c rev60573 (with small changes to make it self-contained) to src folder of this pkg; in addition, we now use the shakier .C - interface again... + in v 2.5.1 reverted the changes in /src/library/stats/src/ks.c: + including R.h etc is easier than thought... + BUGFIXES: + fixed .makedotsPt -issue discovered by Gerald --> thx + moved generics to "distribution" and "samplesize" to pkg distr to avoid - conflict with pkg distrMod + conflict between pkgs distrMod and distrSim + v 2.5.1: same with "samplesize<-" to avoid conflict between pkgs + distrSim and RobAStBase - ############## v 2.4 ############## Modified: pkg/distr/man/internalGenerics.Rd =================================================================== --- pkg/distr/man/internalGenerics.Rd 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distr/man/internalGenerics.Rd 2013-09-12 08:04:46 UTC (rev 908) @@ -2,18 +2,22 @@ \alias{internalGenerics} \alias{distribution} \alias{samplesize} -\title{Internal: Common Generics 'distribution' and 'samplesize'} +\alias{samplesize<-} +\title{Internal: Common Generics 'distribution' and 'samplesize', 'samplesize<-'} \description{ - In order to be able to use packages \pkg{distrSim} and \pkg{distrMod} independently, + In order to be able to use packages \pkg{distrSim} and \pkg{distrMod} + resp. \pkg{RobAStBase} independently, it is necessary to import the respective generic from a prior package, i.e., \pkg{distr}. } \usage{ distribution(object) samplesize(object, ...) +x <- samplesize(object, value) } \arguments{ \item{object}{ the first argument to dispatch on in the actual methods. } + \item{value}{ the value to be assigned. } \item{\dots}{ additional arguments for function \code{samplesize}. } } Modified: pkg/distr/src/ks.c =================================================================== --- pkg/distr/src/ks.c 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distr/src/ks.c 2013-09-12 08:04:46 UTC (rev 908) @@ -26,67 +26,17 @@ in the two-sided one-sample and two-sample cases. */ -#include -#include -#define PI 3.141592653589793 -#ifndef M_1_SQRT_2PI -#define M_1_SQRT_2PI 0.398942280401432677939946059934 /* 1/sqrt(2pi) */ -#endif -#ifndef M_PI_2 -#define M_PI_2 1.570796326794896619231321691640 /* pi/2 */ -#endif +#include +#include +#include /* constants */ -#ifndef M_PI_4 -#define M_PI_4 0.785398163397448309615660845820 /* pi/4 */ -#endif - -/* - * taken from R Core: /src/include/R_ext/RS.h rev60573 - */ -extern void *R_chk_calloc(size_t, size_t); -extern void *R_chk_realloc(void *, size_t); -extern void R_chk_free(void *); - -/* - * taken from R Core: /src/main/memory.c rev60573 - */ -void *R_chk_calloc(size_t nelem, size_t elsize) -{ - void *p; - p = calloc(nelem, elsize); - return(p); -} - -void *R_chk_realloc(void *ptr, size_t size) -{ - void *p; - /* Protect against broken realloc */ - if(ptr) p = realloc(ptr, size); else p = malloc(size); - return(p); -} - -void R_chk_free(void *ptr) -{ - /* S-PLUS warns here, but there seems no reason to do so */ - /* if(!ptr) warning("attempt to free NULL pointer by Free"); */ - if(ptr) free(ptr); /* ANSI C says free has no effect on NULL, but - better to be safe here */ -} - -#define Calloc(n, t) (t *) R_chk_calloc( (size_t) (n), sizeof(t) ) -#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) ) -#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) - -/*static void pkolmogorov2x(double *x, int *n); -static void pkstwo(int n, double *x, double tol); -*/ static double K(int n, double d); static void m_multiply(double *A, double *B, double *C, int m); static void m_power(double *A, int eA, double *V, int *eV, int m, int n); /* Two-sample two-sided asymptotic distribution */ -void -pkstwo(int *n, double *x, double *tol) +static void +pkstwo(int n, double *x, double tol) { /* x[1:n] is input and output * @@ -111,9 +61,9 @@ double new, old, s, w, z; int i, k, k_max; - k_max = (int) sqrt(2 - log(*tol)); + k_max = (int) sqrt(2 - log(tol)); - for(i = 0; i < *n; i++) { + for(i = 0; i < n; i++) { if(x[i] < 1) { z = - (M_PI_2 * M_PI_4) / (x[i] * x[i]); w = log(x[i]); @@ -129,7 +79,7 @@ k = 1; old = 0; new = 1; - while(fabs(old - new) > *tol) { + while(fabs(old - new) > tol) { old = new; new += 2 * s * exp(z * k * k); s *= -1; @@ -140,6 +90,44 @@ } } +/* Two-sided two-sample */ +static double psmirnov2x(double *x, int m, int n) +{ + double md, nd, q, *u, w; + int i, j; + + if(m > n) { + i = n; n = m; m = i; + } + md = (double) m; + nd = (double) n; + /* + q has 0.5/mn added to ensure that rounding error doesn't + turn an equality into an inequality, eg abs(1/2-4/5)>3/10 + + */ + q = (0.5 + floor(*x * md * nd - 1e-7)) / (md * nd); + u = (double *) R_alloc(n + 1, sizeof(double)); + + for(j = 0; j <= n; j++) { + u[j] = ((j / nd) > q) ? 0 : 1; + } + for(i = 1; i <= m; i++) { + w = (double)(i) / ((double)(i + n)); + if((i / md) > q) + u[0] = 0; + else + u[0] = w * u[0]; + for(j = 1; j <= n; j++) { + if(fabs(i / md - j / nd) > q) + u[j] = 0; + else + u[j] = w * u[j] + u[j - 1]; + } + } + return u[n]; +} + static double K(int n, double d) { @@ -249,13 +237,31 @@ } Free(B); } -/* - * taken from R Core: /src/library/stats/src/ks.c rev56090 -*/ -void pkolmogorov2x(double *x, int *n) + +/* Two-sided two-sample */ +SEXP pSmirnov2x(SEXP statistic, SEXP snx, SEXP sny) { - /* x is input and output. */ + int nx = asInteger(snx), ny = asInteger(sny); + double st = asReal(statistic); + return ScalarReal(psmirnov2x(&st, nx, ny)); +} - *x = K(*n, *x); +/* Two-sample two-sided asymptotic distribution */ +SEXP pKS2(SEXP statistic, SEXP stol) +{ + int n = LENGTH(statistic); + double tol = asReal(stol); + SEXP ans = duplicate(statistic); + pkstwo(n, REAL(ans), tol); + return ans; } + +/* The two-sided one-sample 'exact' distribution */ +SEXP pKolmogorov2x(SEXP statistic, SEXP sn) +{ + int n = asInteger(sn); + double st = asReal(statistic), p; + p = K(n, st); + return ScalarReal(p); +} Modified: pkg/distrMod/DESCRIPTION =================================================================== --- pkg/distrMod/DESCRIPTION 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distrMod/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) @@ -1,16 +1,16 @@ Package: distrMod -Version: 2.5 -Date: 2013-09-11 +Version: 2.5.1 +Date: 2013-09-12 Title: Object oriented implementation of probability models Description: Object oriented implementation of probability models based on packages 'distr' and 'distrEx' Author: Matthias Kohl, Peter Ruckdeschel Maintainer: Peter Ruckdeschel -Depends: R(>= 2.14.0), distr(>= 2.2), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, methods +Depends: R(>= 2.14.0), distr(>= 2.5.1), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, methods ByteCompile: yes License: LGPL-3 Encoding: latin1 URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 904 +SVNRevision: 905 Modified: pkg/distrSim/DESCRIPTION =================================================================== --- pkg/distrSim/DESCRIPTION 2013-09-11 16:47:07 UTC (rev 907) +++ pkg/distrSim/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) @@ -1,8 +1,8 @@ Package: distrSim -Version: 2.5 -Date: 2013-09-11 +Version: 2.5.1 +Date: 2013-09-12 Title: Simulation classes based on package distr -Depends: R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.2) +Depends: R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.5.1) Suggests: distrEx(>= 2.2) Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Description: Simulation (S4-)classes based on package distr @@ -13,4 +13,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 904 +SVNRevision: 905 From noreply at r-forge.r-project.org Thu Sep 12 10:07:03 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Sep 2013 10:07:03 +0200 (CEST) Subject: [Distr-commits] r909 - in pkg: distr distrMod distrSim Message-ID: <20130912080703.CECCF1813BB@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-12 10:07:03 +0200 (Thu, 12 Sep 2013) New Revision: 909 Modified: pkg/distr/DESCRIPTION pkg/distrMod/DESCRIPTION pkg/distrSim/DESCRIPTION Log: fixed date and SVN Rev information Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) +++ pkg/distr/DESCRIPTION 2013-09-12 08:07:03 UTC (rev 909) @@ -1,6 +1,6 @@ Package: distr Version: 2.5.1 -Date: 2013-01-09 +Date: 2013-09-12 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions Author: person("Florian", "Camphausen", role=c("cre")), @@ -18,4 +18,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 904 +SVNRevision: 909 Modified: pkg/distrMod/DESCRIPTION =================================================================== --- pkg/distrMod/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) +++ pkg/distrMod/DESCRIPTION 2013-09-12 08:07:03 UTC (rev 909) @@ -13,4 +13,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 905 +SVNRevision: 909 Modified: pkg/distrSim/DESCRIPTION =================================================================== --- pkg/distrSim/DESCRIPTION 2013-09-12 08:04:46 UTC (rev 908) +++ pkg/distrSim/DESCRIPTION 2013-09-12 08:07:03 UTC (rev 909) @@ -13,4 +13,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 905 +SVNRevision: 909 From noreply at r-forge.r-project.org Thu Sep 12 10:29:01 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Sep 2013 10:29:01 +0200 (CEST) Subject: [Distr-commits] r910 - pkg/distr Message-ID: <20130912082901.67FEF18513E@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-12 10:29:01 +0200 (Thu, 12 Sep 2013) New Revision: 910 Modified: pkg/distr/DESCRIPTION Log: distr: appended comment as to authorship of R-Core in DESCRIPTION Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2013-09-12 08:07:03 UTC (rev 909) +++ pkg/distr/DESCRIPTION 2013-09-12 08:29:01 UTC (rev 910) @@ -7,7 +7,8 @@ person("Matthias", "Kohl", role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("aut", "cph"), person("Thomas", "Stabla", role=c("aut", "cph")), - person("R Core Team", role = c("ctb", "cph")) + person("R Core Team", role = c("ctb", "cph"), + comment="for source file ks.c/ routines 'pKS2' and 'pKolmogorov2x'") Maintainer: Peter Ruckdeschel Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils Suggests: distrEx @@ -18,4 +19,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 909 +SVNRevision: 910 From noreply at r-forge.r-project.org Thu Sep 12 10:54:25 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Sep 2013 10:54:25 +0200 (CEST) Subject: [Distr-commits] r911 - pkg/distr Message-ID: <20130912085426.041921859EC@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-12 10:54:25 +0200 (Thu, 12 Sep 2013) New Revision: 911 Modified: pkg/distr/NAMESPACE Log: distr (trunk): missed samplesize<- in exports Modified: pkg/distr/NAMESPACE =================================================================== --- pkg/distr/NAMESPACE 2013-09-12 08:29:01 UTC (rev 910) +++ pkg/distr/NAMESPACE 2013-09-12 08:54:25 UTC (rev 911) @@ -97,4 +97,4 @@ exportMethods("qqplot") export(".isEqual",".isEqual01", ".inArgs", ".fillList", ".presubs", ".makeLenAndOrder", ".DistrCollapse") -export("samplesize", "distribution") \ No newline at end of file +export("samplesize", "distribution", "samplesize<-") \ No newline at end of file From noreply at r-forge.r-project.org Thu Sep 12 11:25:48 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Sep 2013 11:25:48 +0200 (CEST) Subject: [Distr-commits] r912 - in pkg: distr distrMod distrSim utils Message-ID: <20130912092548.BA2EB185667@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-12 11:25:48 +0200 (Thu, 12 Sep 2013) New Revision: 912 Modified: pkg/distr/DESCRIPTION pkg/distrMod/DESCRIPTION pkg/distrSim/DESCRIPTION pkg/utils/DESCRIPTIONutils.R Log: updated version to 2.5.2 Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2013-09-12 08:54:25 UTC (rev 911) +++ pkg/distr/DESCRIPTION 2013-09-12 09:25:48 UTC (rev 912) @@ -1,5 +1,5 @@ Package: distr -Version: 2.5.1 +Version: 2.5.2 Date: 2013-09-12 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions Modified: pkg/distrMod/DESCRIPTION =================================================================== --- pkg/distrMod/DESCRIPTION 2013-09-12 08:54:25 UTC (rev 911) +++ pkg/distrMod/DESCRIPTION 2013-09-12 09:25:48 UTC (rev 912) @@ -1,12 +1,12 @@ Package: distrMod -Version: 2.5.1 +Version: 2.5.2 Date: 2013-09-12 Title: Object oriented implementation of probability models Description: Object oriented implementation of probability models based on packages 'distr' and 'distrEx' Author: Matthias Kohl, Peter Ruckdeschel Maintainer: Peter Ruckdeschel -Depends: R(>= 2.14.0), distr(>= 2.5.1), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, methods +Depends: R(>= 2.14.0), distr(>= 2.5.2), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, methods ByteCompile: yes License: LGPL-3 Encoding: latin1 Modified: pkg/distrSim/DESCRIPTION =================================================================== --- pkg/distrSim/DESCRIPTION 2013-09-12 08:54:25 UTC (rev 911) +++ pkg/distrSim/DESCRIPTION 2013-09-12 09:25:48 UTC (rev 912) @@ -1,8 +1,8 @@ Package: distrSim -Version: 2.5.1 +Version: 2.5.2 Date: 2013-09-12 Title: Simulation classes based on package distr -Depends: R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.5.1) +Depends: R(>= 2.14.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.5.2) Suggests: distrEx(>= 2.2) Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla Description: Simulation (S4-)classes based on package distr Modified: pkg/utils/DESCRIPTIONutils.R =================================================================== --- pkg/utils/DESCRIPTIONutils.R 2013-09-12 08:54:25 UTC (rev 911) +++ pkg/utils/DESCRIPTIONutils.R 2013-09-12 09:25:48 UTC (rev 912) @@ -145,14 +145,25 @@ pkgs=Pkgs, values=Values) } if(FALSE){### Version 0.9.1 +Pkgs <- c("RobLox", "RobLoxBioC", "RobRex", "ROptRegTS") +Names <- c("Version","License") +Values <- matrix(c("0.9","LGPL-3"),2,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/robast",names=Names, + pkgs=Pkgs, values=Values) +} +if(FALSE){ Pkgs <- c("RandVar", "ROptEstOld") -Names <- c("Version") -Values <- matrix("0.9.1",1,length(Pkgs)) +Names <- c("Version","License") +Values <- matrix(c("0.9.1","LGPL-3"),2,length(Pkgs)) colnames(Values) <- Pkgs rownames(Values) <- Names changeDescription(startDir = "C:/rtest/robast",names=Names, pkgs=Pkgs, values=Values) + } + ############################################################################## From noreply at r-forge.r-project.org Thu Sep 12 15:15:18 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Sep 2013 15:15:18 +0200 (CEST) Subject: [Distr-commits] r913 - in pkg: distr utils Message-ID: <20130912131519.0FE1E185B55@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-12 15:15:18 +0200 (Thu, 12 Sep 2013) New Revision: 913 Modified: pkg/distr/DESCRIPTION pkg/utils/DESCRIPTIONutils.R Log: DESCRIPTION ge?\195?\164ndert Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2013-09-12 09:25:48 UTC (rev 912) +++ pkg/distr/DESCRIPTION 2013-09-12 13:15:18 UTC (rev 913) @@ -3,13 +3,12 @@ Date: 2013-09-12 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions -Author: person("Florian", "Camphausen", role=c("cre")), +Authors at R: c(person("Florian", "Camphausen", role=c("aut")), person("Matthias", "Kohl", role=c("aut", "cph")), - person("Peter", "Ruckdeschel", role=c("aut", "cph"), + person("Peter", "Ruckdeschel", role=c("cre", "cph"), email="Peter.Ruckdeschel at itwm.fraunhofer.de"), person("Thomas", "Stabla", role=c("aut", "cph")), person("R Core Team", role = c("ctb", "cph"), - comment="for source file ks.c/ routines 'pKS2' and 'pKolmogorov2x'") -Maintainer: Peter Ruckdeschel + comment="for source file ks.c/ routines 'pKS2' and 'pKolmogorov2x'")) Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils Suggests: distrEx Imports: stats Modified: pkg/utils/DESCRIPTIONutils.R =================================================================== --- pkg/utils/DESCRIPTIONutils.R 2013-09-12 09:25:48 UTC (rev 912) +++ pkg/utils/DESCRIPTIONutils.R 2013-09-12 13:15:18 UTC (rev 913) @@ -162,6 +162,13 @@ changeDescription(startDir = "C:/rtest/robast",names=Names, pkgs=Pkgs, values=Values) +Pkgs <- c("RandVar", "ROptEstOld", "RobAStBase", "RobAStRDA", "RobLox", "RobRex", "RobLoxBioC", "ROptEst", "RobExtremes", "ROptRegTS") +Names <- c("Version") +Values <- matrix(c("1.0"),1,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/robast/branches/robast-1.0",names=Names, + pkgs=Pkgs, values=Values) } ############################################################################## From noreply at r-forge.r-project.org Thu Sep 12 23:37:25 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Sep 2013 23:37:25 +0200 (CEST) Subject: [Distr-commits] r914 - in pkg: SweaveListingUtils SweaveListingUtils/R SweaveListingUtils/inst SweaveListingUtils/man SweaveListingUtils/tests/Examples distrDoc distrDoc/inst distrDoc/man distrDoc/vignettes distrEllipse distrEllipse/inst distrEllipse/man distrEllipse/tests/Examples distrEx distrEx/R distrEx/inst distrEx/man distrEx/tests/Examples distrRmetrics distrRmetrics/inst distrRmetrics/man distrRmetrics/tests/Examples distrTEst distrTEst/inst distrTEst/man distrTEst/tests/Examples distrTeach distrTeach/inst distrTeach/man distrTeach/tests/Examples startupmsg startupmsg/inst startupmsg/tests/Examples utils Message-ID: <20130912213725.DF279183E14@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-12 23:37:25 +0200 (Thu, 12 Sep 2013) New Revision: 914 Added: pkg/distrDoc/.Rinstignore pkg/distrEllipse/.Rbuildignore pkg/distrEx/.Rbuildignore pkg/distrRmetrics/.Rbuildignore pkg/distrTEst/.Rbuildignore pkg/distrTeach/.Rbuildignore pkg/startupmsg/.Rbuildignore Modified: pkg/SweaveListingUtils/.Rbuildignore pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/R/SweaveListingOptions.R pkg/SweaveListingUtils/inst/NEWS pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save pkg/distrDoc/DESCRIPTION pkg/distrDoc/NAMESPACE pkg/distrDoc/inst/NEWS pkg/distrDoc/man/0distrDoc-package.Rd pkg/distrDoc/vignettes/distr.Rnw pkg/distrEllipse/DESCRIPTION pkg/distrEllipse/NAMESPACE pkg/distrEllipse/inst/NEWS pkg/distrEllipse/man/0distrEllipse-package.Rd pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save pkg/distrEx/DESCRIPTION pkg/distrEx/NAMESPACE pkg/distrEx/R/AllClass.R pkg/distrEx/R/ClippedMoments.R pkg/distrEx/R/ConvexContamination.R pkg/distrEx/R/Expectation.R pkg/distrEx/R/Functionals.R pkg/distrEx/R/Kurtosis.R pkg/distrEx/inst/NEWS pkg/distrEx/man/0distrEx-package.Rd pkg/distrEx/man/E.Rd pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save pkg/distrRmetrics/DESCRIPTION pkg/distrRmetrics/NAMESPACE pkg/distrRmetrics/inst/NEWS pkg/distrRmetrics/man/0distrRmetrics-package.Rd pkg/distrRmetrics/man/SNorm-class.Rd pkg/distrRmetrics/man/SNorm.Rd pkg/distrRmetrics/man/SSTd-class.Rd pkg/distrRmetrics/man/SSTd.Rd pkg/distrRmetrics/man/STd.Rd pkg/distrRmetrics/tests/Examples/distrRmetrics-Ex.Rout.save pkg/distrTEst/DESCRIPTION pkg/distrTEst/NAMESPACE pkg/distrTEst/inst/NEWS pkg/distrTEst/man/0distrTEst-package.Rd pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save pkg/distrTeach/DESCRIPTION pkg/distrTeach/NAMESPACE pkg/distrTeach/inst/NEWS pkg/distrTeach/man/0distrTeach-package.Rd pkg/distrTeach/man/IllustCLT.Rd pkg/distrTeach/tests/Examples/distrTeach-Ex.Rout.save pkg/startupmsg/DESCRIPTION pkg/startupmsg/inst/NEWS pkg/startupmsg/tests/Examples/startupmsg-Ex.Rout.save pkg/utils/DESCRIPTIONutils.R Log: moved the rest of pkgs from branches/distr-2.5 to trunk Modified: pkg/SweaveListingUtils/.Rbuildignore =================================================================== --- pkg/SweaveListingUtils/.Rbuildignore 2013-09-12 13:15:18 UTC (rev 913) +++ pkg/SweaveListingUtils/.Rbuildignore 2013-09-12 21:37:25 UTC (rev 914) @@ -1 +1,2 @@ -^.