From noreply at r-forge.r-project.org Sat Apr 23 12:24:20 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 12:24:20 +0200 (CEST) Subject: [Distr-commits] r1088 - in pkg: SweaveListingUtils SweaveListingUtils/man SweaveListingUtils/tests/Examples startupmsg startupmsg/tests/Examples utils Message-ID: <20160423102420.9AA85187692@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 12:24:20 +0200 (Sat, 23 Apr 2016) New Revision: 1088 Modified: pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save pkg/startupmsg/DESCRIPTION pkg/startupmsg/tests/Examples/startupmsg-Ex.Rout.save pkg/utils/DESCRIPTIONutils.R pkg/utils/showsvnlog.R Log: first round for CRAN submissions: updated utils/DESCRIPTIONutils.R utils/showsvnlog.R updated DESCRIPTION and .Rout.save files Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2016-03-07 15:00:28 UTC (rev 1087) +++ pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 10:24:20 UTC (rev 1088) @@ -1,11 +1,12 @@ Package: SweaveListingUtils Title: Utilities for Sweave Together with TeX 'listings' Package -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. +Description: Package SweaveListingUtils provides utilities for defining R / Rd as "language" + for Tex-package-listings and for 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. +Version: 0.7 Encoding: latin1 -Version: 0.7 +Date: 2016-04-23 Depends: R(>= 2.14.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines Imports: methods @@ -13,7 +14,6 @@ Authors at R: person("Peter", "Ruckdeschel", role=c("cre", "cph"), email="peter.ruckdeschel at uni-oldenburg.de") License: LGPL-3 -Date: 2015-11-07 LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1087 Modified: pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd =================================================================== --- pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2016-03-07 15:00:28 UTC (rev 1087) +++ pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2016-04-23 10:24:20 UTC (rev 1088) @@ -16,13 +16,13 @@ \tabular{ll}{ Package: \tab SweaveListingUtils \cr Version: \tab 0.7 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.14.0), startupmsg \cr Suggests: \tab distr, MASS, survival, distrEx, Matrix, splines \cr Imports: \tab methods \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1087 \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 2016-03-07 15:00:28 UTC (rev 1087) +++ pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-23 10:24:20 UTC (rev 1088) @@ -1,82 +1,83 @@ - -R version 3.2.2 Patched (2015-11-06 r69612) -- "Fire Safety" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-pc-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> pkgname <- "SweaveListingUtils" -> source(file.path(R.home("share"), "R", "examples-header.R")) -> options(warn = 1) -> library('SweaveListingUtils') -Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) -:startupmsg> -:startupmsg> For more information see ?"startupmsg", -:startupmsg> NEWS("startupmsg") - -:SweaveListingUtils> Utilities for Sweave Together with -:SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7) -:SweaveListingUtils> -:SweaveListingUtils> NOTE: Support for this package -:SweaveListingUtils> will stop soon. -:SweaveListingUtils> -:SweaveListingUtils> Package 'knitr' is providing the -:SweaveListingUtils> same functionality in a better -:SweaveListingUtils> way. -: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 objects are masked from ?package:base?: - - library, require - -> -> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') -> cleanEx() -> nameEx("SweaveListingMASK") -> ### * SweaveListingMASK -> -> flush(stderr()); flush(stdout()) -> -> ### Name: SweaveListingMASK -> ### Title: Masking of/by other functions in package "SweaveListingUtils" -> ### Aliases: SweaveListingMASK MASKING -> ### Keywords: programming documentation -> -> ### ** Examples -> -> SweaveListingMASK() + +R Under development (unstable) (2016-04-22 r70532) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing +Platform: i386-w64-mingw32/i386 (32-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 <- "SweaveListingUtils" +> source(file.path(R.home("share"), "R", "examples-header.R")) +> options(warn = 1) +> options(pager = "console") +> library('SweaveListingUtils') +Loading required package: startupmsg +:startupmsg> Utilities for Start-Up Messages (version 0.9.2) +:startupmsg> +:startupmsg> For more information see ?"startupmsg", +:startupmsg> NEWS("startupmsg") + +:SweaveListingUtils> Utilities for Sweave Together with +:SweaveListingUtils> TeX 'listings' Package (version +:SweaveListingUtils> 0.7) +:SweaveListingUtils> +:SweaveListingUtils> NOTE: Support for this package +:SweaveListingUtils> will stop soon. +:SweaveListingUtils> +:SweaveListingUtils> Package 'knitr' is providing the +:SweaveListingUtils> same functionality in a better +:SweaveListingUtils> way. +: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 objects are masked from 'package:base': + + library, require + +> +> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') +> cleanEx() +> nameEx("SweaveListingMASK") +> ### * SweaveListingMASK +> +> flush(stderr()); flush(stdout()) +> +> ### Name: SweaveListingMASK +> ### Title: Masking of/by other functions in package "SweaveListingUtils" +> ### Aliases: SweaveListingMASK MASKING +> ### Keywords: programming documentation +> +> ### ** Examples +> +> SweaveListingMASK() ###################################################################### # On masking of and by other functions in package "SweaveListingUtils" ###################################################################### @@ -105,3230 +106,3241 @@ *** non-intentional masking: *** -... nothing discovered so far ... -> -> -> -> cleanEx() -> nameEx("SweaveListingOptions") -> ### * SweaveListingOptions -> -> flush(stderr()); flush(stdout()) -> -> ### Name: SweaveListingOptions -> ### Title: Function to change the global options of the package -> ### 'SweaveListingUtils' -> ### Aliases: SweaveListingOptions SweaveListingoptions -> ### getSweaveListingOption Rset Rdset Rin Rout Rcode Rcolor Rbcolor -> ### Routcolor RRecomdcolor Rcommentcolor pkg pkv Keywordstyle -> ### Recomd.Keywordstyle interm.Keywordstyle intermediate overwrite -> ### inSweave fromRForge base.url addRset addRdset fileCommand pkgCommand -> ### Keywords: misc utilities -> -> ### ** Examples -> -> SweaveListingOptions() -$Rset -$Rset$fancyvrb -[1] "true" - -$Rset$escapechar -[1] "`" - -$Rset$extendedchars -[1] "false" - -$Rset$language -[1] "R" - -$Rset$basicstyle -[1] "{\\color{Rcolor}\\small}" - -$Rset$keywordstyle -[1] "{\\bf\\color{Rcolor}}" - -$Rset$commentstyle -[1] "{\\color{Rcommentcolor}\\ttfamily\\itshape}" - -$Rset$literate -[1] "{\"}{\\texttt{\"}}1{<-}{{$\\leftarrow$}}2{<<-}{{$\\twoheadleftarrow$}}2{~}{{$\\sim$}}1{<=}{{$\\leq$}}2{>=}{{$\\geq$}}2{^}{{$\\scriptstyle\\wedge$}}1" - -$Rset$alsoother -[1] "{$}" - -$Rset$alsoletter -[1] "{.<-}" - -$Rset$otherkeywords -[1] "{!,!