*\.svn.+ +^.*\.svn.+ +.*-Ex\.R \ No newline at end of file Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2013-09-12 13:15:18 UTC (rev 913) +++ pkg/SweaveListingUtils/DESCRIPTION 2013-09-12 21:37:25 UTC (rev 914) @@ -1,10 +1,9 @@ Package: SweaveListingUtils Title: Utilities for Sweave together with TeX listings package Encoding: latin1 -Version: 0.6.2 -Depends: R(> 2.13.2), startupmsg +Version: 0.7 +Depends: R(>= 2.14.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines -Imports: stats ByteCompile: yes Author: Peter Ruckdeschel Description: provides utilities for defining R / Rd as Tex-package-listings "language" and @@ -13,7 +12,7 @@ source code Maintainer: Peter Ruckdeschel License: LGPL-3 -Date: 2013-02-09 +Date: 2013-09-12 LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 882 +SVNRevision: 913 Modified: pkg/SweaveListingUtils/R/SweaveListingOptions.R =================================================================== --- pkg/SweaveListingUtils/R/SweaveListingOptions.R 2013-09-12 13:15:18 UTC (rev 913) +++ pkg/SweaveListingUtils/R/SweaveListingOptions.R 2013-09-12 21:37:25 UTC (rev 914) @@ -36,7 +36,7 @@ Rbcolor = c(0,0.6,0.6), Routcolor = c(0.461,0.039,0.102), Rcommentcolor = c(0.101,0.043,0.432), -pkv = "2.1.4", +pkv = "2.5", pkg = "distr", Keywordstyle = "{\\bf}", Recomd.Keywordstyle = "{\\bf\\color{RRecomdcolor}}", @@ -45,8 +45,6 @@ intermediate = TRUE, inSweave = FALSE, fromRForge = TRUE, -#base.url = paste("http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/", -# "*checkout*/pkg/", sep = ""), base.url = paste("http://r-forge.r-project.org/scm/viewvc.php/", "*checkout*/pkg/", sep = ""), Modified: pkg/SweaveListingUtils/inst/NEWS =================================================================== --- pkg/SweaveListingUtils/inst/NEWS 2013-09-12 13:15:18 UTC (rev 913) +++ pkg/SweaveListingUtils/inst/NEWS 2013-09-12 21:37:25 UTC (rev 914) @@ -3,6 +3,20 @@ ###################################################################### ############## +v 0.7 +############## + +user-visible CHANGES: + +GENERAL ENHANCEMENTS: ++ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends + +under the hood: ++ added .Rbuildignore + +BUGFIXES: + +############## v 0.6 ############## Modified: pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd =================================================================== --- pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2013-09-12 13:15:18 UTC (rev 913) +++ pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2013-09-12 21:37:25 UTC (rev 914) @@ -15,12 +15,12 @@ \details{ \tabular{ll}{ Package: \tab SweaveListingUtils \cr -Version: \tab 0.6.2 \cr -Date: \tab 2013-02-08 \cr -Depends: \tab R(> 2.13.2), startupmsg \cr +Version: \tab 0.7 \cr +Date: \tab 2013-09-12 \cr +Depends: \tab R(>= 2.14.0), startupmsg \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr -SVNRevision: \tab 881 \cr +SVNRevision: \tab 913 \cr } TeX-package \file{listings}, confer \url{http://www.ctan.org/tex-archive/macros/latex/contrib/listings/}, Modified: pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save =================================================================== --- pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2013-09-12 13:15:18 UTC (rev 913) +++ pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2013-09-12 21:37:25 UTC (rev 914) @@ -1,7 +1,6 @@ -R Under development (unstable) (2013-01-05 r61562) -- "Unsuffered Consequences" +R version 3.0.1 Patched (2013-09-02 r63805) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. @@ -22,16 +21,27 @@ > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > options(pager = "console") +> base::assign(".ExTimings", "SweaveListingUtils-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') +> +> ### * > library('SweaveListingUtils') Loading required package: startupmsg -:startupmsg> Utilities for start-up messages (version 0.8) +:startupmsg> Utilities for start-up messages (version 0.9) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") :SweaveListingUtils> Utilities for Sweave together with -:SweaveListingUtils> TeX listings package (version -:SweaveListingUtils> 0.6.1) +:SweaveListingUtils> TeX listings package (version 0.7) :SweaveListingUtils> :SweaveListingUtils> NOTE: Support for this package :SweaveListingUtils> will stop soon. @@ -59,18 +69,19 @@ Attaching package: 'SweaveListingUtils' -The following object is masked from 'package:base': +The following objects are masked from 'package:base': library, require > -> assign(".oldSearch", search(), pos = 'CheckExEnv') +> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > cleanEx() > nameEx("SweaveListingMASK") > ### * SweaveListingMASK > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: SweaveListingMASK > ### Title: Masking of/by other functions in package "SweaveListingUtils" > ### Aliases: SweaveListingMASK MASKING @@ -110,12 +121,15 @@ ... nothing discovered so far ...> > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("SweaveListingMASK", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("SweaveListingOptions") > ### * SweaveListingOptions > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: SweaveListingOptions > ### Title: Function to change the global options of the package > ### 'SweaveListingUtils' @@ -236,7 +250,7 @@ [1] 0.101 0.043 0.432 $pkv -[1] "2.1.4" +[1] "2.5" $pkg [1] "distr" @@ -303,12 +317,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("SweaveListingOptions", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("SweaveListingPreparations") > ### * SweaveListingPreparations > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: SweaveListingPreparations > ### Title: SweaveListingPreparations > ### Aliases: SweaveListingPreparations @@ -428,7 +445,7 @@ \def\Code#1{{\tt\color{Rcolor} #1}} \def\file#1{{\tt #1}} \def\pkg#1{{\tt "#1"}} -\newcommand{\pkgversion}{{\tt 2.4}} +\newcommand{\pkgversion}{{\tt 2.5.2}} %------------------------------------------------------------------------------% Warning in setBaseOrRecommended(pkgs = pkgs) : number of items to replace is not a multiple of replacement length @@ -549,20 +566,20 @@ win.graph,trans3d,topo.colors,tiff,terrain.colors,% svg,setPS,setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,% savePlot,rgb2hsv,replayPlot,recordPlot,recordGraphics,% -ps.options,postscriptFonts,postscriptFont,png,pdfFonts,% -pdf.options,pdf,nclass.scott,nclass.Sturges,nclass.FD,% -n2mfrow,msgWindow,make.rgb,jpeg,is.raster,% -heat.colors,hcl,grey.colors,gray.colors,graphics.off,% -getGraphicsEventEnv,getGraphicsEvent,extendrange,embedFonts,deviceIsInteractive,% -devAskNewPage,dev.size,dev.set,dev.print,dev.prev,% -dev.off,dev.next,dev.new,dev.list,dev.interactive,% -dev.hold,dev.flush,dev.cur,dev.copy2pdf,dev.copy2eps,% -dev.copy,dev.control,dev.capture,dev.capabilities,densCols,% -convertColor,contourLines,colorspaces,colorRampPalette,colorRamp,% -colorConverter,col2rgb,cm.colors,check.options,cairo_ps,% -cairo_pdf,bringToTop,boxplot.stats,bmp,blues9,% -bitmap,axisTicks,as.raster,as.graphicsAnnot,adjustcolor,% -Type1Font,Hershey,CIDFont% +ps.options,postscriptFonts,png,pdfFonts,pdf.options,% +pdf,nclass.scott,nclass.Sturges,nclass.FD,n2mfrow,% +msgWindow,make.rgb,jpeg,is.raster,heat.colors,% +hcl,grey.colors,gray.colors,graphics.off,getGraphicsEventEnv,% +getGraphicsEvent,extendrange,embedFonts,deviceIsInteractive,devAskNewPage,% +dev.size,dev.set,dev.print,dev.prev,dev.off,% +dev.next,dev.new,dev.list,dev.interactive,dev.hold,% +dev.flush,dev.cur,dev.copy2pdf,dev.copy2eps,dev.copy,% +dev.control,dev.capture,dev.capabilities,densCols,convertColor,% +contourLines,colorspaces,colorRampPalette,colorRamp,colorConverter,% +col2rgb,cm.colors,check.options,cairo_ps,cairo_pdf,% +bringToTop,boxplot.stats,bmp,blues9,bitmap,% +axisTicks,as.raster,as.graphicsAnnot,adjustcolor,Type1Font,% +Hershey,CIDFont% },% keywordstyle={[6]{\bf\color{RRecomdcolor}}},% % @@ -584,32 +601,33 @@ read.delim,read.csv2,read.csv,read.DIF,rc.status,% rc.settings,rc.options,rc.getOption,promptPackage,promptData,% process.events,personList,person,packageVersion,packageStatus,% -packageDescription,package.skeleton,old.packages,object.size,news,% -new.packages,modifyList,mirror2html,memory.size,memory.limit,% -makeRweaveLatexCodeRunner,make.socket,make.packages.html,maintainer,lsf.str,% -ls.str,localeToCharset,loadhistory,loadRconsole,limitedLabels,% -is.relistable,installed.packages,install.packages,history,help.start,% -help.search,help.request,head.matrix,head,globalVariables,% -glob2rx,getWindowsHandles,getWindowsHandle,getWindowTitle,getWinProgressBar,% -getTxtProgressBar,getSrcref,getSrcLocation,getSrcFilename,getSrcDirectory,% -getS3method,getParseText,getParseData,getIdentification,getFromNamespace,% -getClipboardFormats,getCRANmirrors,getAnywhere,formatUL,formatOL,% -flush.console,fixInNamespace,findLineNum,file_test,file.edit,% -dump.frames,download.packages,download.file,de.setup,de.restore,% -de.ncols,data.entry,create.post,count.fields,contrib.url,% -compareVersion,combn,close.socket,citeNatbib,cite,% -citation,citHeader,citFooter,citEntry,chooseCRANmirror,% -chooseBioCmirror,choose.files,choose.dir,checkCRAN,capture.output,% -bug.report,browseVignettes,browseURL,browseEnv,bibentry,% -available.packages,assignInNamespace,assignInMyNamespace,aspell_write_personal_dictionary_file,aspell_package_vignettes,% -aspell_package_Rd_files,aspell_package_R_files,aspell_package_C_files,aspell,as.roman,% -as.relistable,as.personList,as.person,arrangeWindows,argsAnywhere,% -aregexec,alarm,adist,View,URLencode,% -URLdecode,SweaveSyntaxNoweb,SweaveSyntaxLatex,SweaveSyntConv,SweaveHooks,% -Sweave,Stangle,RweaveTryStop,RweaveLatexWritedoc,RweaveLatexSetup,% -RweaveLatexOptions,RweaveLatexFinish,RweaveLatex,RweaveEvalWithOpt,RweaveChunkPrefix,% -RtangleWritedoc,RtangleSetup,Rtangle,Rprofmem,Rprof,% -RSiteSearch,RShowDoc,Filters,DLL.version,CRAN.packages% +packageName,packageDescription,package.skeleton,old.packages,object.size,% +news,new.packages,modifyList,mirror2html,memory.size,% +memory.limit,makeRweaveLatexCodeRunner,make.socket,make.packages.html,maintainer,% +lsf.str,ls.str,localeToCharset,loadhistory,loadRconsole,% +limitedLabels,is.relistable,installed.packages,install.packages,history,% +help.start,help.search,help.request,head.matrix,head,% +globalVariables,glob2rx,getWindowsHandles,getWindowsHandle,getWindowTitle,% +getWinProgressBar,getTxtProgressBar,getSrcref,getSrcLocation,getSrcFilename,% +getSrcDirectory,getS3method,getParseText,getParseData,getIdentification,% +getFromNamespace,getClipboardFormats,getCRANmirrors,getAnywhere,formatUL,% +formatOL,flush.console,fixInNamespace,findLineNum,file_test,% +file.edit,dump.frames,download.packages,download.file,de.setup,% +de.restore,de.ncols,data.entry,create.post,count.fields,% +contrib.url,compareVersion,combn,close.socket,citeNatbib,% +cite,citation,citHeader,citFooter,citEntry,% +chooseCRANmirror,chooseBioCmirror,choose.files,choose.dir,checkCRAN,% +capture.output,bug.report,browseVignettes,browseURL,browseEnv,% +bibentry,available.packages,assignInNamespace,assignInMyNamespace,aspell_write_personal_dictionary_file,% +aspell_package_vignettes,aspell_package_Rd_files,aspell_package_R_files,aspell_package_C_files,aspell,% +as.roman,as.relistable,as.personList,as.person,arrangeWindows,% +argsAnywhere,aregexec,alarm,adist,View,% +URLencode,URLdecode,SweaveSyntaxNoweb,SweaveSyntaxLatex,SweaveSyntConv,% +SweaveHooks,Sweave,Stangle,RweaveTryStop,RweaveLatexWritedoc,% +RweaveLatexSetup,RweaveLatexOptions,RweaveLatexFinish,RweaveLatex,RweaveEvalWithOpt,% +RweaveChunkPrefix,RtangleWritedoc,RtangleSetup,Rtangle,Rprofmem,% +Rprof,RSiteSearch,RShowDoc,Filters,DLL.version,% +CRAN.packages% },% keywordstyle={[7]{\bf\color{RRecomdcolor}}},% % @@ -621,22 +639,22 @@ state.x77,state.region,state.name,state.division,state.center,% state.area,state.abb,stackloss,stack.x,stack.loss,% sleep,rock,rivers,randu,quakes,% -pressure,presidents,precip,occupationalStatus,nottem,% -nhtemp,mtcars,morley,mdeaths,lynx,% -longley,lh,ldeaths,islands,iris3,% -iris,infert,freeny.y,freeny.x,freeny,% -fdeaths,faithful,eurodist,euro.cross,euro,% -esoph,discoveries,crimtab,co2,chickwts,% -cars,beaver2,beaver1,austres,attitude,% -attenu,anscombe,airquality,airmiles,ability.cov,% -WorldPhones,WWWusage,VADeaths,USPersonalExpenditure,USJudgeRatings,% -USArrests,USAccDeaths,UKgas,UKDriverDeaths,UCBAdmissions,% -ToothGrowth,Titanic,Theoph,Seatbelts,Puromycin,% -PlantGrowth,OrchardSprays,Orange,Nile,Loblolly,% -LifeCycleSavings,LakeHuron,JohnsonJohnson,InsectSprays,Indometh,% -Harman74.cor,Harman23.cor,HairEyeColor,Formaldehyde,EuStockMarkets,% -DNase,ChickWeight,CO2,BOD,BJsales.lead,% -BJsales,AirPassengers% +pressure,presidents,precip,occupationalStatus,npk,% +nottem,nhtemp,mtcars,morley,mdeaths,% +lynx,longley,lh,ldeaths,islands,% +iris3,iris,infert,freeny.y,freeny.x,% +freeny,fdeaths,faithful,eurodist,euro.cross,% +euro,esoph,discoveries,crimtab,co2,% +chickwts,cars,beaver2,beaver1,austres,% +attitude,attenu,anscombe,airquality,airmiles,% +ability.cov,WorldPhones,WWWusage,VADeaths,USPersonalExpenditure,% +USJudgeRatings,USArrests,USAccDeaths,UKgas,UKDriverDeaths,% +UCBAdmissions,ToothGrowth,Titanic,Theoph,Seatbelts,% +Puromycin,PlantGrowth,OrchardSprays,Orange,Nile,% +Loblolly,LifeCycleSavings,LakeHuron,JohnsonJohnson,InsectSprays,% +Indometh,Harman74.cor,Harman23.cor,HairEyeColor,Formaldehyde,% +EuStockMarkets,DNase,ChickWeight,CO2,BOD,% +BJsales.lead,BJsales,AirPassengers% },% keywordstyle={[8]{\bf\color{RRecomdcolor}}},% % @@ -678,13 +696,13 @@ el,dumpMethods,dumpMethod,doPrimitiveMethod,defaultPrototype,% defaultDumpName,conformMethod,completeSubclasses,completeExtends,completeClassDefinition,% coerce<-,coerce,classesToAM,className,classMetaName,% -classLabel,checkSlotAssignment,cbind2,canCoerce,callNextMethod,% -callGeneric,cacheMethod,cacheMetaData,cacheGenericsMetaData,body<-,% -balanceMethodsList,assignMethodsMetaData,assignClassDef,asMethodDefinition,as<-,% -allNames,allGenerics,addNextMethod,Summary,SignatureMethod,% -S3Part<-,S3Part,S3Class<-,S3Class,Quote,% -MethodsListSelect,MethodsList,MethodAddCoerce,Math2,Logic,% -Complex,Compare,Arith% +classLabel,checkSlotAssignment,checkAtAssignment,cbind2,canCoerce,% +callNextMethod,callGeneric,cacheMethod,cacheMetaData,cacheGenericsMetaData,% +body<-,balanceMethodsList,assignMethodsMetaData,assignClassDef,asMethodDefinition,% +as<-,allNames,allGenerics,addNextMethod,Summary,% +SignatureMethod,S3Part<-,S3Part,S3Class<-,S3Class,% +Quote,MethodsListSelect,MethodsList,MethodAddCoerce,Math2,% +Logic,Complex,Compare,Arith% },% keywordstyle={[9]{\bf\color{RRecomdcolor}}},% % @@ -710,152 +728,151 @@ sys.parents,sys.parent,sys.on.exit,sys.nframe,sys.load.image,% sys.function,sys.frames,sys.frame,sys.calls,sys.call,% suppressWarnings,suppressPackageStartupMessages,suppressMessages,summary.table,summary.srcref,% -summary.srcfile,summary.matrix,summary.factor,summary.default,summary.data.frame,% -summary.connection,summary.POSIXlt,summary.POSIXct,summary.Date,substring<-,% -substr<-,subset.matrix,subset.default,subset.data.frame,strwrap,% -strtrim,strtoi,strptime,strftime,storage.mode<-,% -storage.mode,stopifnot,stdout,stdin,stderr,% -standardGeneric,srcref,srcfilecopy,srcfilealias,srcfile,% -sprintf,split<-.default,split<-.data.frame,split<-,split.default,% -split.data.frame,split.POSIXct,split.Date,sort.list,sort.int,% -sort.default,sort.POSIXlt,solve.qr,solve.default,socketSelect,% -socketConnection,slice.index,sink.number,simplify2array,simpleWarning,% -simpleMessage,simpleError,simpleCondition,signalCondition,showConnections,% -shell.exec,shell,shQuote,setTimeLimit,setSessionTimeLimit,% -setNamespaceInfo,setHook,set.seed,serialize,seq_len,% -seq_along,seq.int,seq.default,seq.POSIXt,seq.Date,% -seek.connection,seek,scale.default,saveRDS,save.image,% -sample.int,sQuote,rowsum.default,rowsum.data.frame,rownames<-,% -rowSums,rowMeans,row.names<-.default,row.names<-.data.frame,row.names<-,% -row.names.default,row.names.data.frame,row.names,round.POSIXt,round.Date,% -rev.default,retracemem,restartFormals,restartDescription,requireNamespace,% -replicate,rep_len,rep.numeric_version,rep.int,rep.factor,% -rep.POSIXlt,rep.POSIXct,rep.Date,removeTaskCallback,regmatches<-,% -regmatches,registerS3methods,registerS3method,regexec,reg.finalizer,% -readRenviron,readRDS,readLines,readChar,readBin,% -read.dcf,rcond,rbind.data.frame,rawToChar,rawToBits,% -rawShift,rawConnectionValue,rawConnection,raw,rapply,% -range.default,quarters.POSIXt,quarters.Date,quarters,qr.solve,% -qr.resid,qr.qy,qr.qty,qr.fitted,qr.default,% -qr.coef,qr.X,qr.R,qr.Q,pushBackLength,% -pushBack,psigamma,provideDimnames,prop.table,proc.time,% -print.warnings,print.table,print.summaryDefault,print.summary.table,print.srcref,% -print.srcfile,print.simple.list,print.rle,print.restart,print.proc_time,% -print.packageInfo,print.octmode,print.numeric_version,print.noquote,print.listof,% -print.libraryIQR,print.hexmode,print.function,print.factor,print.difftime,% -print.default,print.data.frame,print.connection,print.condition,print.by,% -print.POSIXlt,print.POSIXct,print.NativeRoutineList,print.Date,print.DLLRegisteredRoutines,% -print.DLLInfoList,print.DLLInfo,print.AsIs,prettyNum,pretty.default,% -pos.to.env,pmin.int,pmax.int,pipe,pi,% -path.package,path.expand,paste0,parseNamespaceFile,parent.frame,% -parent.env<-,parent.env,package_version,packageStartupMessage,packageHasNamespace,% -packageEvent,packBits,open.srcfilecopy,open.srcfilealias,open.srcfile,% -open.connection,open,on.exit,oldClass<-,oldClass,% -nzchar,numeric_version,normalizePath,norm,ngettext,% -new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,namespaceImport,% -namespaceExport,names<-.POSIXlt,names<-,names.POSIXlt,mostattributes<-,% -months.POSIXt,months.Date,months,month.name,month.abb,% -mode<-,mget,message,merge.default,merge.data.frame,% -memory.profile,memDecompress,memCompress,mem.limits,mean.difftime,% -mean.default,mean.data.frame,mean.POSIXlt,mean.POSIXct,mean.Date,% +summary.srcfile,summary.proc_time,summary.matrix,summary.factor,summary.default,% +summary.data.frame,summary.connection,summary.POSIXlt,summary.POSIXct,summary.Date,% +substring<-,substr<-,subset.matrix,subset.default,subset.data.frame,% +strwrap,strtrim,strtoi,strptime,strftime,% +storage.mode<-,storage.mode,stopifnot,stdout,stdin,% +stderr,standardGeneric,srcref,srcfilecopy,srcfilealias,% +srcfile,sprintf,split<-.default,split<-.data.frame,split<-,% +split.default,split.data.frame,split.POSIXct,split.Date,sort.list,% +sort.int,sort.default,sort.POSIXlt,solve.qr,solve.default,% +socketSelect,socketConnection,slice.index,sink.number,simplify2array,% +simpleWarning,simpleMessage,simpleError,simpleCondition,signalCondition,% +showConnections,shell.exec,shell,shQuote,setTimeLimit,% +setSessionTimeLimit,setNamespaceInfo,setHook,set.seed,serialize,% +seq_len,seq_along,seq.int,seq.default,seq.POSIXt,% +seq.Date,seek.connection,seek,scale.default,saveRDS,% +save.image,sample.int,sQuote,rowsum.default,rowsum.data.frame,% +rownames<-,rowSums,rowMeans,row.names<-.default,row.names<-.data.frame,% +row.names<-,row.names.default,row.names.data.frame,row.names,round.POSIXt,% +round.Date,rev.default,retracemem,restartFormals,restartDescription,% +requireNamespace,replicate,rep_len,rep.numeric_version,rep.int,% +rep.factor,rep.POSIXlt,rep.POSIXct,rep.Date,removeTaskCallback,% +regmatches<-,regmatches,registerS3methods,registerS3method,regexec,% +reg.finalizer,readRenviron,readRDS,readLines,readChar,% +readBin,read.dcf,rcond,rbind.data.frame,rawToChar,% +rawToBits,rawShift,rawConnectionValue,rawConnection,raw,% +rapply,range.default,quarters.POSIXt,quarters.Date,quarters,% +qr.solve,qr.resid,qr.qy,qr.qty,qr.fitted,% +qr.default,qr.coef,qr.X,qr.R,qr.Q,% +pushBackLength,pushBack,psigamma,provideDimnames,prop.table,% +proc.time,print.warnings,print.table,print.summaryDefault,print.summary.table,% +print.srcref,print.srcfile,print.simple.list,print.rle,print.restart,% +print.proc_time,print.packageInfo,print.octmode,print.numeric_version,print.noquote,% +print.listof,print.libraryIQR,print.hexmode,print.function,print.factor,% +print.difftime,print.default,print.data.frame,print.connection,print.condition,% +print.by,print.POSIXlt,print.POSIXct,print.NativeRoutineList,print.Date,% +print.DLLRegisteredRoutines,print.DLLInfoList,print.DLLInfo,print.AsIs,prettyNum,% +pretty.default,pos.to.env,pmin.int,pmax.int,pipe,% +pi,path.package,path.expand,paste0,parseNamespaceFile,% +parent.frame,parent.env<-,parent.env,package_version,packageStartupMessage,% +packageHasNamespace,packageEvent,packBits,open.srcfilecopy,open.srcfilealias,% +open.srcfile,open.connection,open,on.exit,oldClass<-,% +oldClass,nzchar,numeric_version,normalizePath,norm,% +ngettext,new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,% +namespaceImport,namespaceExport,names<-.POSIXlt,names<-,names.POSIXlt,% +mostattributes<-,months.POSIXt,months.Date,months,month.name,% +month.abb,mode<-,mget,message,merge.default,% +merge.data.frame,memory.profile,memDecompress,memCompress,mem.limits,% +mean.difftime,mean.default,mean.POSIXlt,mean.POSIXct,mean.Date,% max.col,match.fun,match.call,match.arg,mat.or.vec,% -margin.table,mapply,manglePackageName,makeActiveBinding,make.unique,% -make.names,lower.tri,logb,lockEnvironment,lockBinding,% -loadingNamespaceInfo,loadedNamespaces,loadNamespace,list2env,list.files,% -list.dirs,library.dynam.unload,library.dynam,lfactorial,levels<-.factor,% -levels<-,levels.default,letters,length<-.factor,length<-,% -length.POSIXlt,lazyLoadDBfetch,lazyLoadDBexec,lazyLoad,labels.default,% -l10n_info,kappa.qr,kappa.lm,kappa.default,julian.POSIXt,% -julian.Date,julian,isdebugged,isatty,isTRUE,% -isSymmetric.matrix,isSymmetric,isSeekable,isS4,isRestart,% -isOpen,isNamespace,isIncomplete,isBaseNamespace,is.vector,% -is.unsorted,is.table,is.symbol,is.single,is.recursive,% -is.real,is.raw,is.qr,is.primitive,is.pairlist,% -is.package_version,is.ordered,is.object,is.numeric_version,is.numeric.difftime,% -is.numeric.POSIXt,is.numeric.Date,is.numeric,is.null,is.nan,% -is.name,is.na<-.factor,is.na<-.default,is.na<-,is.na.numeric_version,% -is.na.data.frame,is.na.POSIXlt,is.na,is.matrix,is.logical,% -is.loaded,is.list,is.language,is.integer,is.infinite,% -is.function,is.finite,is.factor,is.expression,is.environment,% -is.element,is.double,is.data.frame,is.complex,is.character,% -is.call,is.atomic,is.array,is.R,invokeRestartInteractively,% -invokeRestart,inverse.rle,intToUtf8,intToBits,importIntoEnv,% -identity,identical,icuSetCollate,iconvlist,iconv,% -gzfile,gzcon,grepl,grepRaw,gregexpr,% -gettextf,gettext,getTaskCallbackNames,getSrcLines,getRversion,% -getNativeSymbolInfo,getNamespaceVersion,getNamespaceUsers,getNamespaceName,getNamespaceInfo,% -getNamespaceImports,getNamespaceExports,getNamespace,getLoadedDLLs,getHook,% -getExportedValue,getElement,getDLLRegisteredRoutines.character,getDLLRegisteredRoutines.DLLInfo,getDLLRegisteredRoutines,% -getConnection,getCallingDLLe,getCallingDLL,getAllConnections,gctorture2,% -gc.time,formatDL,format.summaryDefault,format.pval,format.packageInfo,% -format.octmode,format.numeric_version,format.libraryIQR,format.info,format.hexmode,% -format.factor,format.difftime,format.default,format.data.frame,format.POSIXlt,% -format.POSIXct,format.Date,format.AsIs,formals<-,force,% -flush.connection,flush,findRestart,findPackageEnv,findInterval,% -find.package,file.symlink,file.show,file.rename,file.remove,% -file.path,file.link,file.info,file.exists,file.create,% -file.copy,file.choose,file.append,file.access,fifo,% -factorial,expm1,expand.grid,eval.parent,environmentName,% -environmentIsLocked,environment<-,env.profile,enquote,encodeString,% -enc2utf8,enc2native,emptyenv,eapply,dyn.unload,% -dyn.load,duplicated.numeric_version,duplicated.matrix,duplicated.default,duplicated.data.frame,% -duplicated.array,duplicated.POSIXlt,droplevels.factor,droplevels.data.frame,droplevels,% -do.call,dir.create,dimnames<-.data.frame,dimnames<-,dimnames.data.frame,% -dim<-,dim.data.frame,difftime,diff.default,diff.POSIXt,% -diff.Date,diag<-,determinant.matrix,determinant,det,% -delayedAssign,default.stringsAsFactors,debugonce,data.matrix,data.frame,% -data.class,dQuote,cut.default,cut.POSIXt,cut.Date,% -contributors,conditionMessage.condition,conditionMessage,conditionCall.condition,conditionCall,% -computeRestarts,comment<-,colnames<-,colSums,colMeans,% -closeAllConnections,close.srcfilealias,close.srcfile,close.connection,clearPushBack,% -class<-,chol.default,check_tzones,chartr,charToRaw,% -char.expand,cbind.data.frame,casefold,capabilities,callCC,% -c.numeric_version,c.noquote,c.POSIXlt,c.POSIXct,c.Date,% -bzfile,by.default,by.data.frame,browserText,browserSetDebug,% -browserCondition,bquote,body<-,bitwXor,bitwShiftR,% -bitwShiftL,bitwOr,bitwNot,bitwAnd,bindtextdomain,% -bindingIsLocked,bindingIsActive,baseenv,attributes<-,attr<-,% -attr.all.equal,attachNamespace,assign,asS4,asS3,% -asNamespace,as.vector.factor,as.vector,as.table.default,as.table,% -as.symbol,as.single.default,as.single,as.real,as.raw,% -as.qr,as.pairlist,as.package_version,as.ordered,as.octmode,% -as.numeric_version,as.numeric,as.null.default,as.null,as.name,% -as.matrix.noquote,as.matrix.default,as.matrix.data.frame,as.matrix.POSIXlt,as.matrix,% -as.logical.factor,as.logical,as.list.numeric_version,as.list.function,as.list.factor,% -as.list.environment,as.list.default,as.list.data.frame,as.list.POSIXct,as.list.Date,% -as.list,as.integer,as.hexmode,as.function.default,as.function,% -as.factor,as.expression.default,as.expression,as.environment,as.double.difftime,% -as.double.POSIXlt,as.double,as.difftime,as.data.frame.vector,as.data.frame.ts,% -as.data.frame.table,as.data.frame.raw,as.data.frame.ordered,as.data.frame.numeric_version,as.data.frame.numeric,% -as.data.frame.model.matrix,as.data.frame.matrix,as.data.frame.logical,as.data.frame.list,as.data.frame.integer,% -as.data.frame.factor,as.data.frame.difftime,as.data.frame.default,as.data.frame.data.frame,as.data.frame.complex,% -as.data.frame.character,as.data.frame.array,as.data.frame.POSIXlt,as.data.frame.POSIXct,as.data.frame.Date,% -as.data.frame.AsIs,as.data.frame,as.complex,as.character.srcref,as.character.octmode,% -as.character.numeric_version,as.character.hexmode,as.character.factor,as.character.error,as.character.default,% -as.character.condition,as.character.POSIXt,as.character.Date,as.character,as.call,% -as.array.default,as.array,as.POSIXlt.numeric,as.POSIXlt.factor,as.POSIXlt.default,% -as.POSIXlt.dates,as.POSIXlt.date,as.POSIXlt.character,as.POSIXlt.POSIXct,as.POSIXlt.Date,% -as.POSIXlt,as.POSIXct.numeric,as.POSIXct.default,as.POSIXct.dates,as.POSIXct.date,% -as.POSIXct.POSIXlt,as.POSIXct.Date,as.POSIXct,as.Date.numeric,as.Date.factor,% -as.Date.default,as.Date.dates,as.Date.date,as.Date.character,as.Date.POSIXlt,% -as.Date.POSIXct,as.Date,arrayInd,aperm.table,aperm.default,% -anyDuplicated.matrix,anyDuplicated.default,anyDuplicated.data.frame,anyDuplicated.array,anyDuplicated,% -all.vars,all.names,all.equal.raw,all.equal.numeric,all.equal.list,% -all.equal.language,all.equal.formula,all.equal.factor,all.equal.default,all.equal.character,% -all.equal.POSIXct,all.equal,agrep,addTaskCallback,addNA,% -Vectorize,T,Sys.which,Sys.unsetenv,Sys.umask,% -Sys.timezone,Sys.time,Sys.sleep,Sys.setlocale,Sys.setenv,% -Sys.setFileTime,Sys.readlink,Sys.localeconv,Sys.junction,Sys.info,% -Sys.glob,Sys.getpid,Sys.getlocale,Sys.getenv,Sys.chmod,% -Sys.Date,Summary.ordered,Summary.numeric_version,Summary.factor,Summary.difftime,% -Summary.data.frame,Summary.POSIXlt,Summary.POSIXct,Summary.Date,Reduce,% -R_system_version,RNGversion,R.version.string,R.version,R.home,% -R.Version,Position,Ops.ordered,Ops.numeric_version,Ops.factor,% -Ops.difftime,Ops.data.frame,Ops.POSIXt,Ops.Date,Negate,% -Math.factor,Math.difftime,Math.data.frame,Math.POSIXt,Math.Date,% -Map,La.svd,LETTERS,ISOdatetime,ISOdate,% -Find,Filter,F,Encoding<-,Encoding,% -Cstack_info% +margin.table,mapply,makeActiveBinding,make.unique,make.names,% +lower.tri,logb,lockEnvironment,lockBinding,loadingNamespaceInfo,% +loadedNamespaces,loadNamespace,list2env,list.files,list.dirs,% +library.dynam.unload,library.dynam,lfactorial,levels<-.factor,levels<-,% +levels.default,letters,length<-.factor,length<-,length.POSIXlt,% +lazyLoadDBfetch,lazyLoadDBexec,lazyLoad,labels.default,l10n_info,% +kappa.qr,kappa.lm,kappa.default,julian.POSIXt,julian.Date,% +julian,isdebugged,isatty,isTRUE,isSymmetric.matrix,% +isSymmetric,isSeekable,isS4,isRestart,isOpen,% +isNamespace,isIncomplete,isBaseNamespace,is.vector,is.unsorted,% +is.table,is.symbol,is.single,is.recursive,is.raw,% +is.qr,is.primitive,is.pairlist,is.package_version,is.ordered,% +is.object,is.numeric_version,is.numeric.difftime,is.numeric.POSIXt,is.numeric.Date,% +is.numeric,is.null,is.nan,is.name,is.na<-.factor,% +is.na<-.default,is.na<-,is.na.numeric_version,is.na.data.frame,is.na.POSIXlt,% +is.na,is.matrix,is.logical,is.loaded,is.list,% +is.language,is.integer,is.infinite,is.function,is.finite,% +is.factor,is.expression,is.environment,is.element,is.double,% +is.data.frame,is.complex,is.character,is.call,is.atomic,% +is.array,is.R,invokeRestartInteractively,invokeRestart,inverse.rle,% +intToUtf8,intToBits,importIntoEnv,identity,identical,% +icuSetCollate,iconvlist,iconv,gzfile,gzcon,% +grepl,grepRaw,gregexpr,gettextf,gettext,% +getTaskCallbackNames,getSrcLines,getRversion,getNativeSymbolInfo,getNamespaceVersion,% +getNamespaceUsers,getNamespaceName,getNamespaceInfo,getNamespaceImports,getNamespaceExports,% +getNamespace,getLoadedDLLs,getHook,getExportedValue,getElement,% +getDLLRegisteredRoutines.character,getDLLRegisteredRoutines.DLLInfo,getDLLRegisteredRoutines,getConnection,getCallingDLLe,% +getCallingDLL,getAllConnections,gctorture2,gc.time,formatDL,% +format.summaryDefault,format.pval,format.packageInfo,format.octmode,format.numeric_version,% +format.libraryIQR,format.info,format.hexmode,format.factor,format.difftime,% +format.default,format.data.frame,format.POSIXlt,format.POSIXct,format.Date,% +format.AsIs,formals<-,force,flush.connection,flush,% +findRestart,findPackageEnv,findInterval,find.package,file.symlink,% +file.show,file.rename,file.remove,file.path,file.link,% +file.info,file.exists,file.create,file.copy,file.choose,% +file.append,file.access,fifo,factorial,expm1,% +expand.grid,eval.parent,environmentName,environmentIsLocked,environment<-,% +env.profile,enquote,encodeString,enc2utf8,enc2native,% +emptyenv,eapply,dyn.unload,dyn.load,duplicated.numeric_version,% +duplicated.matrix,duplicated.default,duplicated.data.frame,duplicated.array,duplicated.POSIXlt,% +droplevels.factor,droplevels.data.frame,droplevels,do.call,dir.create,% +dimnames<-.data.frame,dimnames<-,dimnames.data.frame,dim<-,dim.data.frame,% +difftime,diff.default,diff.POSIXt,diff.Date,diag<-,% +determinant.matrix,determinant,det,delayedAssign,default.stringsAsFactors,% +debugonce,data.matrix,data.frame,data.class,dQuote,% +cut.default,cut.POSIXt,cut.Date,contributors,conditionMessage.condition,% +conditionMessage,conditionCall.condition,conditionCall,computeRestarts,comment<-,% +colnames<-,colSums,colMeans,closeAllConnections,close.srcfilealias,% +close.srcfile,close.connection,clearPushBack,class<-,chol.default,% [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 914 From noreply at r-forge.r-project.org Fri Sep 13 01:35:11 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 01:35:11 +0200 (CEST) Subject: [Distr-commits] r915 - branches/distr-2.6 branches/distr-2.6/pkg branches/distr-2.6/pkg/distr branches/distr-2.6/pkg/distr/man branches/distr-2.6/pkg/distrMod branches/distr-2.6/pkg/distrMod/man branches/distr-2.6/pkg/distrSim branches/distr-2.6/pkg/distrSim/man pkg/utils Message-ID: <20130912233511.83C9E184288@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-13 01:35:11 +0200 (Fri, 13 Sep 2013) New Revision: 915 Added: branches/distr-2.6/pkg/ branches/distr-2.6/pkg/distr/ branches/distr-2.6/pkg/distrMod/ branches/distr-2.6/pkg/distrSim/ Modified: branches/distr-2.6/pkg/distr/DESCRIPTION branches/distr-2.6/pkg/distr/man/0distr-package.Rd branches/distr-2.6/pkg/distrMod/DESCRIPTION branches/distr-2.6/pkg/distrMod/man/0distrMod-package.Rd branches/distr-2.6/pkg/distrSim/DESCRIPTION branches/distr-2.6/pkg/distrSim/man/0distrSim-package.Rd pkg/utils/DESCRIPTIONutils.R Log: after acceptance on CRAN, generated branches/distr-2.6/pkg versions of distr, distrSim, distrMod Modified: branches/distr-2.6/pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2013-09-12 13:15:18 UTC (rev 913) +++ branches/distr-2.6/pkg/distr/DESCRIPTION 2013-09-12 23:35:11 UTC (rev 915) @@ -1,14 +1,13 @@ Package: distr -Version: 2.5.2 -Date: 2013-09-12 +Version: 2.6 +Date: 2013-09-13 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions -Authors at R: c(person("Florian", "Camphausen", role=c("aut")), - 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=c("aut", "cph")), - person("R Core Team", role = c("ctb", "cph"), - comment="for source file ks.c/ routines 'pKS2' and 'pKolmogorov2x'")) +Authors at R: c(person("Florian", "Camphausen", role=c("aut")), 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=c("aut", + "cph")), person("R Core Team", role = c("ctb", "cph"), comment="for source file ks.c/ + routines 'pKS2' and 'pKolmogorov2x'")) Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils Suggests: distrEx Imports: stats @@ -18,4 +17,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 910 +SVNRevision: 914 Modified: branches/distr-2.6/pkg/distr/man/0distr-package.Rd =================================================================== --- pkg/distr/man/0distr-package.Rd 2013-09-12 13:15:18 UTC (rev 913) +++ branches/distr-2.6/pkg/distr/man/0distr-package.Rd 2013-09-12 23:35:11 UTC (rev 915) @@ -43,14 +43,14 @@ \details{ \tabular{ll}{ Package: \tab distr \cr -Version: \tab 2.5 \cr -Date: \tab 2013-09-11 \cr +Version: \tab 2.6 \cr +Date: \tab 2013-09-13 \cr Depends: \tab R(>= 2.2.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils\cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 904 \cr +SVNRevision: \tab 914 \cr }} Modified: branches/distr-2.6/pkg/distrMod/DESCRIPTION =================================================================== --- pkg/distrMod/DESCRIPTION 2013-09-12 13:15:18 UTC (rev 913) +++ branches/distr-2.6/pkg/distrMod/DESCRIPTION 2013-09-12 23:35:11 UTC (rev 915) @@ -1,16 +1,17 @@ Package: distrMod -Version: 2.5.2 -Date: 2013-09-12 +Version: 2.6 +Date: 2013-09-13 Title: Object oriented implementation of probability models Description: Object oriented implementation of probability models based on packages 'distr' and 'distrEx' Author: Matthias Kohl, Peter Ruckdeschel Maintainer: Peter Ruckdeschel -Depends: R(>= 2.14.0), distr(>= 2.5.2), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, methods +Depends: R(>= 2.14.0), distr(>= 2.5.2), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, + methods ByteCompile: yes License: LGPL-3 Encoding: latin1 URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 909 +SVNRevision: 914 Modified: branches/distr-2.6/pkg/distrMod/man/0distrMod-package.Rd =================================================================== --- pkg/distrMod/man/0distrMod-package.Rd 2013-09-12 13:15:18 UTC (rev 913) +++ branches/distr-2.6/pkg/distrMod/man/0distrMod-package.Rd 2013-09-12 23:35:11 UTC (rev 915) @@ -15,14 +15,14 @@ \details{ \tabular{ll}{ Package: \tab distrMod \cr -Version: \tab 2.5 \cr -Date: \tab 2013-09-11 \cr +Version: \tab 2.6 \cr +Date: \tab 2013-09-13 \cr Depends: \tab R(>= 2.6.0), methods, startupmsg, distr(>= 2.2), distrEx(>= 2.2), RandVar(>= 0.6.3), MASS, stats4 \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 904 \cr +SVNRevision: \tab 914 \cr }} \section{Classes}{ Modified: branches/distr-2.6/pkg/distrSim/DESCRIPTION =================================================================== --- pkg/distrSim/DESCRIPTION 2013-09-12 13:15:18 UTC (rev 913) +++ branches/distr-2.6/pkg/distrSim/DESCRIPTION 2013-09-12 23:35:11 UTC (rev 915) @@ -1,6 +1,6 @@ Package: distrSim -Version: 2.5.2 -Date: 2013-09-12 +Version: 2.6 +Date: 2013-09-13 Title: Simulation classes based on package distr Depends: R(>= 2.14.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.5.2) Suggests: distrEx(>= 2.2) @@ -13,4 +13,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 909 +SVNRevision: 914 Modified: branches/distr-2.6/pkg/distrSim/man/0distrSim-package.Rd =================================================================== --- pkg/distrSim/man/0distrSim-package.Rd 2013-09-12 13:15:18 UTC (rev 913) +++ branches/distr-2.6/pkg/distrSim/man/0distrSim-package.Rd 2013-09-12 23:35:11 UTC (rev 915) @@ -13,14 +13,14 @@ \details{ \tabular{ll}{ Package: \tab distrSim \cr -Version: \tab 2.5 \cr -Date: \tab 2013-09-11 \cr +Version: \tab 2.6 \cr +Date: \tab 2013-09-13 \cr Depends: \tab R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.0), startupmsg\cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 904 \cr +SVNRevision: \tab 914 \cr } } \section{Classes}{ Modified: pkg/utils/DESCRIPTIONutils.R =================================================================== --- pkg/utils/DESCRIPTIONutils.R 2013-09-12 21:37:25 UTC (rev 914) +++ pkg/utils/DESCRIPTIONutils.R 2013-09-12 23:35:11 UTC (rev 915) @@ -35,9 +35,10 @@ oldDir <- getwd() on.exit(setwd(oldDir)) setwd(startDir) - if(is.null(pathRepo)) pathRepo <- gsub(".*/([^/]+)/*$","\\1", startDir) if(withSVNread){ - svnrev <- getRevNr(startDir, pathRepo)[[1]] + startD <- gsub("/branches/[^/]+","",startDir) + if(is.null(pathRepo)) pathRepo <- gsub(".*/([^/]+)/*$","\\1", startD) + svnrev <- getRevNr(startD, pathRepo)[[1]] print(svnrev) if("SVNRevision" %in% names){ values[which(names=="SVNRevision"),] <- svnrev @@ -177,12 +178,20 @@ "distrTeach", "distrTEst", "distrEllipse", "distrRmetrics") Names <- c("Version") -Values <- matrix(c("2.5",1,length(Pkgs)) +Values <- matrix(c("2.5"),1,length(Pkgs)) colnames(Values) <- Pkgs rownames(Values) <- Names Values["Version",,drop=FALSE] <- c("0.9", "0.7", rep("2.5",6)) changeDescription(startDir = "C:/rtest/distr",names=Names, pkgs=Pkgs, values=Values) + +Pkgs <- c("distr", "distrSim","distrMod") +Names <- c("Version") +Values <- matrix(c("2.6"),1,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/branches/distr-2.6",names=Names, + pkgs=Pkgs, values=Values) } ############################################################################## From noreply at r-forge.r-project.org Fri Sep 13 03:09:12 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 03:09:12 +0200 (CEST) Subject: [Distr-commits] r916 - pkg/setRNG/man Message-ID: <20130913010913.0F3B4185CE9@r-forge.r-project.org> Author: pgilbert Date: 2013-09-13 03:09:11 +0200 (Fri, 13 Sep 2013) New Revision: 916 Modified: pkg/setRNG/man/getRNG.Rd Log: minor edit. Modified: pkg/setRNG/man/getRNG.Rd =================================================================== --- pkg/setRNG/man/getRNG.Rd 2013-09-12 23:35:11 UTC (rev 915) +++ pkg/setRNG/man/getRNG.Rd 2013-09-13 01:09:11 UTC (rev 916) @@ -2,7 +2,7 @@ \alias{getRNG} \alias{getRNG.default} -\title{get the RND and seed from an object} +\title{get the RNG and seed from an object} \description{ Get the random number generator and seed used to generate an object. } From noreply at r-forge.r-project.org Fri Sep 13 09:29:17 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 09:29:17 +0200 (CEST) Subject: [Distr-commits] r917 - branches/distr-2.5/pkg/distr Message-ID: <20130913072917.2227F1851A9@r-forge.r-project.org> Author: kroisand Date: 2013-09-13 09:29:16 +0200 (Fri, 13 Sep 2013) New Revision: 917 Modified: branches/distr-2.5/pkg/distr/DESCRIPTION Log: Beschreibungsdatei mit falschem Authors at R verbessert Modified: branches/distr-2.5/pkg/distr/DESCRIPTION =================================================================== --- branches/distr-2.5/pkg/distr/DESCRIPTION 2013-09-13 01:09:11 UTC (rev 916) +++ branches/distr-2.5/pkg/distr/DESCRIPTION 2013-09-13 07:29:16 UTC (rev 917) @@ -3,12 +3,13 @@ Date: 2013-09-12 Title: Object oriented implementation of distributions Description: S4 Classes and Methods for distributions -Authors at R: c(person("Florian", "Camphausen", role=c("cre")), - person("Matthias", "Kohl", role=c("aut", "cph")), - person("Peter", "Ruckdeschel", role=c("aut", "cph")), - person("Thomas", "Stabla", role=c("aut", "cph")), - person("R Core Team", role = c("ctb", "cph"))) -Maintainer: Peter Ruckdeschel +Authors at R: c(person("Peter", "Ruckdeschel", role=c("cre", "cph"), + email="Peter.Ruckdeschel at itwm.fraunhofer.de"), + person("Florian", "Camphausen", role=c("aut")), + person("Matthias", "Kohl", role=c("aut", "cph")), + person("Thomas", "Stabla", role=c("aut", "cph")), + person("R Core Team", role = c("ctb", "cph"), + comment="for source file ks.c/ routines 'pKS2' and 'pKolmogorov2x'")) Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils Suggests: distrEx Imports: stats From noreply at r-forge.r-project.org Fri Sep 13 09:42:25 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 09:42:25 +0200 (CEST) Subject: [Distr-commits] r918 - pkg/utils Message-ID: <20130913074225.5743F185A14@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-13 09:42:25 +0200 (Fri, 13 Sep 2013) New Revision: 918 Added: pkg/utils/RCRAN.bat Log: neues Makro RCRAN.bat Added: pkg/utils/RCRAN.bat =================================================================== --- pkg/utils/RCRAN.bat (rev 0) +++ pkg/utils/RCRAN.bat 2013-09-13 07:42:25 UTC (rev 918) @@ -0,0 +1,7 @@ + at echo off +if not "%2"=="" ( +call R CMD check --as-cran --outdir=%2 %1 +) else ( +call R CMD check --as-cran %1 +) +echo on From noreply at r-forge.r-project.org Fri Sep 13 09:45:17 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 09:45:17 +0200 (CEST) Subject: [Distr-commits] r919 - pkg/utils Message-ID: <20130913074517.2239C185B55@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-13 09:45:16 +0200 (Fri, 13 Sep 2013) New Revision: 919 Added: pkg/utils/README_dt_PkgCheck Log: README_dt_PkgCheck erstellt Added: pkg/utils/README_dt_PkgCheck =================================================================== --- pkg/utils/README_dt_PkgCheck (rev 0) +++ pkg/utils/README_dt_PkgCheck 2013-09-13 07:45:16 UTC (rev 919) @@ -0,0 +1,44 @@ +Zum Paketbauen etc verwende ich/Peter derzeit die unten genannten Schritte 1-6. + +Neu ist seit knapp einem Jahr, dass Schritte 2,5,6 nun auf den tar-ball, also +_.tar.gz und nicht mehr auf den Ordner angewendet +werden; Schritte 1 und 4 hingegen weiter auf den Ordner . + +1. Paket bauen -> Ergebnis _.tar.gz +2. Checken von _.tar.gz +falls "fehlerfrei" stehen Ergebnisse in Ordner .Rcheck +3. Kopieren von -Ex.Rout aus Ordner .Rcheck + in Ordner /tests/Examples und Umbenennen in + -Ex.Rout.save / bzw ?berschreiben der alten + Datei -Ex.Rout.save +4. noch mal Paket bauen +5. Installieren von _.tar.gz +6. Bauen des Windows Zip Files _.tar.gz + +Hierzu habe ich die Makros RBuild.bat (Schritte 1 und 4) RCheck.bat +(Schritt 2), RInstall.bat (Schritt 5) und RZip.bat (Schritt 6) in +distrXXX-svn-Repo unter pkg/utils. + + at Matthias: vllt kannst Du die Linux Shell Skripten darin mal +aktualisieren ;-) + +Dieses Verzeichnis liegt bei mir im Pfad so dass ich die Makros einfach +in der Kommandozeile aufrufen kann. + +F?r Schritte 1,4 verwende ich RBuild +F?r Schritt 2 verwende ich RCheck _.tar.gz +bzw R CMD check --as-cran _.tar.gz +F?r Schritt 5 RInstall _.tar.gz +F?r Schritt 6 RZip _.tar.gz + +im einzelnen: + +RBuild: = R CMD build --compact-vignettes="gs+qpdf" --resave-data +RCheck: = R CMD check --multiarch --timings --install-args="--byte-compile \ + --with-keep.source --compact-docs --resave-data --install-tests --example \ + --html --latex --clean --preclean --compile-both" +RInstall: = R CMD INSTALL --byte-compile --with-keep.source --compact-docs \ + --resave-data --install-tests --example --html --latex --clean --preclean \ + --compile-both +RZip: = R CMD INSTALL --build --byte-compile --with-keep.source --compact-docs \ + --resave-data --install-tests --example --html --latex --clean --preclean --compile-both From noreply at r-forge.r-project.org Fri Sep 13 10:38:35 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 10:38:35 +0200 (CEST) Subject: [Distr-commits] r920 - pkg/utils Message-ID: <20130913083835.C8B1C184F9A@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-13 10:38:35 +0200 (Fri, 13 Sep 2013) New Revision: 920 Added: pkg/utils/DESCRIPTIONutilsExamples.R Modified: pkg/utils/DESCRIPTIONutils.R Log: updated DESCRIPTIONutils.R -> pls check if also works on Linux / in particular whether getRevNr() works (in file getRevNr.R) Modified: pkg/utils/DESCRIPTIONutils.R =================================================================== --- pkg/utils/DESCRIPTIONutils.R 2013-09-13 07:45:16 UTC (rev 919) +++ pkg/utils/DESCRIPTIONutils.R 2013-09-13 08:38:35 UTC (rev 920) @@ -1,7 +1,5 @@ ### some utils for unified treatment of DESCRIPTION files from R -source("C:/rtest/distr/branches/distr-2.4/pkg/utils/getRevNr.R") - updatePackageHelp <- function(package){ if(file.exists(file.path(package, "DESCRIPTION"))){ DFF <- read.dcf(file = file.path(package, "DESCRIPTION")) @@ -25,76 +23,98 @@ }} } +## needs: getRevNr() in getRevNr.R in utils/ e.g. +## source("C:/rtest/distr/branches/distr-2.4/pkg/utils/getRevNr.R") -changeDescription <- function(startDir, names, values, - pkgs = NULL, - withSVNread = TRUE, - withPackageHelpUpdate = TRUE, - pathRepo = NULL, - withDate = TRUE){ - oldDir <- getwd() - on.exit(setwd(oldDir)) - setwd(startDir) - if(withSVNread){ - startD <- gsub("/branches/[^/]+","",startDir) - if(is.null(pathRepo)) pathRepo <- gsub(".*/([^/]+)/*$","\\1", startD) - svnrev <- getRevNr(startD, pathRepo)[[1]] - print(svnrev) - if("SVNRevision" %in% names){ - values[which(names=="SVNRevision"),] <- svnrev - }else{ - nr <- nrow(values) - names <- c(names,"SVNRevision") - values <- rbind(values,rep(svnrev,ncol(values))) - rownames(values)[nr+1] <- "SVNRevision" - } - } - if(withDate){ - if(!"Date" %in% names){ - nr <- nrow(values) - dat <- format(Sys.time(), format="%Y-%m-%d") - names <- c(names,"Date") - values <- rbind(values,rep(dat,ncol(values))) - rownames(values)[nr+1] <- "Date" - } - } -# print(names) -# print(values) - - if(is.matrix(values) && is.null(colnames(values))) - colnames(values) <- rep(pkgs, length.out = ncol(values)) - - if(is.null(pkgs)) { - pkgs <- pkgs <- dir("pkg/") - idx <- grep(".+\\.",pkgs) - if(length(idx)) idx <- -idx else idx <- TRUE - pkgs <- pkgs[idx] - } - if (length(pkgs) && length(names) && length(values)){ - pkgs <- pkgs[sapply(pkgs, function(x) - file.exists(paste("pkg/",x,"/DESCRIPTION",sep="")))] + changeDescription <- function(startDir ## folder with pkgs to be updated, + ### e.g. "C:/rtest/distr/branches/distr-2.6" + ,names ### names of the DESCRIPTION tags to be updated + ,values ### values of the DESCRIPTION tags to be updated + ## (a matrix, columns = pkgs and row = tags see examples) + ,pkgs = NULL ## pkgs to be updated; if NULL all pkgs in startfolder + ,withSVNread = TRUE ### should SVNRevision be updated + ,withPackageHelpUpdate = TRUE ### should file -package.Rd in man + ## be updated + ,pathRepo = NULL ### path to svn repo; if NULL deduced from startDir + ### assuming r-forge + ,withDate = TRUE, ### shall date be updated? + inRforge = TRUE, ### shall we use r-forge as repository + ## (otherwise need full URL as arg pathRepo + withlogin = TRUE, ### do we need option --login (yes in cygwin, don't know in Linux) + PathToBash = "C:/cygwin/bin/bash", ## path to bash + PathToreadsvnlog.sh="C:/rtest/distr/branches/distr-2.4/pkg/utils", + ### path to shell script readsvnlog.sh + tmpfile = "C:/rtest/tmp-svnlog5.txt", ### some tmpfile to which we write the + ## results temporarily; is deleted afterwords + verbose=FALSE + verbose = FALSE){ + oldDir <- getwd() + on.exit(setwd(oldDir)) + setwd(startDir) + if(withSVNread){ + startD <- gsub("/branches/[^/]+","",startDir) + if(is.null(pathRepo)) pathRepo <- gsub(".*/([^/]+)/*$","\\1", startD) + svnrev <- getRevNr(startD, pathRepo, inRforge, withlogin, + PathToBash, PathToreadsvnlog.sh)[[1]] + print(svnrev) + if("SVNRevision" %in% names){ + values[which(names=="SVNRevision"),] <- svnrev + }else{ + nr <- nrow(values) + names <- c(names,"SVNRevision") + values <- rbind(values,rep(svnrev,ncol(values))) + rownames(values)[nr+1] <- "SVNRevision" + } + } + if(withDate){ + if(!"Date" %in% names){ + nr <- nrow(values) + dat <- format(Sys.time(), format="%Y-%m-%d") + names <- c(names,"Date") + values <- rbind(values,rep(dat,ncol(values))) + rownames(values)[nr+1] <- "Date" + } + } + # print(names) + # print(values) - if(!is.matrix(values)) - values <- matrix(values, length(names), length(pkgs), - dimnames = list(names, pkgs)) - else values <- values[,pkgs,drop=F] - # get packages - sapply(pkgs, function(x){ - FN <- file.path("pkg",x,"DESCRIPTION") - xx <- read.dcf(FN) -# print(xx) -# print(values) -# print(names) -# print(values[names,x]) -# print(xx[,names]) - xx[,names] <- values[names,x] - write.dcf(xx, file=FN,width=1.2*getOption("width")) - if(withPackageHelpUpdate) - updatePackageHelp(package=file.path("pkg",x)) - }) + if(is.matrix(values) && is.null(colnames(values))) + colnames(values) <- rep(pkgs, length.out = ncol(values)) + if(is.null(pkgs)) { + pkgs <- pkgs <- dir("pkg/") + idx <- grep(".+\\.",pkgs) + if(length(idx)) idx <- -idx else idx <- TRUE + pkgs <- pkgs[idx] + } + if (length(pkgs) && length(names) && length(values)){ + pkgs <- pkgs[sapply(pkgs, function(x) + file.exists(file.path("pkg",x,"DESCRIPTION")))] + print(pkgs) + if(!is.matrix(values)) + values <- matrix(values, length(names), length(pkgs), + dimnames = list(names, pkgs)) + else values <- values[,pkgs,drop=F] + # get packages + sapply(pkgs, function(x){ + FN <- file.path("pkg",x,"DESCRIPTION") + xx <- read.dcf(FN) + if(verbose){ + print(xx) + print(values) + print(names) + print(values[names,x]) + print(xx[,names]) + } + xx[,names] <- values[names,x] + print(xx[,names]) + write.dcf(xx, file=FN,width=1.2*getOption("width")) + if(withPackageHelpUpdate) + updatePackageHelp(package=file.path("pkg",x)) + }) + } + return(invisible()) } - return(invisible()) -} +### Examples see DESCRIPTIONutilsExamples.R in same folder getVersions <- function(startDir = "C:/rtest/robast/branches/robast-0.7", pkgs){ @@ -104,98 +124,8 @@ ff[1,"Version"]}))} -############################################################################## -# EXAMPLES -############################################################################## -if(FALSE){## Example 1 -Pkgs <- c("startupmsg", "SweaveListingUtils", - "distr", "distrEx", "distrDoc", - "distrMod", "distrTeach", "distrSim", "distrTEst") -Names <- c("Version", "License", "Date") -Values <- matrix(c("2.0.2","LGPL-3"),3,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -Values["Version",] <- c("0.5.2", "0.1.1", "2.0.3", "2.0.2", "2.0.3", - rep("2.0.2",4)) -changeDescription(startDir = "C:/rtest/distr",names=Names, - pkgs=Pkgs, values=Values) -} -if(FALSE){## Example 2 -Pkgs <- c("SweaveListingUtils", "distr", "distrEx", - "distrMod", "distrTeach", "distrSim", "distrTEst") -Names <- c("Date") -Values <- matrix((format(Sys.time(), format="%Y-%m-%d")),1,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -changeDescription(startDir = "C:/rtest/distr",names="Date", - pkgs=Pkgs, values=format(Sys.time(), format="%Y-%m-%d")) -} -if(FALSE){### Version 2.4.1 -Pkgs <- c("startupmsg", "SweaveListingUtils", - "distr", "distrEx", "distrDoc", - "distrMod", "distrTeach", "distrSim", - "distrTEst", "distrEllipse", "distrRmetrics") -Names <- c("Version") -Values <- matrix(c("2.4.1",1,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -Values["Version",,drop=FALSE] <- c("0.8.1", "0.6.1", rep("2.4.1",9)) -changeDescription(startDir = "C:/rtest/distr",names=Names, - pkgs=Pkgs, values=Values) -} -if(FALSE){### Version 0.9.1 -Pkgs <- c("RobLox", "RobLoxBioC", "RobRex", "ROptRegTS") -Names <- c("Version","License") -Values <- matrix(c("0.9","LGPL-3"),2,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -changeDescription(startDir = "C:/rtest/robast",names=Names, - pkgs=Pkgs, values=Values) -} -if(FALSE){ -Pkgs <- c("RandVar", "ROptEstOld") -Names <- c("Version","License") -Values <- matrix(c("0.9.1","LGPL-3"),2,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -changeDescription(startDir = "C:/rtest/robast",names=Names, - pkgs=Pkgs, values=Values) - -Pkgs <- c("RandVar", "ROptEstOld", "RobAStBase", "RobAStRDA", "RobLox", "RobRex", "RobLoxBioC", "ROptEst", "RobExtremes", "ROptRegTS") -Names <- c("Version") -Values <- matrix(c("1.0"),1,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -changeDescription(startDir = "C:/rtest/robast/branches/robast-1.0",names=Names, - pkgs=Pkgs, values=Values) -} - -if(FALSE){### Version 2.5 -Pkgs <- c("startupmsg", "SweaveListingUtils", - "distrEx", "distrDoc", - "distrTeach", - "distrTEst", "distrEllipse", "distrRmetrics") -Names <- c("Version") -Values <- matrix(c("2.5"),1,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -Values["Version",,drop=FALSE] <- c("0.9", "0.7", rep("2.5",6)) -changeDescription(startDir = "C:/rtest/distr",names=Names, - pkgs=Pkgs, values=Values) - -Pkgs <- c("distr", "distrSim","distrMod") -Names <- c("Version") -Values <- matrix(c("2.6"),1,length(Pkgs)) -colnames(Values) <- Pkgs -rownames(Values) <- Names -changeDescription(startDir = "C:/rtest/distr/branches/distr-2.6",names=Names, - pkgs=Pkgs, values=Values) -} -############################################################################## - - copyDescription <- function(startDir){ oldDir <- getwd() on.exit(setwd(oldDir)) Added: pkg/utils/DESCRIPTIONutilsExamples.R =================================================================== --- pkg/utils/DESCRIPTIONutilsExamples.R (rev 0) +++ pkg/utils/DESCRIPTIONutilsExamples.R 2013-09-13 08:38:35 UTC (rev 920) @@ -0,0 +1,90 @@ +############################################################################## +# EXAMPLES +############################################################################## +if(FALSE){## Example 1 +Pkgs <- c("startupmsg", "SweaveListingUtils", + "distr", "distrEx", "distrDoc", + "distrMod", "distrTeach", "distrSim", "distrTEst") +Names <- c("Version", "License", "Date") +Values <- matrix(c("2.0.2","LGPL-3"),3,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +Values["Version",] <- c("0.5.2", "0.1.1", "2.0.3", "2.0.2", "2.0.3", + rep("2.0.2",4)) +changeDescription(startDir = "C:/rtest/distr",names=Names, + pkgs=Pkgs, values=Values) +} + +if(FALSE){## Example 2 +Pkgs <- c("SweaveListingUtils", "distr", "distrEx", + "distrMod", "distrTeach", "distrSim", "distrTEst") +Names <- c("Date") +Values <- matrix((format(Sys.time(), format="%Y-%m-%d")),1,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr",names="Date", + pkgs=Pkgs, values=format(Sys.time(), format="%Y-%m-%d")) +} + +if(FALSE){### Version 2.4.1 +Pkgs <- c("startupmsg", "SweaveListingUtils", + "distr", "distrEx", "distrDoc", + "distrMod", "distrTeach", "distrSim", + "distrTEst", "distrEllipse", "distrRmetrics") +Names <- c("Version") +Values <- matrix(c("2.4.1",1,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +Values["Version",,drop=FALSE] <- c("0.8.1", "0.6.1", rep("2.4.1",9)) +changeDescription(startDir = "C:/rtest/distr",names=Names, + pkgs=Pkgs, values=Values) +} +if(FALSE){### Version 0.9.1 +Pkgs <- c("RobLox", "RobLoxBioC", "RobRex", "ROptRegTS") +Names <- c("Version","License") +Values <- matrix(c("0.9","LGPL-3"),2,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/robast",names=Names, + pkgs=Pkgs, values=Values) +} +if(FALSE){ +Pkgs <- c("RandVar", "ROptEstOld") +Names <- c("Version","License") +Values <- matrix(c("0.9.1","LGPL-3"),2,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/robast",names=Names, + pkgs=Pkgs, values=Values) + +Pkgs <- c("RandVar", "ROptEstOld", "RobAStBase", "RobAStRDA", "RobLox", "RobRex", "RobLoxBioC", "ROptEst", "RobExtremes", "ROptRegTS") +Names <- c("Version") +Values <- matrix(c("1.0"),1,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/robast/branches/robast-1.0",names=Names, + pkgs=Pkgs, values=Values) +} + +if(FALSE){### Version 2.5 +Pkgs <- c("startupmsg", "SweaveListingUtils", + "distrEx", "distrDoc", + "distrTeach", + "distrTEst", "distrEllipse", "distrRmetrics") +Names <- c("Version") +Values <- matrix(c("2.5"),1,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +Values["Version",,drop=FALSE] <- c("0.9", "0.7", rep("2.5",6)) +changeDescription(startDir = "C:/rtest/distr",names=Names, + pkgs=Pkgs, values=Values) + +Pkgs <- c("distr", "distrSim","distrMod") +Names <- c("Version") +Values <- matrix(c("2.6"),1,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/branches/distr-2.6",names=Names, + pkgs=Pkgs, values=Values) +} +############################################################################## From noreply at r-forge.r-project.org Fri Sep 13 11:00:26 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 11:00:26 +0200 (CEST) Subject: [Distr-commits] r921 - pkg/utils Message-ID: <20130913090027.041BF183B43@r-forge.r-project.org> Author: kroisand Date: 2013-09-13 11:00:26 +0200 (Fri, 13 Sep 2013) New Revision: 921 Modified: pkg/utils/Rpkgcheck.sh Log: Rpkgcheck.sh daran angepasst, dass tar.gz genommen werden muss; auch Reihenfolge vertauscht, d.h. zuerst bauen, dann testen und danach erst entfernen und installieren Modified: pkg/utils/Rpkgcheck.sh =================================================================== --- pkg/utils/Rpkgcheck.sh 2013-09-13 08:38:35 UTC (rev 920) +++ pkg/utils/Rpkgcheck.sh 2013-09-13 09:00:26 UTC (rev 921) @@ -8,11 +8,26 @@ echo --------------------------------------------- # echo --------------------------------------------- +echo remove old tar.gz +echo --------------------------------------------- +rm -f $2*.tar.gz +# +echo --------------------------------------------- echo build echo --------------------------------------------- -$1 CMD build --compact-vignettes $2 +$1 CMD build --compact-vignettes="gs+qpdf" --resave-data $2 # +tarGz=`ls $2*.tar.gz` echo --------------------------------------------- +echo tar.gz is $tarGz +echo --------------------------------------------- +# +echo --------------------------------------------- +echo check as cran +echo --------------------------------------------- +$1 CMD check --as-cran --timings $tarGz +# +echo --------------------------------------------- echo REMOVE echo --------------------------------------------- $1 CMD REMOVE $2 @@ -20,9 +35,10 @@ echo --------------------------------------------- echo INSTALL echo --------------------------------------------- -$1 CMD INSTALL $2 -# -echo --------------------------------------------- -echo check -echo --------------------------------------------- -$1 CMD check --as-cran --timings $2 +$1 CMD INSTALL \ + --byte-compile --with-keep.source --compact-docs \ + --resave-data --install-tests --example \ + --html --latex --clean --preclean \ + --compile-both \ + $tarGz + From noreply at r-forge.r-project.org Fri Sep 13 11:58:41 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 11:58:41 +0200 (CEST) Subject: [Distr-commits] r922 - pkg/utils Message-ID: <20130913095841.820201855D8@r-forge.r-project.org> Author: kroisand Date: 2013-09-13 11:58:41 +0200 (Fri, 13 Sep 2013) New Revision: 922 Modified: pkg/utils/Rpkgcheck.sh Log: check routine adapted such that removing the old version of a library and installing the new happens only if the check succeeded Modified: pkg/utils/Rpkgcheck.sh =================================================================== --- pkg/utils/Rpkgcheck.sh 2013-09-13 09:00:26 UTC (rev 921) +++ pkg/utils/Rpkgcheck.sh 2013-09-13 09:58:41 UTC (rev 922) @@ -4,16 +4,16 @@ export _R_CHECK_SUGGESTS_ONLY_=true # echo --------------------------------------------- -echo start full package check +echo start full package check of $2 echo --------------------------------------------- # echo --------------------------------------------- -echo remove old tar.gz +echo remove old tar.gz of $2 echo --------------------------------------------- rm -f $2*.tar.gz # echo --------------------------------------------- -echo build +echo build $2 echo --------------------------------------------- $1 CMD build --compact-vignettes="gs+qpdf" --resave-data $2 # @@ -23,22 +23,34 @@ echo --------------------------------------------- # echo --------------------------------------------- -echo check as cran +echo check as cran $tarGz echo --------------------------------------------- $1 CMD check --as-cran --timings $tarGz +result=$? # echo --------------------------------------------- -echo REMOVE +echo we test that the check of $2 was successful +echo i.e. whether the value of check, +echo which is $result, is 0 +echo before removing the old version +echo and installing the new version echo --------------------------------------------- -$1 CMD REMOVE $2 -# -echo --------------------------------------------- -echo INSTALL -echo --------------------------------------------- -$1 CMD INSTALL \ - --byte-compile --with-keep.source --compact-docs \ - --resave-data --install-tests --example \ - --html --latex --clean --preclean \ - --compile-both \ - $tarGz +zero=0 +if [ $result -eq $zero ]; then + # + echo --------------------------------------------- + echo REMOVE $2 + echo --------------------------------------------- + $1 CMD REMOVE $2 + # + echo --------------------------------------------- + echo INSTALL $2 + echo --------------------------------------------- + $1 CMD INSTALL \ + --byte-compile --with-keep.source --compact-docs \ + --resave-data --install-tests --example \ + --html --latex --clean --preclean \ + --compile-both \ + $tarGz +fi From noreply at r-forge.r-project.org Fri Sep 13 13:37:32 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 13:37:32 +0200 (CEST) Subject: [Distr-commits] r923 - pkg/utils Message-ID: <20130913113733.0AB0D1852C2@r-forge.r-project.org> Author: kroisand Date: 2013-09-13 13:37:32 +0200 (Fri, 13 Sep 2013) New Revision: 923 Modified: pkg/utils/Rpkgcheck.sh Log: the checkscript was changed again, because a warning in the checks also gives that the library is not installed again Modified: pkg/utils/Rpkgcheck.sh =================================================================== --- pkg/utils/Rpkgcheck.sh 2013-09-13 09:58:41 UTC (rev 922) +++ pkg/utils/Rpkgcheck.sh 2013-09-13 11:37:32 UTC (rev 923) @@ -26,17 +26,13 @@ echo check as cran $tarGz echo --------------------------------------------- $1 CMD check --as-cran --timings $tarGz -result=$? # echo --------------------------------------------- -echo we test that the check of $2 was successful -echo i.e. whether the value of check, -echo which is $result, is 0 +echo we test that the .tar.gz file of $2 exists echo before removing the old version echo and installing the new version echo --------------------------------------------- -zero=0 -if [ $result -eq $zero ]; then +if [ -r $tarGz ]; then # echo --------------------------------------------- echo REMOVE $2 From noreply at r-forge.r-project.org Fri Sep 13 15:26:29 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 15:26:29 +0200 (CEST) Subject: [Distr-commits] r924 - / branches/distr-2.4/pkg/utils Message-ID: <20130913132629.3A4FA1854F2@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-13 15:26:28 +0200 (Fri, 13 Sep 2013) New Revision: 924 Modified: branches/distr-2.4/pkg/utils/getRevNr.R package_depends.txt Log: updated package_depends.txt Modified: branches/distr-2.4/pkg/utils/getRevNr.R =================================================================== --- branches/distr-2.4/pkg/utils/getRevNr.R 2013-09-13 11:37:32 UTC (rev 923) +++ branches/distr-2.4/pkg/utils/getRevNr.R 2013-09-13 13:26:28 UTC (rev 924) @@ -4,7 +4,7 @@ ## (otherwise need full URL as arg pathRepo withlogin = TRUE, ### do we need option --login (yes in cygwin, don't know in Linux) PathToBash = "C:/cygwin/bin/bash", ## path to bash - PathToUtils="C:/rtest/distr/branches/distr-2.4/pkg/utils", + PathToUtils="C:/rtest/distr/pkg/utils", ### path to shell script readsvnlog.sh tmpfile = "C:/rtest/tmp-svnlog5.txt", ### some tmpfile to which we write the ## results temporarily; is deleted afterwords Modified: package_depends.txt =================================================================== --- package_depends.txt 2013-09-13 11:37:32 UTC (rev 923) +++ package_depends.txt 2013-09-13 13:26:28 UTC (rev 924) @@ -9,4 +9,6 @@ distrDoc RobAStBase ROptEstOld ROptEst ROptRegTS RobExtremes RobLox RobRex - ROptReg RobLoxBioC \ No newline at end of file + ROptReg RobLoxBioC + +unconnected: RobAStRDA \ No newline at end of file From noreply at r-forge.r-project.org Fri Sep 13 17:29:52 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 17:29:52 +0200 (CEST) Subject: [Distr-commits] r925 - pkg/distrDoc/vignettes Message-ID: <20130913152952.8355B185A12@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-13 17:29:52 +0200 (Fri, 13 Sep 2013) New Revision: 925 Modified: pkg/distrDoc/vignettes/distr.Rnw Log: [distrDoc]commented out some outdated references from uni-bayreuth Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2013-09-13 13:26:28 UTC (rev 924) +++ pkg/distrDoc/vignettes/distr.Rnw 2013-09-13 15:29:52 UTC (rev 925) @@ -81,7 +81,7 @@ @ % % ------------------------------------------------------------------------------- -%\newcommand{\pkgversion}{{\tt 2.4}} +\renewcommand{\pkgversion}{{\tt 2.5}} \newcommand{\pkgExversion}{{\tt 2.5}} \newcommand{\Reals}{\mathbb{R}} \newcommand{\R}{\mathbb{R}} @@ -2893,14 +2893,14 @@ % \section{Examples} \subsection{$12$-fold convolution of uniform $(0,1)$ variables} -\begin{footnotesize} - Code also available under\newline % - {\href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/NormApprox.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}$% - {\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}% - {\tt /mathe7/DISTR/NormApprox.R}}}}}\\[2ex] -\end{footnotesize} +%\begin{footnotesize} +% Code also available under\newline % +% {\href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/NormApprox.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}$% +% {\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}% +% {\tt /mathe7/DISTR/NormApprox.R}}}}}\\[2ex] +%\end{footnotesize} \begin{small} This example shows how easily we may get the distribution of the sum of $12$ ${\rm i.i.d.}$ ${\rm ufo}(0,1)$--variables minus $6$--- which was used as a @@ -2949,11 +2949,11 @@ par(opar) @ \subsection{Comparison of exact convolution to FFT for normal distributions}\label{Convex} -\begin{footnotesize} - Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/ConvolutionNormalDistr.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/ConvolutionNormalDistr.R}}}}\\[2ex] -\end{footnotesize} +%\begin{footnotesize} +% Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/ConvolutionNormalDistr.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/ConvolutionNormalDistr.R}}}}\\[2ex] +%\end{footnotesize} \begin{small} This example illustrates the exactness of the numerical algorithm used to compute the convolution: We know that ${\cal L}({\tt A+B})={\cal N}(5,13)$ --- @@ -3047,11 +3047,11 @@ @ \subsection{Comparison of FFT to {\tt RtoDPQ}}\label{compex} -\begin{footnotesize} - Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/ComparisonFFTandRtoDPQ.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/ComparisonFFTandRtoDPQ.R}}}}\\[2ex] -\end{footnotesize} +%\begin{footnotesize} +% Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/ComparisonFFTandRtoDPQ.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/ComparisonFFTandRtoDPQ.R}}}}\\[2ex] +%\end{footnotesize} \begin{small} This example illustrates the exactness (or rather not--so--exactness) of the simulational default algorithm used to compute the distribution of @@ -3123,11 +3123,11 @@ fill = c("black", "red")) @ \subsection{Comparison of exact and approximate stationary regressor distribution}\label{statex} -\begin{footnotesize} - Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/StationaryRegressorDistr.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/StationaryRegressorDistr.R}}}}\\[2ex] -\end{footnotesize} +%\begin{footnotesize} +% Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/StationaryRegressorDistr.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/StationaryRegressorDistr.R}}}}\\[2ex] +%\end{footnotesize} \begin{small} Another illustration for the use of package {\tt "distr"}. In case of a stationary AR(1)--model, for non--normal innovation distribution, @@ -3245,11 +3245,11 @@ \subsection{Distribution of minimum and maximum of two independent random variables}\label{minmaxex} has been integrated to the package itself, see section~\ref{TruncMin} \subsection{Instructive destructive example}\label{destrex} -\begin{footnotesize} - Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/destructive.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/destructive.R}}}}\\[2ex] -\end{footnotesize} +%\begin{footnotesize} +% Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/destructive.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/destructive.R}}}}\\[2ex] +%\end{footnotesize} <>= ########################################################## ## Demo: Instructive destructive example @@ -3269,11 +3269,11 @@ @ \subsection{A simulation example}\label{simex} {\bf needs packages \pkg{distrSim}/\pkg{distrTEst}}\\[2ex] -\begin{footnotesize} - Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/SimulateandEstimate.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/SimulateandEstimate.R}}}}\\[2ex] -\end{footnotesize} +%\begin{footnotesize} +% Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/SimulateandEstimate.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/SimulateandEstimate.R}}}}\\[2ex] +%\end{footnotesize} <>= require(distrTEst) ### also loads distrSim @@ -3351,9 +3351,9 @@ \end{small} \subsection{Expectation of a given function under a given distribution} \begin{footnotesize} - Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/Expectation.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/Expectation.R}}}}\\[2ex] +% Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/Expectation.