=,~,$,*,\\&,\\%/\\%,\\%*\\%,\\%\\%,<-,<<-,/}" - -$Rset$escapeinside -[1] "{(*}{*)}" - - -$Rdset -$Rdset$fancyvrb -[1] "true" - -$Rdset$language -[1] "Rd" - -$Rdset$keywordstyle -[1] "{\\bf}" - -$Rdset$basicstyle -[1] "{\\color{black}\\footnotesize}" - -$Rdset$commentstyle -[1] "{\\ttfamily\\itshape}" - -$Rdset$alsolanguage -[1] "R" - - -$Rin -$Rin$style -[1] "Rstyle" - -$Rin$fancyvrb -[1] "true" - -$Rin$basicstyle -[1] "\\color{Rcolor}\\small" - - -$Rout -$Rout$fancyvrb -[1] "false" - -$Rout$basicstyle -[1] "\\color{Routcolor}\\small" - - -$Rcode -$Rcode$style -[1] "Rstyle" - -$Rcode$fancyvrb -[1] "true" - -$Rcode$fontshape -[1] "sl" - -$Rcode$basicstyle -[1] "\\color{Rcolor}" - - -$Rcolor -[1] 0.0 0.5 0.5 - -$RRecomdcolor -[1] 0.0 0.6 0.4 - -$Rbcolor -[1] 0.0 0.6 0.6 - -$Routcolor -[1] 0.461 0.039 0.102 - -$Rcommentcolor -[1] 0.101 0.043 0.432 - -$pkv -[1] "2.5" - -$pkg -[1] "distr" - -$Keywordstyle -[1] "{\\bf}" - -$Recomd.Keywordstyle -[1] "{\\bf\\color{RRecomdcolor}}" - -$interm.Keywordstyle -[1] "{\\bf\\color{Rbcolor}}" - -$overwrite -[1] FALSE - -$intermediate -[1] TRUE - -$inSweave -[1] FALSE - -$fromRForge -[1] TRUE - -$base.url -[1] "http://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/" - -$addRset -[1] TRUE - -$addRdset -[1] TRUE - -$addRinset -[1] TRUE - -$addRoutset -[1] TRUE - -$addRcodeset -[1] TRUE - -$fileCommand -[1] "\\def\\file#1{{\\tt #1}}" - -$pkgCommand -[1] "\\def\\pkg#1{{\\tt \"#1\"}}" - -> SweaveListingOptions("Rout") -$Rout -$Rout$fancyvrb -[1] "false" - -$Rout$basicstyle -[1] "\\color{Routcolor}\\small" - - -> SweaveListingOptions("Rout" = c(0,0,0)) -> # or -> SweaveListingOptions(Rout = c(0,1,0)) -> getSweaveListingOption("Rout") -[1] 0 1 0 -> -> -> -> cleanEx() -> nameEx("SweaveListingPreparations") -> ### * SweaveListingPreparations -> -> flush(stderr()); flush(stdout()) -> -> ### Name: SweaveListingPreparations -> ### Title: SweaveListingPreparations -> ### Aliases: SweaveListingPreparations -> ### Keywords: utilities -> -> ### ** Examples -> -> SweaveListingPreparations() -%------------------------------------------------------------------------------% -%Preparations for Sweave and Listings -%------------------------------------------------------------------------------% -% -\RequirePackage{color} -\definecolor{Rcolor}{rgb}{0, 0.5, 0.5} -\definecolor{RRecomdcolor}{rgb}{0, 0.6, 0.4} -\definecolor{Rbcolor}{rgb}{0, 0.6, 0.6} -\definecolor{Routcolor}{rgb}{0.461, 0.039, 0.102} -\definecolor{Rcommentcolor}{rgb}{0.101, 0.043, 0.432} -%------------------------------------------------------------------------------% -\lstdefinelanguage{Rd}[common]{TeX}% -{moretexcs={acronym,alias,arguments,author,bold,cite,% - code,command,concept,cr,deqn,describe,% - description,details,dfn,doctype,dots,% - dontrun,dontshow,donttest,dQuote,% - email,emph,enc,encoding,enumerate,env,eqn,% - examples,file,format,if,ifelse,item,itemize,kbd,keyword,% - ldots,link,linkS4class,method,name,note,% - option,out,pkg,preformatted,R,Rdopts,Rdversion,% - references,S3method,S4method,Sexpr,samp,section,% - seealso,source,sp,special,sQuote,strong,% - subsection,synopsis,tab,tabular,testonly,% - title,url,usage,value,var,verb}, - sensitive=true,% - morecomment=[l]\%% 2008/9 Peter Ruckdeschel -}[keywords,comments]%% -%------------------------------------------------------------------------------% - -%---------------- -\lstdefinestyle{RstyleO1}{fancyvrb=true,escapechar=`,extendedchars=false,% - language=R,% - basicstyle={\color{Rcolor}\small},% - keywordstyle={\bf\color{Rcolor}},%Warning in print.taglist(taglist, LineLength = LineLength, offset.start = nchar(startS), : - Some elements of taglist are too long - - commentstyle={\color{Rcommentcolor}\ttfamily\itshape},% - literate={"}{\texttt{"}}1{<-}{{$\leftarrow$}}2{<<-}{{$\twoheadleftarrow$}}2{~}{{$\sim$}}1{<=}{{$\leq$}}2{>=}{{$\geq$}}2{^}{{$\scriptstyle\wedge$}}1,% - alsoother={$},% - alsoletter={.<-},% - otherkeywords={!,!=,~,$,*,\&,\%/\%,\%*\%,\%\%,<-,<<-,/},% - escapeinside={(*}{*)}}% -%---------------- -\lstdefinestyle{Rstyle}{style=RstyleO1} - -%---------------- -\lstdefinestyle{Rdstyle}{fancyvrb=true,language=Rd,keywordstyle={\bf},% - basicstyle={\color{black}\footnotesize},% - commentstyle={\ttfamily\itshape},% - alsolanguage=R}% -%---------------- -%------------------------------------------------------------------------------% -\global\def\Rlstset{\lstset{style=Rstyle}}% -\global\def\Rdlstset{\lstset{style=Rdstyle}}% -%------------------------------------------------------------------------------% -\global\def\Rinlstset{\lstset{style=Rinstyle}}% -\global\def\Routlstset{\lstset{style=Routstyle}}% -\global\def\Rcodelstset{\lstset{style=Rcodestyle}}% -%------------------------------------------------------------------------------% -\Rlstset -%------------------------------------------------------------------------------% -%copying relevant parts of Sweave.sty -%------------------------------------------------------------------------------% -% -\RequirePackage{graphicx,fancyvrb}% -\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}% - -\RequirePackage{ifthen}% -\newboolean{Sweave at gin}% -\setboolean{Sweave at gin}{true}% -\setkeys{Gin}{width=0.8\textwidth}% -\newboolean{Sweave at ae} -\setboolean{Sweave at ae}{true}% -\RequirePackage[T1]{fontenc} -\RequirePackage{ae} -% -\newenvironment{Schunk}{}{} - -\newcommand{\Sconcordance}[1]{% -\ifx\pdfoutput\undefined% -\csname newcount\endcsname\pdfoutput\fi% -\ifcase\pdfoutput\special{#1}% -\else\immediate\pdfobj{#1}\fi} - -%------------------------------------------------------------------------------% -% ---- end of parts of Sweave.sty -%------------------------------------------------------------------------------% -% -% ---- input -\lstdefinestyle{RinstyleO}{style=Rstyle,fancyvrb=true,% - basicstyle=\color{Rcolor}\small}% -\lstdefinestyle{Rinstyle}{style=RinstyleO} -\lstnewenvironment{Sinput}{\Rinlstset}{\Rlstset} -% -% ---- output -\lstdefinestyle{RoutstyleO}{ -V1=0,V2=1,V3=0}% -\lstdefinestyle{Routstyle}{style=RoutstyleO} -\lstnewenvironment{Soutput}{\Routlstset}{\Rlstset} -% -% ---- code -\lstdefinestyle{RcodestyleO}{style=Rstyle,fancyvrb=true,fontshape=sl,% - basicstyle=\color{Rcolor}}% -\lstdefinestyle{Rcodestyle}{style=RcodestyleO} -\lstnewenvironment{Scode}{\Rcodelstset}{\Rlstset} -% -%------------------------------------------------------------------------------% -\let\code\lstinline -\def\Code#1{{\tt\color{Rcolor} #1}} -\def\file#1{{\tt #1}} -\def\pkg#1{{\tt "#1"}} -\newcommand{\pkgversion}{{\tt 2.6}} -%------------------------------------------------------------------------------% -Warning in setBaseOrRecommended(pkgs = pkgs) : - number of items to replace is not a multiple of replacement length - -\lstdefinestyle{RstyleO2}{style=RstyleO1,% -% -------------------------- -% Registration of package SweaveListingUtils -% -------------------------- -morekeywords={[2]taglist,setToBeDefinedPkgs,setBaseOrRecommended,readSourceFromRForge,readPkgVersion,% -lstsetRout,lstsetRin,lstsetRd,lstsetRcode,lstsetRall,% -lstsetR,lstsetLanguage,lstset,lstinputSourceFromRForge,lstdefRstyle,% -isBaseOrRecommended,getSweaveListingOption,copySourceFromRForge,changeKeywordstyles,SweaveListingoptions,% -SweaveListingPreparations,SweaveListingOptions,SweaveListingMASK% -},% -keywordstyle={[2]{\bf}},% -% -% -------------------------- -% Registration of package startupmsg -% -------------------------- -morekeywords={[3]suppressStartupMessages,startupType,startupPackage,startupMessage,startupEndline,% -readVersionInformation,readURLInformation,pointertoNEWS,onlytypeStartupMessages,mystartupMessage,% -mySMHandler,infoShow,buildStartupMessage,TOBEDONE,StartupMessage,% -NEWS% -},% -keywordstyle={[3]{\bf}},% -% -% -------------------------- -% Registration of package stats [recommended or base] -% -------------------------- -morekeywords={[4]xtabs,write.ftable,window<-,wilcox.test,weighted.residuals,% -weighted.mean,vcov,varimax,variable.names,var.test,% -update.formula,update.default,tsp<-,tsdiag,tsSmooth,% -ts.union,ts.plot,ts.intersect,toeplitz,terms.formula,% -termplot,t.test,supsmu,summary.stepfun,summary.manova,% -summary.lm,summary.glm,summary.aov,stl,stepfun,% -stat.anova,splinefunH,spectrum,spec.taper,spec.pgram,% -spec.ar,sortedXyData,smoothEnds,smooth.spline,smooth,% -simulate,shapiro.test,setNames,selfStart,se.contrast,% -screeplot,scatter.smooth,runmed,rmultinom,residuals.lm,% -residuals.glm,reshape,reorder,rect.hclust,read.ftable,% -rWishart,r2dtable,quasipoisson,quasibinomial,quade.test,% -qbirthday,prop.trend.test,prop.test,promax,printCoefmat,% -princomp,predict.lm,predict.glm,prcomp,ppr,% -power.t.test,power.prop.test,power.anova.test,polym,poisson.test,% -plot.ts,plot.stepfun,plot.spec.phase,plot.spec.coherency,plot.ecdf,% -plclust,pbirthday,pairwise.wilcox.test,pairwise.table,pairwise.t.test,% -pairwise.prop.test,pacf,p.adjust.methods,p.adjust,order.dendrogram,% -optimHess,oneway.test,numericDeriv,nobs,nls.control,% -nls,nlminb,naresid,naprint,napredict,% -na.pass,na.omit,na.fail,na.exclude,na.contiguous,% -na.action,mood.test,monthplot,model.weights,model.tables,% -model.response,model.offset,model.matrix.lm,model.matrix.default,model.matrix,% -model.frame.default,model.frame,model.extract,medpolish,median.default,% -mcnemar.test,mauchly.test,mantelhaen.test,manova,makepredictcall,% -makeARIMA,make.link,ls.print,ls.diag,logLik,% -loess.smooth,loess.control,loess,loadings,lm.wfit,% -lm.influence,lm.fit,line,lag.plot,lag,% -ksmooth,ks.test,kruskal.test,knots,kmeans,% -kernel,kernapply,isoreg,is.tskernel,is.ts,% -is.stepfun,is.mts,is.leaf,is.empty.model,inverse.gaussian,% -interaction.plot,integrate,influence.measures,heatmap,hclust,% -hatvalues,glm.fit,glm.control,get_all_vars,getInitial,% -getCall,friedman.test,fligner.test,fitted.values,fisher.test,% -filter,factor.scope,factanal,expand.model.frame,estVar,% -embed,eff.aovlist,ecdf,dummy.coef.lm,dummy.coef,% -drop.terms,drop.scope,dmultinom,dist,diffinv,% -dfbeta,df.residual,df.kernel,deriv3,density.default,% -dendrapply,delete.response,decompose,cutree,cpgram,% -cov2cor,cov.wt,cor.test,cophenetic,cooks.distance,% -contrasts<-,contr.treatment,contr.sum,contr.poly,contr.helmert,% -contr.SAS,constrOptim,confint.lm,confint.default,confint,% -complete.cases,cmdscale,chisq.test,ccf,case.names,% -cancor,bw.ucv,bw.nrd0,bw.nrd,bw.bcv,% -bw.SJ,biplot,binom.test,bartlett.test,bandwidth.kernel,% -asOneSidedFormula,as.ts,as.stepfun,as.hclust,as.formula,% -as.dist,as.dendrogram,arima0.diag,arima0,arima.sim,% -arima,ar.yw,ar.ols,ar.mle,ar.burg,% -ar,ansari.test,aggregate.ts,aggregate.data.frame,addmargins,% -add.scope,acf2AR,acf,TukeyHSD,StructTS,% -SSweibull,SSmicmen,SSlogis,SSgompertz,SSfpl,% -SSfol,SSbiexp,SSasympOrig,SSasympOff,SSasymp,% -SSD,PP.test,NLSstRtAsymptote,NLSstLfAsymptote,NLSstClosestX,% -NLSstAsymptotic,KalmanSmooth,KalmanRun,KalmanLike,KalmanForecast,% -HoltWinters,Box.test,BIC,ARMAtoMA,ARMAacf,% -AIC% -},% -keywordstyle={[4]{\bf\color{RRecomdcolor}}},% -% -% -------------------------- -% Registration of package graphics [recommended or base] -% -------------------------- -morekeywords={[5]xspline,text.default,stripchart,strheight,split.screen,% -spineplot,smoothScatter,rasterImage,polypath,points.default,% -plot.xy,plot.window,plot.new,plot.function,plot.design,% -plot.default,pie,panel.smooth,pairs.default,lines.default,% -layout.show,image.default,hist.default,grconvertY,grconvertX,% -fourfoldplot,filled.contour,erase.screen,dotchart,contour.default,% -co.intervals,close.screen,clip,cdplot,boxplot.matrix,% -boxplot.default,barplot.default,axis.POSIXct,axis.Date,axTicks,% -assocplot,Axis% -},% -keywordstyle={[5]{\bf\color{RRecomdcolor}}},% -% -% -------------------------- -% Registration of package grDevices [recommended or base] -% -------------------------- -morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,trans3d,% -topo.colors,tiff,terrain.colors,svg,setPS,% -setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,savePlot,rgb2hsv,% -replayPlot,recordPlot,recordGraphics,quartzFonts,quartzFont,% -quartz.save,quartz.options,quartz,ps.options,postscriptFonts,% -png,pdfFonts,pdf.options,pdf,nclass.scott,% -nclass.Sturges,nclass.FD,n2mfrow,make.rgb,jpeg,% -is.raster,heat.colors,hcl,grey.colors,gray.colors,% -graphics.off,grSoftVersion,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,boxplot.stats,bmp,% -blues9,bitmap,axisTicks,as.raster,as.graphicsAnnot,% -adjustcolor,X11Fonts,X11Font,X11.options,Type1Font,% -Hershey,CIDFont% -},% -keywordstyle={[6]{\bf\color{RRecomdcolor}}},% -% -% -------------------------- -% Registration of package utils [recommended or base] -% -------------------------- -morekeywords={[7]write.table,write.socket,write.csv2,write.csv,vignette,% -url.show,upgrade,update.packages,update.packageStatus,unzip,% -untar,unstack,type.convert,txtProgressBar,toLatex,% -toBibtex,timestamp,tar,tail.matrix,tail,% -suppressForeignCheck,summaryRprof,strOptions,str,stack,% -setTxtProgressBar,setRepositories,setBreakpoint,sessionInfo,select.list,% -savehistory,rtags,removeSource,remove.packages,relist,% -recover,readCitationFile,read.table,read.socket,read.fwf,% -read.fortran,read.delim2,read.delim,read.csv2,read.csv,% -read.DIF,rc.status,rc.settings,rc.options,rc.getOption,% -promptPackage,promptImport,promptData,process.events,personList,% -person,packageVersion,packageStatus,packageName,packageDescription,% -package.skeleton,old.packages,object.size,nsl,news,% -new.packages,modifyList,mirror2html,memory.size,memory.limit,% -makeRweaveLatexCodeRunner,make.socket,make.packages.html,maintainer,lsf.str,% -ls.str,localeToCharset,loadhistory,limitedLabels,is.relistable,% -installed.packages,install.packages,hsearch_db_keywords,hsearch_db_concepts,hsearch_db,% -history,help.start,help.search,help.request,head.matrix,% -head,globalVariables,glob2rx,getTxtProgressBar,getSrcref,% -getSrcLocation,getSrcFilename,getSrcDirectory,getS3method,getParseText,% -getParseData,getFromNamespace,getCRANmirrors,getAnywhere,formatUL,% -formatOL,flush.console,fixInNamespace,findLineNum,file_test,% -fileSnapshot,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,checkCRAN,changedFiles,% -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,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,CRAN.packages% -},% -keywordstyle={[7]{\bf\color{RRecomdcolor}}},% -% -% -------------------------- -% Registration of package datasets [recommended or base] -% -------------------------- -morekeywords={[8]women,warpbreaks,volcano,uspop,trees,% -treering,swiss,sunspots,sunspot.year,sunspot.month,% -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,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,UScitiesD,% -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}}},% -% -% -------------------------- -% Registration of