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/Expectation.R}}}}\\[2ex] This code is for illustration only; in the mean-time, the expectation- and variance operators implemented in this example have been included to package \pkg{distrEx} where their functionality has further been extended. @@ -3380,11 +3380,11 @@ E(N, sq) - E(N, id)^2 @ \subsection{$n$-fold convolution of absolutely continuous distributions}\label{exe10} -\begin{footnotesize} - Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/nFoldConvolution.R}% - {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% - {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/nFoldConvolution.R}}}}\\[2ex] -\end{footnotesize} +%\begin{footnotesize} +% Code also available under\newline \href{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/nFoldConvolution.R}% +% {\parbox[t]{12cm}{$\mbox{\hspace{2cm}}${\tt http://www.uni-bayreuth.de/departments/math/org/}\\% +% {$\mbox{\hspace{2cm}}$\hphantom{\tt http:/}{\tt /mathe7/DISTR/nFoldConvolution.R}}}}\\[2ex] +%\end{footnotesize} \begin{small} Might be useful for teaching the CLT: a straightforward implementation of the $n$--fold convolution of an From noreply at r-forge.r-project.org Fri Sep 13 17:34:59 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Sep 2013 17:34:59 +0200 (CEST) Subject: [Distr-commits] r926 - pkg/distrDoc/vignettes Message-ID: <20130913153459.EC40E185A12@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-13 17:34:59 +0200 (Fri, 13 Sep 2013) New Revision: 926 Modified: pkg/distrDoc/vignettes/distr.Rnw Log: [distrDoc] added svn-properties to distr.Rnw Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2013-09-13 15:29:52 UTC (rev 925) +++ pkg/distrDoc/vignettes/distr.Rnw 2013-09-13 15:34:59 UTC (rev 926) @@ -8,11 +8,11 @@ \usepackage{svn-multi} % Version control information: \svnidlong -{$HeadURL: svn+ssh://ruckdeschel at svn.r-forge.r-project.org/svnroot/distr/branches/distr-2.4/pkg/distrDoc/vignettes/distr.Rnw $} -{$LastChangedDate: 2012-05-22 14:40:14 +0200 (Di, 22 Mai 2012) $} -{$LastChangedRevision: 816 $} -{$LastChangedBy: ruckdeschel $} -%\svnid{$Id: example_main.tex 146 2008-12-03 13:29:19Z martin $} +{$HeadURL$} +{$LastChangedDate$} +{$LastChangedRevision$} +{$LastChangedBy$} +%\svnid{$Id$} % Don't forget to set the svn property 'svn:keywords' to % 'HeadURL LastChangedDate LastChangedRevision LastChangedBy' or % 'Id' or both depending if you use \svnidlong and/or \svnid Property changes on: pkg/distrDoc/vignettes/distr.Rnw ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision URL Header From noreply at r-forge.r-project.org Wed Sep 18 12:53:13 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 18 Sep 2013 12:53:13 +0200 (CEST) Subject: [Distr-commits] r927 - branches/distr-2.6/pkg branches/distr-2.6/pkg/SweaveListingUtils branches/distr-2.6/pkg/SweaveListingUtils/man branches/distr-2.6/pkg/distrDoc branches/distr-2.6/pkg/distrDoc/man branches/distr-2.6/pkg/distrDoc/vignettes branches/distr-2.6/pkg/distrEllipse branches/distr-2.6/pkg/distrEllipse/man branches/distr-2.6/pkg/distrEx branches/distr-2.6/pkg/distrEx/man branches/distr-2.6/pkg/distrRmetrics branches/distr-2.6/pkg/distrRmetrics/man branches/distr-2.6/pkg/distrTEst branches/distr-2.6/pkg/distrTEst/man branches/distr-2.6/pkg/distrTeach branches/distr-2.6/pkg/distrTeach/man branches/distr-2.6/pkg/startupmsg branches/distr-2.6/pkg/utils pkg/utils Message-ID: <20130918105313.C63351841A4@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-18 12:53:13 +0200 (Wed, 18 Sep 2013) New Revision: 927 Added: branches/distr-2.6/pkg/Mail/ branches/distr-2.6/pkg/SweaveListingUtils/ branches/distr-2.6/pkg/distrDoc/ branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw branches/distr-2.6/pkg/distrEllipse/ branches/distr-2.6/pkg/distrEx/ branches/distr-2.6/pkg/distrRmetrics/ branches/distr-2.6/pkg/distrTEst/ branches/distr-2.6/pkg/distrTeach/ branches/distr-2.6/pkg/startupmsg/ branches/distr-2.6/pkg/utils/ Removed: branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw Modified: branches/distr-2.6/pkg/SweaveListingUtils/DESCRIPTION branches/distr-2.6/pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd branches/distr-2.6/pkg/distrDoc/DESCRIPTION branches/distr-2.6/pkg/distrDoc/man/0distrDoc-package.Rd branches/distr-2.6/pkg/distrEllipse/DESCRIPTION branches/distr-2.6/pkg/distrEllipse/man/0distrEllipse-package.Rd branches/distr-2.6/pkg/distrEx/DESCRIPTION branches/distr-2.6/pkg/distrEx/man/0distrEx-package.Rd branches/distr-2.6/pkg/distrRmetrics/DESCRIPTION branches/distr-2.6/pkg/distrRmetrics/man/0distrRmetrics-package.Rd branches/distr-2.6/pkg/distrTEst/DESCRIPTION branches/distr-2.6/pkg/distrTEst/man/0distrTEst-package.Rd branches/distr-2.6/pkg/distrTeach/DESCRIPTION branches/distr-2.6/pkg/distrTeach/man/0distrTeach-package.Rd branches/distr-2.6/pkg/startupmsg/DESCRIPTION branches/distr-2.6/pkg/utils/DESCRIPTIONutils.R branches/distr-2.6/pkg/utils/DESCRIPTIONutilsExamples.R pkg/utils/DESCRIPTIONutils.R Log: completed branches/distr-2.6 Modified: branches/distr-2.6/pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2013-09-13 11:37:32 UTC (rev 923) +++ branches/distr-2.6/pkg/SweaveListingUtils/DESCRIPTION 2013-09-18 10:53:13 UTC (rev 927) @@ -12,7 +12,7 @@ source code Maintainer: Peter Ruckdeschel License: LGPL-3 -Date: 2013-09-12 +Date: 2013-09-18 LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 913 +SVNRevision: 926 Modified: branches/distr-2.6/pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd =================================================================== --- pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2013-09-13 11:37:32 UTC (rev 923) +++ branches/distr-2.6/pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2013-09-18 10:53:13 UTC (rev 927) @@ -16,11 +16,11 @@ \tabular{ll}{ Package: \tab SweaveListingUtils \cr Version: \tab 0.7 \cr -Date: \tab 2013-09-12 \cr +Date: \tab 2013-09-18 \cr Depends: \tab R(>= 2.14.0), startupmsg \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr -SVNRevision: \tab 913 \cr +SVNRevision: \tab 926 \cr } TeX-package \file{listings}, confer \url{http://www.ctan.org/tex-archive/macros/latex/contrib/listings/}, Modified: branches/distr-2.6/pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2013-09-13 15:29:52 UTC (rev 925) +++ branches/distr-2.6/pkg/distrDoc/DESCRIPTION 2013-09-18 10:53:13 UTC (rev 927) @@ -1,6 +1,6 @@ Package: distrDoc -Version: 2.5 -Date: 2013-09-12 +Version: 2.6 +Date: 2013-09-18 Title: Documentation for packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod, and distrEllipse Description: provides documentation in form of a common vignette to packages distr, distrEx, @@ -18,4 +18,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 913 +SVNRevision: 926 Modified: branches/distr-2.6/pkg/distrDoc/man/0distrDoc-package.Rd =================================================================== --- pkg/distrDoc/man/0distrDoc-package.Rd 2013-09-13 15:29:52 UTC (rev 925) +++ branches/distr-2.6/pkg/distrDoc/man/0distrDoc-package.Rd 2013-09-18 10:53:13 UTC (rev 927) @@ -14,14 +14,14 @@ \details{ \tabular{ll}{ Package: \tab distrDoc \cr -Version: \tab 2.5 \cr -Date: \tab 2013-09-12 \cr +Version: \tab 2.6 \cr +Date: \tab 2013-09-18 \cr Depends: \tab R(>= 2.6.0), tools, distr(>= 2.2.0), startupmsg, distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0), distrTeach(>= 2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 913 \cr +SVNRevision: \tab 926 \cr }} Deleted: branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2013-09-13 15:29:52 UTC (rev 925) +++ branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw 2013-09-18 10:53:13 UTC (rev 927) @@ -1,3621 +0,0 @@ -%\VignetteIndexEntry{distr - manual} -%\VignetteDepends{distr} -%\VignetteKeyword{probability distribution,simulation,estimation} -%\VignettePackage{distr} -% -\documentclass[11pt]{article} -% -\usepackage{svn-multi} -% Version control information: -\svnidlong -{$HeadURL: svn+ssh://ruckdeschel at svn.r-forge.r-project.org/svnroot/distr/branches/distr-2.4/pkg/distrDoc/vignettes/distr.Rnw $} -{$LastChangedDate: 2012-05-22 14:40:14 +0200 (Di, 22 Mai 2012) $} -{$LastChangedRevision: 816 $} -{$LastChangedBy: ruckdeschel $} -%\svnid{$Id: example_main.tex 146 2008-12-03 13:29:19Z martin $} -% Don't forget to set the svn property 'svn:keywords' to -% 'HeadURL LastChangedDate LastChangedRevision LastChangedBy' or -% 'Id' or both depending if you use \svnidlong and/or \svnid -% -\newcommand{\svnfooter}{Last Changed Rev: \svnkw{LastChangedRevision}} -\svnRegisterAuthor{ruckdeschel}{Peter Ruckdeschel} -\svnRegisterAuthor{stamats}{Matthias Kohl} -\svnRegisterAuthor{florian}{Florian Camphausen} -\svnRegisterAuthor{stabla}{Thomas Stabla} -\svnRegisterAuthor{anhuel}{Anja H{\"u}ller} -\svnRegisterAuthor{ifrin}{Eleonara Feist} -\svnRegisterAuthor{jdospina}{Juan David Ospina} -\svnRegisterAuthor{kowzar}{Kouros Owzar} -% -%borrowed from doc/manual/refman.top -% -%% Set PDF 1.5 and compression, including object compression -%% Needed for MiKTeX -- most other distributions default to this -\ifx\pdfoutput\undefined -\else - \ifx\pdfoutput\relax - \else - \ifnum\pdfoutput>0 - % PDF output - \pdfminorversion=5 - \pdfcompresslevel=9 - \pdfobjcompresslevel=2 - \fi - \fi -\fi -% -% -\usepackage{geometry} -\usepackage{ifpdf} -\usepackage{color} -\definecolor{darkblue}{rgb}{0.0,0.0,0.75} -\definecolor{Rcolor}{rgb}{0,0.5,0.5} -\definecolor{Rout}{rgb}{0.461,0.039,0.102} -\definecolor{Rcomment}{rgb}{0.101,0.043,0.432} -\usepackage{amssymb} -\usepackage{url} -\usepackage[% -baseurl={http://www.bioconductor.org},% -pdftitle={S4 Classes for Distributions---a manual for packages distr, distrSim, distrTEst, distrEx, -distrMod, and distrTeach},% -pdfauthor={Peter Ruckdeschel, Matthias Kohl, Thomas Stabla, Florian Camphausen},% -pdfsubject={distr},% -pdfkeywords={probability distribution,simulation,estimation},% -pagebackref,bookmarks,colorlinks,linkcolor=darkblue,citecolor=darkblue,% -pagecolor=darkblue,raiselinks,plainpages,pdftex]{hyperref} -% -% ------------------------------------------------------------------------------- -\RequirePackage{fancyvrb} -\RequirePackage{listings} -%\usepackage{Sweave} no longer needed -% ------------------------------------------------------------------------------- -\SweaveOpts{keep.source=TRUE} -% ------------------------------------------------------------------------------- -\definecolor{distrCol}{rgb}{0.0,0.4,0.4} -<>= -require(SweaveListingUtils) -SweaveListingPreparations() -setToBeDefinedPkgs(pkgs = c("distr","distrEx","distrTEst","distrSim", - "distrDoc","distrTeach","distrMod","RandVar"), - keywordstyles = "\\bf\\color{distrCol}") -@ -% -% ------------------------------------------------------------------------------- -\renewcommand{\pkgversion}{{\tt 2.5}} -\newcommand{\pkgExversion}{{\tt 2.5}} -\newcommand{\Reals}{\mathbb{R}} -\newcommand{\R}{\mathbb{R}} -\newcommand{\N}{\mathbb{N}} -% ------------------------------------------------------------------------------- -% -\markboth{\sl Packages ``{\tt distr}'', ``{\tt distrSim}'', ``{\tt distrTEst}'', -``{\tt distrEx}'', ``{\tt distrEllipse}'', ``{\tt distrTeach}'', ``{\tt distrMod}''}% -{\sl Packages ``{\tt distr}'', ``{\tt distrSim}'', ``{\tt distrTEst}'', -``{\tt distrEx}'', ``{\tt distrEllipse}'', ``{\tt distrTeach}'', ``{\tt distrMod}''} -% -% ------------------------------------------------------------------------------- -% -% ------------------------------------------------------------------------------- -\begin{document} -% ------------------------------------------------------------------------------- -\title{{\tt S4} Classes for Distributions---a manual for packages \pkg{distr}, - \pkg{distrEx}, \pkg{distrEllipse}, \pkg{distrMod}, \pkg{distrSim}, - \pkg{distrTEst}, \pkg{distrTeach}, - version \pkgversion} -%,version \pkgExversion} -\author{\small Peter Ruckdeschel\thanks{Fraunhofer ITWM, Kaiserslautern} -\\[-.5ex] -\small Matthias Kohl\thanks{FH Furtwangen} -\\[-.5ex] -\small Thomas Stabla\thanks{Graf-M\"unster-Gymnasium, Bayreuth} -\\[-.5ex] -\small Florian Camphausen\thanks{West-LB, London} -\smallskip\\ -\small Fraunhofer ITWM\\[-.5ex] -\small Fraunhofer Platz 1\\[-.5ex] -\small 67663 Kaiserslautern\\[-.5ex] -\small Germany\\ -\small e-Mail: {\small \tt Peter.Ruckdeschel at itwm.fraunhofer.de}\medskip\\ -\parbox[t]{5cm}{ -\footnotesize\sffamily - Version control information: -\begin{tabbing} -\footnotesize\sffamily - Last changes revision: \= \kill - Head URL: \> \parbox[t]{6cm}{\url{\svnkw{HeadURL}}}\\[1.2ex] - Last changed date: \> \svndate\\ - Last changes revision: \> \svnrev\\ - Version: \> \svnFullRevision*{\svnrev}\\ - Last changed by: \> \svnFullAuthor*{\svnauthor}\\ -\end{tabbing} -} -} -\maketitle -% ------------------------------------------------------------------------------- -\begin{abstract} -% ------------------------------------------------------------------------------- -\pkg{distr} is a package for {\sf R} from version {\tt 1.8.1} onwards that is -distributed under {\tt LGPL-3}. Its own current version is \pkgversion. -% -The aim of this package is to provide a conceptual treatment of random variables -(r.v.'s) by means of {\tt S4}--classes. A mother class \code{Distribution} is -introduced with slots for a parameter and for functions {\tt r}, {\tt d}, -{\tt p}, and {\tt q} for simulation, respectively for evaluation of density / -c.d.f.\ and quantile function of the corresponding distribution. All -distributions of the \pkg{stats} package are implemented as subclasses of either -\code{AbscontDistribution} or \code{DiscreteDistribution}, -which themselves are again subclasses of \code{UnivariateDistribution}. %\\ -% -By means of these classes, we may automatically generate new objects of these -classes for the laws of r.v.'s under standard mathematical univariate -transformations and under standard bivariate arithmetical operations acting -on independent r.v.'s. -% -%From version 1.6 on, \pkg{distr} has been split up into the smaller packages -%\pkg{distr} (only distribution-classes and -methods), \pkg{distrSim} -%(standardized treatment of simulations, also under contaminations) -%and \pkg{distrTEst} \newline(classes and methods for evaluations of statistical -%procedures on such simulations). -Package \pkg{distr} in this setting works as basic package for further extensions. -These start with package \pkg{distrEx}, covering statistical functionals like -expectation, variance and the median evaluated at distributions, as well as -distances between distributions and basic support for multivariate and -conditional distributions. Next, from version 2.0 on, comes package \pkg{distrMod} -which uses these concepts to provide an object orientated competitor to -\code{fitdistr} from package \pkg{MASS} in covering estimation in statistical -models. Further on there are packages \pkg{distrSim} for the standardized -treatment of simulations, also under contaminations and package -\pkg{distrTEst} with classes and methods for evaluations of statistical -procedures on such simulations. Finally, from version 2.0 on, there is package -\pkg{distrTeach} to embody illustrations for basic stats courses using -our distribution classes. - -From version 2.4 on, we have moved support for extreme value distributions, -as well as for certain scale-shape distributions to the new package -\pkg{RobExtremes}. This concerns the Gumbel, Weibull, Pareto distributions. -%\noindent The latter two of them require package \pkg{setRNG} by -%\href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert} -%to be installed from \href{http://cran.r-project.org/mirrors.html}{\tt CRAN}. -% \\ - -%\noindent Additionally, mainly contributed by \cite{MK:05}, in \pkg{distrEx} we -%extend the functionality of \pkg{distr}, providing functionals like expectation -%or variance and distances for distributions. Also, this package contains some -%first steps to multivariate distributions, providing classes for discrete -%multivariate distributions and for factorized, conditional -%distributions. -% ------------------------------------------------------------------------------- -\end{abstract} -% ------------------------------------------------------------------------------- -\tableofcontents -\noindent -{\small Parts of this document appeared in an earlier and much shorter form in -{\em R-News\/}, {\bf 6}(2) as {\sf ``S4 Classes for Distributions''}, -c.f.\ \cite{R:K:S:C:04}, which in its -published form refers to package versions 1.6, resp.\ 0.4-2. This present document -takes into account the subsequent revisions and versions.}\medskip -% ------------------------------------------------------------------------------- -\addtocounter{section}{-1} -\section{Motivation} -% ------------------------------------------------------------------------------- -{\sf R} up to now contains powerful techniques for virtually -any useful distribution using the suggestive naming convention -{\tt [prefix]} as functions where {\tt [prefix]} stands for - {\tt r}, {\tt d}, {\tt p}, or {\tt q} - and {\tt } is the name of the distribution.\\ -There are limitations of this concept, however: -You can only use distributions which are implemented in some library -already or for which you yourself have provided an implementation. -In many natural settings you want to formulate algorithms once for -all distributions, so you should be able to treat the actual distribution -{\tt } as sort of a variable.\\ -You may of course paste together prefix and the value of {\tt } as a -string and then use \code{eval(parse(....))}. This is neither very elegant nor -flexible, however.\\ -% -Instead, we would rather like to implement the algorithm by passing an object of -some distribution class as argument to the function. Even better though, we -would use a generic function and let the {\tt S4}-dispatching mechanism decide -what to do at run-time. In particular, we would like to automatically generate -the corresponding functions {\tt r}, {\tt d}, {\tt p}, and {\tt q} for the law -of expressions like \code{X+3Y} for objects \code{X} and \code{Y} of class -\code{Distribution}, or, more general, of a transformation of $X$, $Y$ under a -function $f\colon \Reals^2 \to \Reals$ which is already realized as a function -in {\sf R}.\\ -This is possible with package \pkg{distr}. As an example, try -<>= -## preparation: set option withSweave to true -require(distrTEst) -require(distrEx) -require(distrTeach) -require(distrMod) -distroptions(withSweave = TRUE) -options("newDevice" = TRUE) -@ -<>= -require(distr) -N <- Norm(mean = 2, sd = 1.3) -P <- Pois(lambda = 1.2) -Z <- 2*N + 3 + P -Z -plot(Z) -p(Z)(0.4) -q(Z)(0.3) -Zs <- r(Z)(50) -Zs -@ -\par -\begin{small} -\noindent{\bf Comment:}\\ -Let \code{N} an object of class \code{"Norm"} with parameters \code{mean=2}, -\code{sd=1.3} and let \code{P} an object of class \code{"Pois"} with parameter -\code{lambda=1.2}. Assigning to \code{Z} the expression \code{2*N+3+P}, a -new distribution object is generated ---of class \code{"AbscontDistribution"} in -our case--- so that identifying \code{N}, \code{P}, \code{Z} with random -variables distributed according to {\tt N}, {\tt P}, {\tt Z}, -${\cal L}({\tt Z})={\cal L}(2*{\tt N}+3+{\tt P})$, and writing \code{p(Z)(0.4)} -we get $P(Z\leq 0.4)$, \code{ q(Z)(0.3)} the $30\%$-quantile of {\tt Z}, -and with \code{r(Z)(50)} we generate $50$ pseudo random numbers distributed -according to {\tt Z}, while the \code{plot} command generates the above figure. -\end{small} -% ------------------------------------------------------------------------------- -\section{Concept} -% ------------------------------------------------------------------------------- -In developing our packages, we had the following principles in mind: -We wanted to be open in our design so that our classes could easily be extended -by any volunteer in the {\sf R} community to provide more complex classes of -distributions as multivariate distributions, times series distributions, -conditional distributions. As an exercise, the reader is encouraged to implement -extrem value distributions from the package \pkg{evd}\footnote{a solution to -this ``homework'' may be found in the sources to \pkg{distrEx}, -resp.