package methods [recommended or base] -% -------------------------- -morekeywords={[9]validSlotNames,validObject,unRematchDefinition,tryNew,traceOn,% -traceOff,testVirtual,testInheritedMethods,superClassDepth,substituteFunctionArgs,% -substituteDirect,slotsFromS3,slotNames,slot<-,slot,% -signature,sigToEnv,showMlist,showMethods,showExtends,% -showDefault,showClass,setValidity,setReplaceMethod,setRefClass,% -setPrimitiveMethods,setPackageName,setOldClass,setMethod,setLoadActions,% -setLoadAction,setIs,setGroupGeneric,setGenericImplicit,setGeneric,% -setDataPart,setClassUnion,setClass,setAs,selectSuperClasses,% -selectMethod,seemsS4Object,sealClass,resetGeneric,resetClass,% -requireMethods,representation,removeMethodsObject,removeMethods,removeMethod,% -removeGeneric,removeClass,rematchDefinition,registerImplicitGenerics,reconcilePropertiesAndPrototype,% -rbind2,prototype,promptMethods,promptClass,prohibitGeneric,% -possibleExtends,packageSlot<-,packageSlot,newEmptyObject,newClassRepresentation,% -newBasic,multipleClasses,mlistMetaName,missingArg,methodsPackageMetaName,% -methodSignatureMatrix,method.skeleton,metaNameUndo,mergeMethods,matchSignature,% -makeStandardGeneric,makePrototypeFromClassDef,makeMethodsList,makeGeneric,makeExtends,% -makeClassRepresentation,loadMethod,listFromMlist,listFromMethods,linearizeMlist,% -languageEl<-,languageEl,isXS3Class,isVirtualClass,isSealedMethod,% -isSealedClass,isGroup,isGrammarSymbol,isGeneric,isClassUnion,% -isClassDef,isClass,insertSource,insertMethod,insertClassMethods,% -initialize,initRefFields,initFieldArgs,inheritedSlotNames,implicitGeneric,% -hasMethods,hasMethod,hasLoadAction,hasArg,getVirtual,% -getValidity,getSubclasses,getSlots,getRefClass,getPrototype,% -getProperties,getPackageName,getMethodsMetaData,getMethodsForDispatch,getMethods,% -getMethod,getLoadActions,getGroupMembers,getGroup,getGenerics,% -getGeneric,getFunction,getExtends,getDataPart,getClasses,% -getClassPackage,getClassName,getClassDef,getClass,getAllSuperClasses,% -getAllMethods,getAccess,generic.skeleton,functionBody<-,functionBody,% -formalArgs,fixPre1.8,findUnique,findMethods,findMethodSignatures,% -findMethod,findFunction,findClass,finalDefaultMethod,extends,% -existsMethod,existsFunction,evalqOnLoad,evalSource,evalOnLoad,% -emptyMethodsList,empty.dump,elNamed<-,elNamed,el<-,% -el,dumpMethods,dumpMethod,doPrimitiveMethod,defaultPrototype,% -defaultDumpName,conformMethod,completeSubclasses,completeExtends,completeClassDefinition,% -coerce<-,coerce,classesToAM,className,classMetaName,% -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}}},% -% -% -------------------------- -% Registration of package base [recommended or base] -% -------------------------- -morekeywords={[10]xzfile,xtfrm.numeric_version,xtfrm.factor,xtfrm.difftime,xtfrm.default,% -xtfrm.Surv,xtfrm.POSIXlt,xtfrm.POSIXct,xtfrm.Date,xtfrm.AsIs,% -xtfrm,xpdrows.data.frame,xor.octmode,xor.hexmode,writeLines,% -writeChar,writeBin,write.dcf,within.list,within.data.frame,% -within,withVisible,withRestarts,withCallingHandlers,with.default,% -with,which.min,which.max,weekdays.POSIXt,weekdays.Date,% -weekdays,version,vapply,utf8ToInt,upper.tri,% -unz,untracemem,unsplit,unserialize,unlockBinding,% -unloadNamespace,unix.time,units<-.difftime,units<-,units.difftime,% -units,unique.warnings,unique.numeric_version,unique.matrix,unique.default,% -unique.data.frame,unique.array,unique.POSIXlt,tryCatch,truncate.connection,% -truncate,trunc.POSIXt,trunc.Date,trimws,transform.default,% -transform.data.frame,tracingState,tracemem,toupper,topenv,% -tolower,toString.default,toString,textConnectionValue,textConnection,% -testPlatformEquivalence,tempdir,tcrossprod,taskCallbackManager,tanpi,% -t.default,t.data.frame,system2,system.time,system.file,% -sys.status,sys.source,sys.save.image,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.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,sinpi,sink.number,simplify2array,simpleWarning,% -simpleMessage,simpleError,simpleCondition,signalCondition,showConnections,% -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,returnValue,% -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,% [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 1088 From noreply at r-forge.r-project.org Sat Apr 23 13:46:22 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 13:46:22 +0200 (CEST) Subject: [Distr-commits] r1089 - in pkg: distr distr/R distr/inst distr/man distr/tests/Examples utils Message-ID: <20160423114622.8CFAB187E0C@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 13:46:22 +0200 (Sat, 23 Apr 2016) New Revision: 1089 Added: pkg/distr/tests/Examples/distr-Ex_i386.Rout.save pkg/distr/tests/Examples/distr-Ex_x64.Rout.save Removed: pkg/distr/tests/Examples/distr-Ex.Rout.save Modified: pkg/distr/DESCRIPTION pkg/distr/R/qqplot.R pkg/distr/inst/NEWS pkg/distr/man/0distr-package.Rd pkg/distr/man/qqplot.Rd pkg/utils/RCRAN.bat pkg/utils/RCheck.bat Log: distr-2.6 is on CRAN; updated some utilities; qqplot now returns object of class qqplotInfo for later use, eg. in ggplot Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2016-04-23 10:24:20 UTC (rev 1088) +++ pkg/distr/DESCRIPTION 2016-04-23 11:46:22 UTC (rev 1089) @@ -1,6 +1,6 @@ Package: distr Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Object Oriented Implementation of Distributions Description: S4-classes and methods for distributions. Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student in the @@ -19,4 +19,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1088 Modified: pkg/distr/R/qqplot.R =================================================================== --- pkg/distr/R/qqplot.R 2016-04-23 10:24:20 UTC (rev 1088) +++ pkg/distr/R/qqplot.R 2016-04-23 11:46:22 UTC (rev 1089) @@ -118,6 +118,24 @@ xy <- sort(c(xy,xy0,xy1)) } } + qqplotInfo <- list(xy.0=xy, y.0=y, + withConf.pw=withConf.pw, + withConf.sim=withConf.sim, + alpha.CI=alpha.CI , + col.pCI = col.pCI , lty.pCI = lty.pCI , + lwd.pCI = lwd.pCI , pch.pCI = pch.pCI, + cex.pCI = cex.pCI , + col.sCI = col.sCI , lty.sCI = lty.sCI , + lwd.sCI = lwd.sCI , pch.sCI = pch.sCI, + cex.sCI = cex.sCI , + n = n , + exact.sCI = exact.sCI, exact.pCI = exact.pCI, + nosym.pCI = nosym.pCI, with.legend = with.legend, + legend.bg = legend.bg, legend.pos = legend.pos, + legend.cex = legend.cex, legend.pref = legend.pref, + legend.postf = legend.postf, legend.alpha = legend.alpha, debug = debug, + args.stats.qqplot = mcl + ) if(plot.it){ qqb <- .confqq(xy, y, datax=TRUE, withConf.pw, withConf.sim, alpha.CI, col.pCI, lty.pCI, lwd.pCI, pch.pCI, cex.pCI, @@ -134,6 +152,8 @@ } } } - return(invisible(c(ret,qqb))) + qqplotInfo <- c(ret, qqplotInfo, qqb) + class(qqplotInfo) <- c("qqplotInfo","DiagnInfo") + return(invisible(qqplotInfo)) }) Modified: pkg/distr/inst/NEWS =================================================================== --- pkg/distr/inst/NEWS 2016-04-23 10:24:20 UTC (rev 1088) +++ pkg/distr/inst/NEWS 2016-04-23 11:46:22 UTC (rev 1089) @@ -36,6 +36,9 @@ argument has now been enhanced in the sense that now more detailed information about which helper function was the culprit and where (uniroot/optimize) this happens + + now returns an object of S3-classes "qqplotInfo","DiagnInfo" + to be able to recover all information used to produce the plot + for later use in enhanced graphics (e.g. with ggplot) -qqbounds: + the respective helper functions .BinomCI.nosym, .BinomCI, .q2kolmogorov capsulate their calls to uniroot / optimize in Modified: pkg/distr/man/0distr-package.Rd =================================================================== --- pkg/distr/man/0distr-package.Rd 2016-04-23 10:24:20 UTC (rev 1088) +++ pkg/distr/man/0distr-package.Rd 2016-04-23 11:46:22 UTC (rev 1089) @@ -44,14 +44,14 @@ \tabular{ll}{ Package: \tab distr \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils \cr Suggests: \tab distrEx, svUnit (>= 0.7-11) \cr Imports: \tab stats, grDevices, utils, MASS \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1088 \cr }} Modified: pkg/distr/man/qqplot.Rd =================================================================== --- pkg/distr/man/qqplot.Rd 2016-04-23 10:24:20 UTC (rev 1088) +++ pkg/distr/man/qqplot.Rd 2016-04-23 11:46:22 UTC (rev 1089) @@ -110,8 +110,12 @@ } } \value{ - As for function \code{\link[stats:qqnorm]{qqplot}} from package \pkg{stats}: a - list with components + A list of elements containing the information needed to compute the + respective QQ plot, in particular it extends the elements of the + return value of function \code{\link[stats:qqnorm]{qqplot}} + from package \pkg{stats}, i.e., a + list with components \code{x} and \code{y} for x and y coordinates + of the plotted points; more specifically it contains \item{x}{The x coordinates of the points that were/would be plotted} \item{y}{The corresponding quantiles of the second distribution, \emph{including \code{\link{NA}}s}.} @@ -120,6 +124,8 @@ \item{err}{logical vector of length 2.} (elements \code{crit} and \code{err} are taken from the return value(s) of \code{qqbounds}). + The return value allows to recover all information used to produce the plot + for later use in enhanced graphics (e.g. with ggplot). } \references{ Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) Deleted: pkg/distr/tests/Examples/distr-Ex.Rout.save =================================================================== --- pkg/distr/tests/Examples/distr-Ex.Rout.save 2016-04-23 10:24:20 UTC (rev 1088) +++ pkg/distr/tests/Examples/distr-Ex.Rout.save 2016-04-23 11:46:22 UTC (rev 1089) @@ -1,3839 +0,0 @@ - -R version 3.2.2 Patched (2015-11-06 r69612) -- "Fire Safety" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-pc-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> pkgname <- "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 0.9.1) -:startupmsg> -:startupmsg> For more information see ?"startupmsg", -:startupmsg> NEWS("startupmsg") - -Loading required package: sfsmisc -Loading required package: SweaveListingUtils -:SweaveListingUtils> Utilities for Sweave Together with -:SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7) -:SweaveListingUtils> -:SweaveListingUtils> NOTE: Support for this package -:SweaveListingUtils> will stop soon. -:SweaveListingUtils> -:SweaveListingUtils> Package 'knitr' is providing the -:SweaveListingUtils> same functionality in a better -:SweaveListingUtils> way. -: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 objects are masked from ?package:base?: - - library, require - -:distr> Object Oriented Implementation of Distributions (version -:distr> 2.6) -:distr> -:distr> Attention: Arithmetics on distribution objects are -:distr> understood as operations on corresponding random variables -: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 objects are masked from ?package:stats?: - - df, qqplot, sd - -> -> base::assign(".oldSearch", base::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 -> 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 0.43799. -[1] 0.4379965 -> p(A3)(0) # The (approximated) probability that x <= 0 is 0.45620. -[1] 0.4561991 -> q(A3)(.1) # The (approximated) 10 percent quantile is -1.06015. -[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 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 1089 From noreply at r-forge.r-project.org Sat Apr 23 14:00:03 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 14:00:03 +0200 (CEST) Subject: [Distr-commits] r1090 - in pkg: distrEx distrEx/man distrEx/tests/Examples utils Message-ID: <20160423120003.4A06C187EC0@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 14:00:02 +0200 (Sat, 23 Apr 2016) New Revision: 1090 Added: pkg/distrEx/tests/Examples/distrEx-Ex_i386.Rout.save pkg/distrEx/tests/Examples/distrEx-Ex_x64.Rout.save pkg/utils/RCheckOT.bat Removed: pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save Modified: pkg/distrEx/DESCRIPTION pkg/distrEx/man/0distrEx-package.Rd Log: distrEx-2.6 is ready for CRAN; updated some utilities; Modified: pkg/distrEx/DESCRIPTION =================================================================== --- pkg/distrEx/DESCRIPTION 2016-04-23 11:46:22 UTC (rev 1089) +++ pkg/distrEx/DESCRIPTION 2016-04-23 12:00:02 UTC (rev 1090) @@ -1,6 +1,6 @@ Package: distrEx Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Extensions of Package 'distr' Description: Extends package 'distr' by functionals, distances, and conditional distributions. Depends: R(>= 2.10.0), methods, distr(>= 2.2) @@ -15,4 +15,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1089 Modified: pkg/distrEx/man/0distrEx-package.Rd =================================================================== --- pkg/distrEx/man/0distrEx-package.Rd 2016-04-23 11:46:22 UTC (rev 1089) +++ pkg/distrEx/man/0distrEx-package.Rd 2016-04-23 12:00:02 UTC (rev 1090) @@ -28,14 +28,14 @@ \tabular{ll}{ Package: \tab distrEx \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.10.0), methods, distr(>= 2.2) \cr Imports: \tab startupmsg, utils, stats \cr Suggests: \tab tcltk \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1089 \cr } } \section{Classes}{ Deleted: pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save =================================================================== --- pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save 2016-04-23 11:46:22 UTC (rev 1089) +++ pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save 2016-04-23 12:00:02 UTC (rev 1090) @@ -1,1675 +0,0 @@ - -R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -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 <- "distrEx" -> source(file.path(R.home("share"), "R", "examples-header.R")) -> options(warn = 1) -> library('distrEx') -Loading required package: distr -Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) -:startupmsg> -:startupmsg> For more information see ?"startupmsg", -:startupmsg> NEWS("startupmsg") - -Loading required package: sfsmisc -Loading required package: SweaveListingUtils -:SweaveListingUtils> Utilities for Sweave Together with -:SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7) -:SweaveListingUtils> -:SweaveListingUtils> NOTE: Support for this package -:SweaveListingUtils> will stop soon. -:SweaveListingUtils> -:SweaveListingUtils> Package 'knitr' is providing the -:SweaveListingUtils> same functionality in a better -:SweaveListingUtils> way. -: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 objects are masked from ?package:base?: - - library, require - -:distr> Object Oriented Implementation of Distributions (version -:distr> 2.6) -:distr> -:distr> Attention: Arithmetics on distribution objects are -:distr> understood as operations on corresponding random variables -: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 objects are masked from ?package:stats?: - - df, qqplot, sd - -:distrEx> Extensions of Package distr (version 2.6) -: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 objects are masked from ?package:stats?: - - IQR, mad, median, var - -> -> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') -> cleanEx() -> nameEx("AbscontCondDistribution-class") -> ### * AbscontCondDistribution-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: AbscontCondDistribution-class -> ### Title: Absolutely continuous conditional distribution -> ### Aliases: AbscontCondDistribution-class -> ### Keywords: distribution -> -> ### ** Examples -> new("AbscontCondDistribution") -Distribution object of class: AbscontCondDistribution -## cond: -An object of class "Condition" -Slot "name": -[1] "a condition" - -> -> -> cleanEx() -> nameEx("AsymTotalVarDist") -> ### * AsymTotalVarDist -> -> flush(stderr()); flush(stdout()) -> -> ### Name: AsymTotalVarDist -> ### Title: Generic function for the computation of asymmetric total -> ### variation distance of two distributions -> ### Aliases: AsymTotalVarDist AsymTotalVarDist-methods -> ### AsymTotalVarDist,AbscontDistribution,AbscontDistribution-method -> ### AsymTotalVarDist,AbscontDistribution,DiscreteDistribution-method -> ### AsymTotalVarDist,DiscreteDistribution,DiscreteDistribution-method -> ### AsymTotalVarDist,DiscreteDistribution,AbscontDistribution-method -> ### AsymTotalVarDist,LatticeDistribution,DiscreteDistribution-method -> ### AsymTotalVarDist,DiscreteDistribution,LatticeDistribution-method -> ### AsymTotalVarDist,LatticeDistribution,LatticeDistribution-method -> ### AsymTotalVarDist,numeric,DiscreteDistribution-method -> ### AsymTotalVarDist,DiscreteDistribution,numeric-method -> ### AsymTotalVarDist,numeric,AbscontDistribution-method -> ### AsymTotalVarDist,AbscontDistribution,numeric-method -> ### AsymTotalVarDist,AcDcLcDistribution,AcDcLcDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> AsymTotalVarDist(Norm(), UnivarMixingDistribution(Norm(1,2),Norm(0.5,3), -+ mixCoeff=c(0.2,0.8)), rho=0.3) -asym. total variation distance - 0.5311789 -> AsymTotalVarDist(Norm(), Td(10), rho=0.3) -asym. total variation distance - 0.03412602 -> AsymTotalVarDist(Norm(mean = 50, sd = sqrt(25)), Binom(size = 100), rho=0.3) # mutually singular -asym. total variation distance - 1 -> AsymTotalVarDist(Pois(10), Binom(size = 20), rho=0.3) -asym. total variation distance - 0.3093959 -> -> x <- rnorm(100) -> AsymTotalVarDist(Norm(), x, rho=0.3) -asym. total variation distance - 0.3140162 -> AsymTotalVarDist(x, Norm(), asis.smooth.discretize = "smooth", rho=0.3) -asym. total variation distance - 0.2658876 -> -> y <- (rbinom(50, size = 20, prob = 0.5)-10)/sqrt(5) -> AsymTotalVarDist(y, Norm(), rho=0.3) -asym. total variation distance - 0.8343428 -> AsymTotalVarDist(y, Norm(), asis.smooth.discretize = "smooth", rho=0.3) -asym. total variation distance - 0.6326863 -> -> AsymTotalVarDist(rbinom(50, size = 20, prob = 0.5), Binom(size = 20, prob = 0.5), rho=0.3) -asym. total variation distance - 0.292515 -> -> -> -> cleanEx() -> nameEx("Condition-class") -> ### * Condition-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: Condition-class -> ### Title: Conditions -> ### Aliases: Condition-class name,Condition-method name<-,Condition-method -> ### Keywords: distribution -> -> ### ** Examples -> new("Condition") -An object of class "Condition" -Slot "name": -[1] "a condition" - -> -> -> cleanEx() -> nameEx("ContaminationSize") -> ### * ContaminationSize -> -> flush(stderr()); flush(stdout()) -> -> ### Name: ContaminationSize -> ### Title: Generic Function for the Computation of the Convex Contamination -> ### (Pseudo-)Distance of Two Distributions -> ### Aliases: ContaminationSize ContaminationSize-methods -> ### ContaminationSize,AbscontDistribution,AbscontDistribution-method -> ### ContaminationSize,DiscreteDistribution,DiscreteDistribution-method -> ### ContaminationSize,LatticeDistribution,DiscreteDistribution-method -> ### ContaminationSize,DiscreteDistribution,LatticeDistribution-method -> ### ContaminationSize,LatticeDistribution,LatticeDistribution-method -> ### ContaminationSize,AcDcLcDistribution,AcDcLcDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> ContaminationSize(Norm(), Norm(mean=0.1)) -$e1 -Distribution Object of Class: Norm - mean: 0 - sd: 1 - -$e2 -Distribution Object of Class: Norm - mean: 0.1 - sd: 1 - -$size.of.contamination -[1] 0.3504588 - -> ContaminationSize(Pois(), Pois(1.5)) -$e1 -Distribution Object of Class: Pois - lambda: 1 - -$e2 -Distribution Object of Class: Pois - lambda: 1.5 - -$size.of.contamination -[1] 0.3934693 - -> -> -> -> cleanEx() -> nameEx("ConvexContamination") -> ### * ConvexContamination -> -> flush(stderr()); flush(stdout()) -> -> ### Name: ConvexContamination -> ### Title: Generic Function for Generating Convex Contaminations -> ### Aliases: ConvexContamination ConvexContamination-methods -> ### ConvexContamination,UnivariateDistribution,UnivariateDistribution,numeric-method -> ### ConvexContamination,AbscontDistribution,AbscontDistribution,numeric-method -> ### ConvexContamination,AbscontDistribution,UnivariateDistribution,numeric-method -> ### ConvexContamination,DiscreteDistribution,DiscreteDistribution,numeric-method -> ### ConvexContamination,LatticeDistribution,DiscreteDistribution,numeric-method -> ### ConvexContamination,DiscreteDistribution,LatticeDistribution,numeric-method -> ### ConvexContamination,LatticeDistribution,LatticeDistribution,numeric-method -> ### ConvexContamination,AcDcLcDistribution,AcDcLcDistribution,numeric-method -> ### Keywords: distribution methods -> -> ### ** Examples -> -> # Convex combination of two normal distributions -> C1 <- ConvexContamination(e1 = Norm(), e2 = Norm(mean = 5), size = 0.1) -> plot(C1) -> -> -> -> cleanEx() -> nameEx("CvMDist") -> ### * CvMDist -> -> flush(stderr()); flush(stdout()) -> -> ### Name: CvMDist -> ### Title: Generic function for the computation of the Cramer - von Mises -> ### distance of two distributions -> ### Aliases: CvMDist CvMDist-methods -> ### CvMDist,UnivariateDistribution,UnivariateDistribution-method -> ### CvMDist,numeric,UnivariateDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> CvMDist(Norm(), UnivarMixingDistribution(Norm(1,2),Norm(0.5,3), -+ mixCoeff=c(0.2,0.8))) -CvM distance - 0.1812994 -> CvMDist(Norm(), UnivarMixingDistribution(Norm(1,2),Norm(0.5,3), -+ mixCoeff=c(0.2,0.8)),mu=Norm()) -CvM distance - 0.1812994 -> CvMDist(Norm(), Td(10)) -CvM distance - 0.009330691 -> CvMDist(Norm(mean = 50, sd = sqrt(25)), Binom(size = 100)) -CvM distance - 0.01746156 -> CvMDist(Pois(10), Binom(size = 20)) -CvM distance - 0.06107322 -> CvMDist(rnorm(100),Norm()) -CvM distance - 0.04308361 -> CvMDist((rbinom(50, size = 20, prob = 0.5)-10)/sqrt(5), Norm()) -CvM distance - 0.123967 -> CvMDist(rbinom(50, size = 20, prob = 0.5), Binom(size = 20, prob = 0.5)) -CvM distance - 0.1307281 -> CvMDist(rbinom(50, size = 20, prob = 0.5), Binom(size = 20, prob = 0.5), mu = Pois()) -CvM distance - 0.001969063 -> -> -> -> cleanEx() -> nameEx("DiscreteCondDistribution-class") -> ### * DiscreteCondDistribution-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: DiscreteCondDistribution-class -> ### Title: Discrete conditional distribution -> ### Aliases: DiscreteCondDistribution-class -> ### Keywords: distribution -> -> ### ** Examples -> new("DiscreteCondDistribution") -Distribution object of class: DiscreteCondDistribution -## cond: -An object of class "Condition" -Slot "name": -[1] "a condition" - -> -> -> cleanEx() -> nameEx("DiscreteMVDistribution-class") -> ### * DiscreteMVDistribution-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: DiscreteMVDistribution-class -> ### Title: Discrete Multivariate Distributions -> ### Aliases: DiscreteMVDistribution-class -> ### support,DiscreteMVDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> (D1 <- new("MultivariateDistribution")) # Dirac measure in (0,0) -> r(D1)(5) - [,1] [,2] -[1,] 0 0 -[2,] 0 0 -[3,] 0 0 -[4,] 0 0 -[5,] 0 0 -> -> (D2 <- DiscreteMVDistribution(supp = matrix(c(1:5, rep(3, 5)), ncol=2, byrow=TRUE))) -Warning in DiscreteMVDistribution(supp = matrix(c(1:5, rep(3, 5)), ncol = 2, : - collapsing to unique support values -> support(D2) - [,1] [,2] -[1,] 1 2 -[2,] 3 4 -[3,] 5 3 -[4,] 3 3 -> r(D2)(10) - [,1] [,2] - [1,] 3 3 - [2,] 3 3 - [3,] 5 3 - [4,] 1 2 - [5,] 3 3 - [6,] 1 2 - [7,] 1 2 - [8,] 3 4 - [9,] 3 4 -[10,] 3 3 -> d(D2)(support(D2)) -[1] 0.2 0.2 0.2 0.4 -> p(D2)(lower = c(1,1), upper = c(3,3)) -[1] 0.6 -> q(D2) -NULL -> param(D2) -NULL -> img(D2) -An object of class "EuclideanSpace" -Slot "dimension": -[1] 2 - -Slot "name": -[1] "Euclidean Space" - -> -> e1 <- E(D2) # expectation -> -> -> -> cleanEx() -> nameEx("DiscreteMVDistribution") -> ### * DiscreteMVDistribution -> -> flush(stderr()); flush(stdout()) -> -> ### Name: DiscreteMVDistribution -> ### Title: Generating function for multivariate discrete distribution -> ### Aliases: DiscreteMVDistribution -> ### Keywords: distribution -> -> ### ** Examples -> -> # Dirac-measure at (0,0,0) -> D1 <- DiscreteMVDistribution(supp = c(0,0,0)) -> support(D1) - [,1] [,2] [,3] -[1,] 0 0 0 -> -> # simple discrete distribution -> D2 <- DiscreteMVDistribution(supp = matrix(c(0,1,0,2,2,1,1,0), ncol=2), -+ prob = c(0.3, 0.2, 0.2, 0.3)) -> support(D2) - [,1] [,2] -[1,] 0 2 -[2,] 1 1 -[3,] 0 1 -[4,] 2 0 -> r(D2)(10) - [,1] [,2] - [1,] 0 2 - [2,] 2 0 - [3,] 2 0 - [4,] 1 1 - [5,] 0 2 - [6,] 1 1 - [7,] 1 1 - [8,] 0 1 - [9,] 0 1 -[10,] 0 2 -> -> -> -> cleanEx() -> nameEx("E") -> ### * E -> -> flush(stderr()); flush(stdout()) -> -> ### Name: E -> ### Title: Generic Function for the Computation of (Conditional) -> ### Expectations -> ### Aliases: E E-methods E,UnivariateDistribution,missing,missing-method -> ### E,AbscontDistribution,missing,missing-method -> ### E,DiscreteDistribution,missing,missing-method -> ### E,LatticeDistribution,missing,missing-method -> ### E,AffLinDistribution,missing,missing-method -> ### E,AffLinAbscontDistribution,missing,missing-method -> ### E,AffLinDiscreteDistribution,missing,missing-method -> ### E,AffLinLatticeDistribution,missing,missing-method -> ### E,MultivariateDistribution,missing,missing-method -> ### E,DiscreteMVDistribution,missing,missing-method -> ### E,UnivarLebDecDistribution,missing,missing-method -> ### E,AffLinUnivarLebDecDistribution,missing,missing-method -> ### E,UnivarMixingDistribution,missing,missing-method -> ### E,UnivariateDistribution,function,missing-method -> ### E,AbscontDistribution,function,missing-method -> ### E,DiscreteDistribution,function,missing-method -> ### E,LatticeDistribution,function,missing-method -> ### E,MultivariateDistribution,function,missing-method -> ### E,DiscreteMVDistribution,function,missing-method -> ### E,UnivarLebDecDistribution,function,missing-method -> ### E,UnivarMixingDistribution,function,missing-method -> ### E,AcDcLcDistribution,ANY,ANY-method -> ### E,CompoundDistribution,missing,missing-method -> ### E,UnivariateCondDistribution,missing,numeric-method -> ### E,AbscontCondDistribution,missing,numeric-method -> ### E,DiscreteCondDistribution,missing,numeric-method -> ### E,UnivarLebDecDistribution,missing,ANY-method -> ### E,UnivarMixingDistribution,missing,ANY-method -> ### E,UnivarLebDecDistribution,function,ANY-method -> ### E,UnivariateCondDistribution,function,numeric-method -> ### E,UnivarMixingDistribution,function,ANY-method -> ### E,AbscontCondDistribution,function,numeric-method -> ### E,DiscreteCondDistribution,function,numeric-method -> ### E,Arcsine,missing,missing-method E,Beta,missing,missing-method -> ### E,Binom,missing,missing-method E,Cauchy,missing,missing-method -> ### E,Chisq,missing,missing-method E,Dirac,missing,missing-method -> ### E,DExp,missing,missing-method E,Exp,missing,missing-method -> ### E,Fd,missing,missing-method E,Gammad,missing,missing-method -> ### E,Gammad,function,missing-method E,Geom,missing,missing-method -> ### E,Gumbel,missing,missing-method E,GPareto,missing,missing-method -> ### E,GPareto,function,missing-method E,GEV,missing,missing-method -> ### E,GEV,function,missing-method E,Hyper,missing,missing-method -> ### E,Logis,missing,missing-method E,Lnorm,missing,missing-method -> ### E,Nbinom,missing,missing-method E,Norm,missing,missing-method -> ### E,Pareto,missing,missing-method E,Pois,missing,missing-method -> ### E,Td,missing,missing-method E,Unif,missing,missing-method -> ### E,Weibull,missing,missing-method -> ### Keywords: methods distribution -> -> ### ** Examples -> -> # mean of Exp(1) distribution -> E <- Exp() -> -> E(E) ## uses explicit terms -[1] 1 -> E(as(E,"AbscontDistribution")) ## uses numerical integration -[1] 0.9999983 -> E(as(E,"UnivariateDistribution")) ## uses simulations -[1] 1.002698 -> E(E, fun = function(x){2*x^2}) ## uses simulations -[1] 3.999941 -> -> # the same operator for discrete distributions: -> P <- Pois(lambda=2) -> -> E(P) ## uses explicit terms -[1] 2 -> E(as(P,"DiscreteDistribution")) ## uses sums -[1] 1.999997 -> E(as(P,"UnivariateDistribution")) ## uses simulations -[1] 2.00881 -> E(P, fun = function(x){2*x^2}) ## uses simulations -[1] 11.99993 -> -> -> # second moment of N(1,4) -> E(Norm(mean=1, sd=2), fun = function(x){x^2}) -[1] 4.999977 -> E(Norm(mean=1, sd=2), fun = function(x){x^2}, useApply = FALSE) -[1] 4.999977 -> -> # conditional distribution of a linear model -> D1 <- LMCondDistribution(theta = 1) -> E(D1, cond = 1) -[1] 0.9999998 -> E(Norm(mean=1)) -[1] 1 -> E(D1, function(x){x^2}, cond = 1) -[1] 1.999994 -> E(Norm(mean=1), fun = function(x){x^2}) -[1] 1.999994 -> E(D1, function(x, cond){cond*x^2}, cond = 2, withCond = TRUE, useApply = FALSE) -[1] 9.999987 -> E(Norm(mean=2), function(x){2*x^2}) -[1] 9.999987 -> -> E(as(Norm(mean=2),"AbscontDistribution")) -[1] 2 -> ### somewhat less accurate: -> E(as(Norm(mean=2),"AbscontDistribution"), -+ lowerTruncQuantil=1e-4,upperTruncQuantil=1e-4, IQR.fac= 4) -[1] 2 -> ### even less accurate: -> E(as(Norm(mean=2),"AbscontDistribution"), -+ lowerTruncQuantil=1e-2,upperTruncQuantil=1e-2, IQR.fac= 4) -[1] 2 -> ### no good idea, but just as an example: -> E(as(Norm(mean=2),"AbscontDistribution"), -+ lowerTruncQuantil=1e-2,upperTruncQuantil=1e-2, IQR.fac= .1) -[1] 2 -> -> ### truncation of integration range; see also