\ from version 2.4 on, in the sources to \pkg{RobExtremes}}. The largest -effort will in fact be the documentation\ldots\\ -We also wanted to preserve naming and notation from {\sf R}-\pkg{stats} -as far as possible so that any programmer used to {\tt S} could quickly -use our package. Even more so, as the distributions already implemented to -{\sf R} are all well tested and programmed with skills we lack, we use the -existing {\tt r}, {\tt d}, {\tt p}, and {\tt q}-functions wherever possible, -only wrapping them by small code sniplets to our class hierarchy.\\ -Third we wanted to use a suggestive notation for our automatically generated -methods \code{r}, \code{d}, \code{p}, and \code{q}, which we think is now -largely achieved. All this should make intensive use of object orientation in -order to be able to use inheritance and method overloading. -Let us briefly explain why we decided to realize \code{r}, \code{d}, -\code{p}, and \code{q} as part of our class definitions: -Doing so, we place ourselves somewhere between -pure object orientation where methods would be {\it slots\/} ---in the language -of the {\tt S4}-concept, confer \cite{Cham:98}--- and the {\tt S4} paradigm -where methods ``live their own life'' apart from the classes, or, to \code{q}, -which should be regarded use \cite{Beng:03}'s terminology, we use -COOP\footnote{class-object-orientated -programming, as e.g.\ in {\tt C++}}-style for \code{r}, \code{d}, \code{p}, and -\code{q} methods, and FOOP\footnote{function-object-orientated programming, -as in the {\tt S4}-concept} -style for "normal" methods.\\ -The {\tt S4}-paradigm with methods which are not attached to an object but -rather behave differently according to the classes of their arguments is fine -if there are particular user-written methods for only some few general -distribution classes like \code{AbscontDistribution}, as in the case for -\code{plot} or \code{"+"} (c.f.\ \cite{K:R:S:04}, Section 2.2). -During a typical {\sf R} session with \pkg{distr}, however, there will be a lot -of, mostly automatically generated objects of our distribution classes, each -with its own \code{r}, \code{d}, \code{p}, and \code{q}; this even applies to -intermediate expressions like \code{2*N}, \code{2*N+3} to eventually produce -\code{Z} in the example in the motivation. Treating \code{r}, \code{d}, -\code{p}, and \code{q} as generic functions, we would need to generate new -classes for each expression \code{2*N}, \code{2*N+3}, \code{Z} and, -correspondingly, particular {\tt S4}-methods for \code{r}, \code{d}, \code{p}, -and \code{q} for each of these new classes; apparently, this would produce -overly many classes for an effective inheritance structure. \\ -In providing arithmetics for distributions, we have to deviate a little from -the paradigm of {\tt S} as a functional language: For operators like ``$+$'', -additional parameters controlling the precision of the results cannot be handily -passed as arguments. For this purpose we provide global options which may be -inspected and modified by \code{distroptions}, -\code{getdistrOption}\footnote{Upto version 0.4-4, we used a different mechanism -to inspect/modify global options of \pkg{distrEx} (see -section~\ref{distrExoptions}); corresponding functions \code{distrExoptions}, -\code{getdistrExOption} for package \pkg{distrEx} are available from version -1.9 on.} in complete analogy to \code{options}, \code{getOption}. -% -Finally our concept as to parameters: Contrary to the standard {\sf R}-functions -like \code{rnorm} we only permit length $1$ for parameters like \code{mean}, -because we see the objects as implementations of univariate random variables, -for which vector-valued parameters make no sense; rather one could gather -several objects with possibly different parameters to a vector/list of -distributions. Of course, the original functions \code{rnorm} etc.\ remain -unchanged and still allow for vector-valued parameters. -Kouros Owzar in an off-list mail raised the point, that in case of multiple -parameters as in case of the normal or the $\Gamma$-distribution, it might be -useful to be able to pass these multiple parameters in vectorized form to the -generating function. We, too, think that this is a good idea, but have -shifted this question to the new extension package \pkg{distrMod} which covers -more general treatment of statistical models, see section~\ref{distrMod}. -% ------------------------------------------------------------------------------- -\section{Organization in classes} -% ------------------------------------------------------------------------------- -Loosely speaking we have three large groups of classes: distribution classes (in -\pkg{distr}), simulation classes (in \pkg{distrSim}) and an evaluation class (in -\pkg{distrTEst}), where the latter two are to be considered only as tools which -allow a unified treatment of simulations and evaluation of statistical estimation -(perhaps also tests and predictions later) under varying simulation situations. -Additionally, package \pkg{distrEx} provides classes for discrete multivariate -distributions and for factorized, conditional distributions, as well as a bundle -of functionals and distances (see below). -% ------------------------------------------------------------------------------- -\subsection{Distribution classes} -% ------------------------------------------------------------------------------- -The purpose of the classes derived from the class \code{Distribution} is to -implement the concept of a r.v./distribution as such in {\sf R}.\\ -All classes derived from \code{Distribution} have a slot \code{param} for a -parameter, a slot \code{img} for the range and the constitutive slots \code{r}, -\code{d}, \code{p}, and \code{q}.\\ -From version 1.9 on, up to arguments referring to a parameter of the -distribution (like \code{mean} for the normal distribution), these function -slots have the same arguments as those of package \pkg{stats}, i.e.; for a -distribution object \code{X} we may call these functions as - -\begin{itemize} -\item \code{r(X)(n)} $\qquad$ ---except for objects of class \code{Hyper}, -where there is a slot \code{n} already, so here the argument name -to \code{r} is \code{nn}. -\item \code{d(X)(x, log = FALSE)} -\item \code{p(X)(q, lower.tail = TRUE, log.p = FALSE)} -\item \code{q(X)(p, lower.tail = TRUE, log.p = FALSE)} -\end{itemize} - -For the arguments of these function slots see e.g.\ \code{rnorm} -from package \pkg{stats}. -Note that, as usual, slots \code{d}, \code{p}, and \code{q} are vectorized -in their first argument, but are not on the subsequent ones. -The idea is to gain higher precision for the upper tails or when multiplying -probabilities. -% ------------------------------------------------------------------------------- -\subsubsection{Subclasses} -% ------------------------------------------------------------------------------- -To begin with, we have considered univariate distributions giving the -{\tt S4}-class \code{UnivariateDistribution}, and as typical subclasses, we -have introduced classes for absolutely continuous and discrete distributions ----\code{AbscontDistribution} and \code{DiscreteDistribution}.\\ - -The former, from version 1.9 on, has a slot \code{gaps} of class -\code{OptionalMatrix}, i.e.; an object which may either be \code{NULL} or -a \code{matrix}. This slot, if non-\code{NULL}, contains left and right -endpoints of intervals where the density of the object is $0$. This slot -may be inspected by the accessor \code{gaps()} and modified by a corresponding -replacement method. It may also be filled automatically by -\code{setgaps(object, exactq = 6, ngrid = 50000)}, where upon evaluation of -the \code{d}-slot on a grid of length \code{ngrid}, all regions in the -range\footnote{more precisely: between lower and upper \code{TruncQuantile}; - \code{TruncQuantile} is a global option of \pkg{distr} described in - section~\ref{options}} of the distribution where the density is smaller than - $10^{\scriptscriptstyle - {\rm exactq}}$ are set to gaps. - Internally, we have helper functions \code{.consolidategaps} to merge adjacent - intervals and \code{mergegaps} to merge \code{slots} of different objects. - \\ For saved objects - from earlier versions, we provide the functions \code{isOldVersion} and - \linebreak[4]\code{conv2NewVersion} to check whether the -object was generated by an older version of this package and -to convert such an object to the new format, respectively.\\ - -Class \code{DiscreteDistribution} has a slot \code{support}, a vector containing -the support of the distribution, which is truncated to the lower/upper -\code{TruncQuantile} in case of an infinite support. \code{TruncQuantile} is a -global option of \pkg{distr} described in section~{\ref{options}}. - - -Also from version 1.9 on, class \code{DiscreteDistribution} has a subclass -\code{LatticeDistribution} for supports consisting of\footnote{or at least -if filled with points carrying no mass have a representation as an affine linear -lattice} an affine linear lattice of form $p+iw$ for $p\in\R$, $w\in\R$, -$w\not=0$ and $i=0,1,\ldots,L$, -$L\in\N \cup\infty$. This class gains a slot \code{lattice} of -class \code{Lattice} (see below). The purpose of this class is mainly its use -in DFT/FFT methods for convolution. Slot \code{lattice} may be -inspected by the usual accessor function \code{lattice()}. -As by inheritance, all subclasses of \code{LatticeDistribution} which prior to -version 1.9 were direct subclasses of \code{DiscreteDistribution} gain a -slot \code{lattice}, too, we provide again \code{isOldVersion} and -\code{conv2NewVersion} methods to check whether the object was generated by an -older version of this package and to convert such an object to the new -format, respectively. Also note that internally, we suppress lattice points from -the support where the probability is $0$.\\ - - -Objects of classes \code{LatticeDistribution} resp.\ -\code{DiscreteDistribution}, and from version 2.0 on, also -\code{AbscontDistribution}, may be generated using the generating functions -\code{LatticeDistribution()} resp.\ \code{DiscreteDistribution()} -resp.\ \code{AbscontDistribution()}; see also -the corresponding help. E.g., to produce a discrete distribution with -support $(1,5,7,21)$ with corresponding probabilities $(0.1,0.1,0.6,0.2)$ -we may write -<>= -D <- DiscreteDistribution(supp = c(1,5,7,21), prob = c(0.1,0.1,0.6,0.2)) -D -plot(D) -@ -\newline -and to generate an absolutely continuos distribution with density proportional -to $e^{-|x|^3}$, we write -<>= -AC <- AbscontDistribution(d = function(x) exp(-abs(x)^3), withStand = TRUE) -AC -plot(AC) -@ -\newline -As subclasses of these absolutely continuous and discrete classes, we have -implemented all parametric families which already exist in the \pkg{stats} -package of {\sf R} in form of -{\tt [prefix]} functions ---by just providing wrappers to the original -{\sf R}-functions.\\ -% -Schematically, the inheritance relations as well as the slots -of the corresponding classes may be read off from Figure~\ref{fig1c}. -Class \code{LatticeDistribution} and slot \code{gaps}, as well as -additional classes \code{AffLinAbscontDistribution}, -\code{AffLinDiscreteDistribution}, \code{AffLinLatticeDistribution} -(c.f.\ section~\ref{afflin}) are still lacking in this graphic so far, however, -as well as the classes introduced in version 2.0. -\\ - -\ifpdf -\begin{figure}[!ht]\label{fig1} -\vspace{2ex} - \begin{center} -% \includegraphics[viewport=0 0 500 700,width=9cm]{distribution.pdf}% - \includegraphics[viewport=130 150 500 750,width=9cm]{distribution.pdf}% - \caption{\label{fig1c}{\footnotesize Inheritance relations and slots of the - corresponding \mbox{(sub-)}classes for \code{Distribution} where we do not - repeat inherited slots - }} - \end{center} -\vspace{-4ex} -\end{figure} -\else -\begin{figure}[htb]\label{fig1} - \begin{center} - \includegraphics[viewport=130 150 500 730,width=7.5cm]{distribution.ps}% - \caption{\label{fig1c}{\footnotesize Inheritance relations and slots of the - corresponding \mbox{(sub-)}classes for \code{Distribution} where we do not - repeat inherited slots - }} - \end{center} -\vspace{-1ex} -\end{figure} -\fi - -The most powerful use of our package probably consists in operations to -automatically generate new slots \code{r}, \code{d}, \code{p}, and \code{q} ----induced by mathematical transformations. This is discussed in some detail in -subsection~{\ref{methods}}. - -\subsubsection{Classes for Mixture Distributions} - -\paragraph{Lists of distributions} - -As a first step, we allow distributions to be gathered in lists, giving -classes \code{DistrList} and \code{UnivarDistrList}, where in case of the latter, -all elements must be univariate distributions. For these, the usual indexing -operations with \code{[[.]]} are available. As we will use these lists to -construct more general mixture distributions in some subsequent versions, we -have moved these routines to package \pkg{distr} from version 1.9 on. - - -\paragraph{Mixing distributions} - -To be able to work with distributions which are neither purely absolutely continuous -nor purely discrete, like e.g.\ the distribution of $\min(X,1)$ for -$X\sim{\cal N}(0,1)$, from package version 2.0 on, we support mixtures of -distributions. These are realized as subclasses of class \code{UnivariateDistribution}. -To begin with, we introduce a class \code{UnivarMixingDistribution} as subclass of -class \code{UnivariateDistribution} which additionally has two slots \code{MixCoeff} -and \code{MixDistr}. While the former is a numeric vector taking up the mixture -coefficients of the distribution, the latter is an object of class -\code{UnivarDistrList} as described below, taking up the distributions of the -mixture components; as usual, these slots have their respective accessor and -replacement functions. Usually, this mixing distribution will neither have -a Lebesgue density nor be purely discrete, having a counting density. So slot -\code{d} as a rule will be empty. Objects of this class may be generated by -the generating function \code{UnivarMixingDistribution()}, see also -the corresponding help. In addition there is the function \code{flat.mix} -to simplify such an object converting it to an object of class -\code{UnivarLebDecDistribution}; confer subsection~\ref{flat}. -Note that these mixing distributions may be recursive, i.e.\ compoments of -slot \code{MixDistr} may again -be of class \code{UnivarMixingDistribution}. -<>= -library(distr) -M1 <- UnivarMixingDistribution(Norm(), Pois(lambda=1), Norm(), - withSimplify = FALSE) -M2 <- UnivarMixingDistribution(M1, Norm(), M1, Norm(), withSimplify = FALSE) -M2 -@ - -\paragraph{Lebesgue Decomposed distributions} - -As seen in the above example of $\min(X,1)$, classes \code{DiscreteDistribution} -and \code{Abscontdistribution} are not closed under arithmetic operations. To -have such a closure, from version 2.0 on, we introduce class -\code{UnivarLebDecDistribution}, which realizes a Lebesgue decomposition of a -univariate distribution into a discrete and an absolutely continuous distribution. -Of course, we still cannot cover distributions having a non-trivial continuous -but not absolutely continuous part like the Cantor distribution, but class -\code{UnivarLebDecDistribution} provides a sufficiently general compromise. -Class \code{UnivarLebDecDistribution} is a subclass of class -\code{UnivarMixingDistribution}, where in addition we assume that both slots -\code{MixCoeff} and \code{MixDistr} are of length 2, and that the first component -of slot \code{MixDistr} is of class \code{AbscontDistribution} while the second -is of class \code{DiscreteDistribution}. For this class there are particular -accessors \code{acWeight}, \code{discreteWeight} for the respective weights and -\code{acPart}, \code{discretePart} for the respective distributions. Again there -is a generating function \code{UnivarMixingDistribution()}. -In addition there is the function \code{flat.LCD} -to simplify such an object converting it to an object of class -\code{UnivarLebDecDistribution}; confer subsection~\ref{flat}.% -Classes \code{AbscontDistribution}, \code{DiscreteDistribution} and -\code{UnivarLebDecDistribution} are grouped to a virtual class -(more specifically a class union) -\code{AcDcLcDistribution}. - -\paragraph{Compound distributions} -From version 2.1 on, we also support compound distributions, i.e. the distributions -$D$ of form $D={\cal L}(\sum_{i=1}^N X_i)$, $X_i\stackrel{\rm\scriptsize i.i.d.}{\sim} F$, -a distribution on $\R$, and, independent of the $X_i$, $N\sim Q$ a distribution on $\N_0$. -These distributions are implemented as class \code{CompoundDistribution} which is a subclass -of class \code{UnivarMixingDistribution}; in addition this class has [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 927 From noreply at r-forge.r-project.org Wed Sep 18 13:25:52 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 18 Sep 2013 13:25:52 +0200 (CEST) Subject: [Distr-commits] r928 - www Message-ID: <20130918112552.E409C185031@r-forge.r-project.org> Author: ruckdeschel Date: 2013-09-18 13:25:52 +0200 (Wed, 18 Sep 2013) New Revision: 928 Modified: www/RandVar.html www/distr-Familie.html www/distr.html www/distrDoc.html www/distrEllipse.html www/distrEx.html www/distrMod.html www/distrSim.html www/distrTEst.html www/distrTeach.html Log: updated webpages Modified: www/RandVar.html =================================================================== --- www/RandVar.html 2013-09-18 10:53:13 UTC (rev 927) +++ www/RandVar.html 2013-09-18 11:25:52 UTC (rev 928) @@ -1,51 +1,61 @@ - + + + Package "RandVar" + + + + +
-

[Picture: logo]R-Package +

[Picture: logo]R-Package "RandVar" -R-Logo

+R-Logo

+
+
-
Version: 0.5
-Release Date: 11-30-06
-Authors: Matthias +
Version: 0.9.2
+ +Release Date: 2013-09-18
+ +Authors: Matthias Kohl
+ Required R-Version: >=2.4.0
+ Dependencies: requires packages "methods", "startupmsg" available from CRAN;
+ as well as packages  "distr" -version >= 1.6 and "distrEx"  version +version >= 1.6 and "distrEx"  +version >= 0.4-1 by the author of this package also available from CRAN;
+

What is "RandVar" meant for?

+ This package introduces classes and methods for random variables (understood as measurable mappings). -It extends (and requires) package "distr" +It extends (and requires) package "distr" and "distrEx" .
+ A random variable has slots domain and range as well as a slot -map;  For the derived classes "RealRandVector", "EuclRandVector" +map;  For the derived classes "RealRandVector", +"EuclRandVector" and "EuclRandMatrix" virtually (not in the OO-Sense :-)  every mathematical operation that is possible in R with numeric variables is also possible with objects of our class random variable. In particular @@ -54,142 +64,229 @@ of the random variable, and to evaluate it. Together with a distribution on the domain, we have an expectation as well as a factorized conditional expectation method.
+
+
+

Documentation

+
-more on that package may be found in Matthias' PhD Thesis "Numerical Contributions to the Asymptotic +more on that package may be found in Matthias' PhD Thesis "Numerical Contributions to the +Asymptotic Theory of Robustness", App. D
-available on http://stamats.de/ThesisMKohl.pdf + +available on http://stamats.de/ThesisMKohl.pdf
+
+

License

+
-This software is distributed under +This software is +distributed under the terms of the GNU GENERAL
-PUBLIC LICENSE Version 2, June 1991, + +PUBLIC LICENSE Version +2, June 1991, confer http://www.gnu.org/copyleft/gpl.html
+
+
+

Download

+

Windows

+ +
    +
  • to be installed by
      -
    • the R-gui File picker [Packages ->Install package(s) from + +
    • the R-gui File picker [Packages ->Install +package(s) from local zip-files...] or
      +
      • +
    • - 
      install.packages("RandVar", <path to the file distr.zip in your File system>, NULL)
      + 
      install.packages("RandVar", <path to the file distr.zip in your File system>, NULL)
      +
      • +
    +
    • +
  • to be removed by
    + 
    remove.packages("RandVar")
    +
    • +
  • to be used by
    + 
    library("RandVar")
    + or 
    require("RandVar")
    +
    • +
+

Linux

+ +
    +
  • to be installed by
    - 
    R CMD INSTALL RandVar_0.5.tar.gz

    + + 
    R CMD INSTALL RandVar_0.5.tar.gz

    +
    • +
  • to be removed by
    + 
    R CMD REMOVE RandVar
    +
    • +
  • to be used as under Windows
    • +
+

Sources

+
    +
  • included into the .tar.gz.file
    +
    • +
+
-
+ +

Demos

-also see demo("distr") --- after installation of "distr"
+ +also see +demo("distr") --- after +installation of "distr"
+
+ +
+
+
-

Version history:

+

Version +history:

+
-Changes from Version 0.4-1 to Version 0.4-2 + +Changes from Version 0.4-1 to +Version 0.4-2
    +
  • minor changes to increase speed of computation
    • +
+
-
  • introduction of a new parameter useApply in methods for function E + +
  • introduction of a new parameter useApply in methods for +function E with default value TRUE
    +
    -
    -Changes from Version 0.4-2 to Version 0.5
    -     + +
    • + +

  • Changes from Version 0.4-2 to Version 0.5
      +
    • Vignette was added; after loading the package try vignette("RandVar")
      +
      • +
    -
    • +

  • Changes from Version 0.5 onwards
     +
      +
    • see NEWS file +
      • +
    +
    • +
    -

    Our plans for +

    Our +plans for the next versions:

    +
      -
    • use of package Matrix
      • -
    • better use of symmetry and group invariances
      -
      • + +
    • see TOBEDONE file
      • +
    -
    -
    -

    Things we invite -other people to do

    -
      -

    • -
      • -
    +
    +
    -
    This page is -maintained by Peter +
    This +page is +maintained by Peter Ruckdeschel -and last updated on 11-22-05.
    +and last updated on 2013-09-18..
    +
    -
    -
    + Modified: www/distr-Familie.html =================================================================== --- www/distr-Familie.html 2013-09-18 10:53:13 UTC (rev 927) +++ www/distr-Familie.html 2013-09-18 11:25:52 UTC (rev 928) @@ -1,110 +1,161 @@ - + + + + + + + Package "distrTEst" + + +
    -

    [Picture: logo]  The "distrXXX"-Family +

    [Picture: logo]  The "distrXXX"-Family of R-Packages  - R-Logo

    + R-Logo

    +
    +
    -
    Version: 2.0
    -Release Date: 2008-01-17
    -Authors: Peter -Ruckdeschel, Matthias +
    Version: 2.5
    + +Release Date: 2013-09-18
    + +Authors:     Peter +Ruckdeschel, Matthias Kohl, Thomas Stabla, Florian Camphausen, Eleonara Feist, Anja Hueller
    + Required R-Version:
    +
      + +
    • >=2.14 for versions >= 2.5
    • >=2.2.0 for versions 1.6-2.0
      • +
    +

    What is the "distrXXX" family meant for?

    -
    Project distr is an -umbrella project which contains all the packages of the "distrXXX"-family. These in + +
    Project distr is an +umbrella project which contains all the packages of the "distrXXX"-family. These in return are all based on package "distrXXX". This family currently comprises the packages
    + + It also contains package startupmsg
    + Besides the packages the project also contains the following folders
    +
      +
    • pkg/Mail
      + this folder contains important mails sent to Mailing lists R-devel and R-packages
      +
      • +
    • pkg/utils contains
      +
      • + + +
    + Also the informative (non-formatted ASCII-)-Files
    + -should be interesting.
    + +should be interesting, and each pkg has its own NEWS and TOBEDONE file.
    +
    +
    +
    +
      +
    +
    This page is -maintained by Peter +maintained by Peter Ruckdeschel -and last updated on 2008-01-17.
    +and last updated on 2013-09-18.
    +
    + Modified: www/distr.html =================================================================== --- www/distr.html 2013-09-18 10:53:13 UTC (rev 927) +++ www/distr.html 2013-09-18 11:25:52 UTC (rev 928) @@ -2,60 +2,104 @@ + + + + + + + + + + + + Package "distr" + +

    [Picture: logo]R-Package "distr" R-Logo

    + +
    + +
    -
    Version: 2.3.3
    +
    Version: 2.5.2
    -Release Date: 2011-11-19
    + +Release Date: 2013-09-18
    + + + Authors: Peter Ruckdeschel, Matthias Kohl, Thomas Stabla, Florian Camphausen
    + + Required R-Version:
      + + +
    • >=2.14 for version 2.5
      • +
    • >=2.2.0 for version 2.1,
      • + +
    • >=2.2.0 for version 1.6-2.0,
      • + +
    • >=2.0.1 patched for version 1.5,
      • + +
    • >= 1.8.0 for version 1.4,
      • + +
    • >= 1.7.0 for version built from source files
      • + +
    + + Dependencies: requires package "startupmsg" by Peter Ruckdeschel also available from CRAN;
    + +

    What is "distr" meant for?

    + +
    The aim of package "distr" is to provide a conceptual treatment of random variables (r.v.'s) by means of @@ -71,18 +115,30 @@ or "DiscreteDistribution", which themselves are again subclasses of "Distribution".
    + +
    + + This approach seems very appealing to us from a conceptual viewpoint:
    + +
    + + Just pass an object of some derived distribution class to a generic function as argument and let the dispatching mechanism decide what to do on run-time.
    + +
    + + As an example, we may automatically generate new objects of these classes with corresponding "r", "d", "p", and "q"-slots for the laws of @@ -90,20 +146,32 @@ convolution of independent r.v.'s. For "Distribution" objects X and Y expressions like 3*X+sin(exp(-Y/4+3)) have their natural interpretation as corresponding image distributions.
    + +
    + + Note: Arithmetics on distribution objects are understood as operations on corresponding r.v.'s and not on distribution functions or densities.
    + +
    + + You may set global options by distroptions() confer ?distroptions .
    + +
    + + Up to version 1.5, additionally, we also provided classes for a standardized treatment of simulations (also under contaminations) and evaluations of statistical procedures on such simulations. These are @@ -111,384 +179,722 @@ and distrTEst (see below).
    + +
    + +
    + +
    Attention: This package has been reorganized in version 1.6; if you cannot find a class/method/function previously in the package, also search the new packages
    + +
    + + + +
    + +
    Further packages built on top of package "distr":
    + +     -
    RandVar,  distrMod,  distrTeach,   +
    RandVar,  distrMod,  distrTeach, distrEllipse,  (and, without extra web-page: distrRmetrics)
    + +
    + +
    + +
    + +

    + +

    Manual

    + +
    for version prior to 1.8, a somewhat more detailed manual to this package in pdf-format is available here;
    + + from version 1.8 on, we have converted this manual into a common vignette to packages distr, distrEx, distrSim, distrTEst, distrMod, distrTeach,
    + + which is available in the mere documentation package distrDoc. To use it you may type
    + + 
            require("distrDoc"); V<-vignette("distr"); print(V); edit(V)
    + +
    + +
    + +

    License

    + +
    This software is distributed under the terms of the GNU GENERAL
    + + PUBLIC LICENSE LGPL v3, confer http://www.gnu.org/licenses/lgpl-3.0.html
    + +
    + +
    + +

    Download

    + +

    Windows

    + + + +
      + +
    • to be installed by + +
        + +
      • the R-gui File picker [Packages ->Install package(s) from local zip-files...] or
        + +
        • + +
      • + + 
        install.packages("distr", <path to the file distr.zip in your File system>, NULL)
        + +
        • + + + +
      + +
      • + +
    • to be removed by
      + + + + 
      remove.packages("distr")
      + +
      • + +
    • to be used by
      + + + + 
      library("distr")
      + + or + + 
      require("distr")
      + +
      • + +
    + +

    Linux

    + + + +
      + +
    • to be installed by
      + + + + 
      R CMD INSTALL distr_1.x.tar.gz

      + +
      • + +
    • to be removed by
      + + + + 
      R CMD REMOVE distr
      + +
      • + +
    • to be used as under Windows
      • + +
    + +

    Sources

    + +
      + +
    • included into the .tar.gz.file
      + +
      • + +
    • as zipped source  (for Versions <1.8.0)
      + +
      • + +
    • procede as follows:
      • + + + +
        + +
      • unzip the zip File
        + +
        • + +
      • consult the README -File in the zip-archive and follow the instructions therein
        • + + + +
      + +
    • (is the only possiblity for versions 1.7.0 and 1.7.1)
      • + +
    + +
    + +

    Demos

    + + also see demo(package="distr") --- after installation of "distr"
    + +
    + + + +
    + +
    + + [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 928