m1df... -> E(Norm(mean=2), low=2,upp=4) -[1] 1.299451 -> -> E(Cauchy()) -[1] NA -> E(Cauchy(),upp=3,low=-2) -[1] 0 -> # some Lebesgue decomposed distribution -> mymix <- UnivarLebDecDistribution(acPart = Norm(), discretePart = Binom(4,.4), -+ acWeight = 0.4) -> E(mymix) -[1] 0.96 -> -> -> -> cleanEx() -> nameEx("EmpiricalMVDistribution") -> ### * EmpiricalMVDistribution -> -> flush(stderr()); flush(stdout()) -> -> ### Name: EmpiricalMVDistribution -> ### Title: Generating function for mulitvariate discrete distribution -> ### Aliases: EmpiricalMVDistribution -> ### Keywords: distribution -> -> ### ** Examples -> -> ## generate some data -> X <- matrix(rnorm(50), ncol = 5) -> -> ## empirical distribution of X -> D1 <- EmpiricalMVDistribution(data = X) -> support(D1) - [,1] [,2] [,3] [,4] [,5] - [1,] -0.6264538 1.51178117 0.91897737 1.35867955 -0.1645236 - [2,] 0.1836433 0.38984324 0.78213630 -0.10278773 -0.2533617 - [3,] -0.8356286 -0.62124058 0.07456498 0.38767161 0.6969634 - [4,] 1.5952808 -2.21469989 -1.98935170 -0.05380504 0.5566632 - [5,] 0.3295078 1.12493092 0.61982575 -1.37705956 -0.6887557 - [6,] -0.8204684 -0.04493361 -0.05612874 -0.41499456 -0.7074952 - [7,] 0.4874291 -0.01619026 -0.15579551 -0.39428995 0.3645820 - [8,] 0.7383247 0.94383621 -1.47075238 -0.05931340 0.7685329 - [9,] 0.5757814 0.82122120 -0.47815006 1.10002537 -0.1123462 -[10,] -0.3053884 0.59390132 0.41794156 0.76317575 0.8811077 -> r(D1)(10) - [,1] [,2] [,3] [,4] [,5] - [1,] 0.7383247 0.94383621 -1.47075238 -0.05931340 0.7685329 - [2,] 0.3295078 1.12493092 0.61982575 -1.37705956 -0.6887557 - [3,] 1.5952808 -2.21469989 -1.98935170 -0.05380504 0.5566632 - [4,] -0.6264538 1.51178117 0.91897737 1.35867955 -0.1645236 - [5,] 0.7383247 0.94383621 -1.47075238 -0.05931340 0.7685329 - [6,] 1.5952808 -2.21469989 -1.98935170 -0.05380504 0.5566632 - [7,] -0.8356286 -0.62124058 0.07456498 0.38767161 0.6969634 - [8,] -0.8204684 -0.04493361 -0.05612874 -0.41499456 -0.7074952 - [9,] -0.6264538 1.51178117 0.91897737 1.35867955 -0.1645236 -[10,] 0.4874291 -0.01619026 -0.15579551 -0.39428995 0.3645820 -> -> -> -> cleanEx() -> nameEx("EuclCondition-class") -> ### * EuclCondition-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: EuclCondition-class -> ### Title: Conditioning by an Euclidean space. -> ### Aliases: EuclCondition-class Range Range,EuclCondition-method -> ### show,EuclCondition-method -> ### Keywords: distribution -> -> ### ** Examples -> -> new("EuclCondition") -name: conditioning by an Euclidean space -Range: Euclidean Space with dimension 1 -> -> -> -> cleanEx() -> nameEx("EuclCondition") -> ### * EuclCondition -> -> flush(stderr()); flush(stdout()) -> -> ### Name: EuclCondition -> ### Title: Generating function for EuclCondition-class -> ### Aliases: EuclCondition -> ### Keywords: distribution -> -> ### ** Examples -> -> EuclCondition(dimension = 3) -name: conditioning by an Euclidean space -Range: Euclidean Space with dimension 3 -> -> ## The function is currently defined as -> function(dimension){ -+ new("EuclCondition", Range = EuclideanSpace(dimension = dimension)) -+ } -function (dimension) -{ - new("EuclCondition", Range = EuclideanSpace(dimension = dimension)) -} -> -> -> -> cleanEx() -> nameEx("GLIntegrate") -> ### * GLIntegrate -> -> flush(stderr()); flush(stdout()) -> -> ### Name: GLIntegrate -> ### Title: Gauss-Legendre Quadrature -> ### Aliases: GLIntegrate -> ### Keywords: math utilities -> -> ### ** Examples -> -> integrate(dnorm, -1.96, 1.96) -0.9500042 with absolute error < 1e-11 -> GLIntegrate(dnorm, -1.96, 1.96) -[1] 0.9500042 -> -> -> -> cleanEx() -> nameEx("HellingerDist") -> ### * HellingerDist -> -> flush(stderr()); flush(stdout()) -> -> ### Name: HellingerDist -> ### Title: Generic function for the computation of the Hellinger distance -> ### of two distributions -> ### Aliases: HellingerDist HellingerDist-methods -> ### HellingerDist,AbscontDistribution,AbscontDistribution-method -> ### HellingerDist,AbscontDistribution,DiscreteDistribution-method -> ### HellingerDist,DiscreteDistribution,DiscreteDistribution-method -> ### HellingerDist,DiscreteDistribution,AbscontDistribution-method -> ### HellingerDist,LatticeDistribution,DiscreteDistribution-method -> ### HellingerDist,DiscreteDistribution,LatticeDistribution-method -> ### HellingerDist,LatticeDistribution,LatticeDistribution-method -> ### HellingerDist,numeric,DiscreteDistribution-method -> ### HellingerDist,DiscreteDistribution,numeric-method -> ### HellingerDist,numeric,AbscontDistribution-method -> ### HellingerDist,AbscontDistribution,numeric-method -> ### HellingerDist,AcDcLcDistribution,AcDcLcDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> HellingerDist(Norm(), UnivarMixingDistribution(Norm(1,2),Norm(0.5,3), -+ mixCoeff=c(0.2,0.8))) -Hellinger distance - 0.4604849 -> HellingerDist(Norm(), Td(10)) -Hellinger distance - 0.0598968 -> HellingerDist(Norm(mean = 50, sd = sqrt(25)), Binom(size = 100)) # mutually singular -Hellinger distance - 1 -> HellingerDist(Pois(10), Binom(size = 20)) -Hellinger distance - 0.1742254 -> -> x <- rnorm(100) -> HellingerDist(Norm(), x) -Hellinger distance - 0.3287617 -> HellingerDist(x, Norm(), asis.smooth.discretize = "smooth") -Hellinger distance - 0.1904838 -> -> y <- (rbinom(50, size = 20, prob = 0.5)-10)/sqrt(5) -> HellingerDist(y, Norm()) -Hellinger distance - 0.7596996 -> HellingerDist(y, Norm(), asis.smooth.discretize = "smooth") -Hellinger distance - 0.5283272 -> -> HellingerDist(rbinom(50, size = 20, prob = 0.5), Binom(size = 20, prob = 0.5)) -Hellinger distance - 0.1945649 -> -> -> -> cleanEx() -> nameEx("KolmogorovDist") -> ### * KolmogorovDist -> -> flush(stderr()); flush(stdout()) -> -> ### Name: KolmogorovDist -> ### Title: Generic function for the computation of the Kolmogorov distance -> ### of two distributions -> ### Aliases: KolmogorovDist KolmogorovDist-methods -> ### KolmogorovDist,AbscontDistribution,AbscontDistribution-method -> ### KolmogorovDist,AbscontDistribution,DiscreteDistribution-method -> ### KolmogorovDist,DiscreteDistribution,DiscreteDistribution-method -> ### KolmogorovDist,DiscreteDistribution,AbscontDistribution-method -> ### KolmogorovDist,LatticeDistribution,DiscreteDistribution-method -> ### KolmogorovDist,DiscreteDistribution,LatticeDistribution-method -> ### KolmogorovDist,LatticeDistribution,LatticeDistribution-method -> ### KolmogorovDist,numeric,UnivariateDistribution-method -> ### KolmogorovDist,UnivariateDistribution,numeric-method -> ### KolmogorovDist,AcDcLcDistribution,AcDcLcDistribution-method -> ### Keywords: distribution -> -> ### ** Examples -> -> KolmogorovDist(Norm(), UnivarMixingDistribution(Norm(1,2),Norm(0.5,3), -+ mixCoeff=c(0.2,0.8))) -Kolmogorov distance - 0.3092684 -> KolmogorovDist(Norm(), Td(10)) -Kolmogorov distance - 0.01554215 -> KolmogorovDist(Norm(mean = 50, sd = sqrt(25)), Binom(size = 100)) -Kolmogorov distance - 0.03979462 -> KolmogorovDist(Pois(10), Binom(size = 20)) -Kolmogorov distance - 0.08863266 -> KolmogorovDist(Norm(), rnorm(100)) -Kolmogorov distance - 0.1149486 -> KolmogorovDist((rbinom(50, size = 20, prob = 0.5)-10)/sqrt(5), Norm()) -Kolmogorov distance - 0.1673604 -> KolmogorovDist(rbinom(50, size = 20, prob = 0.5), Binom(size = 20, prob = 0.5)) -Kolmogorov distance - 0.03172234 -> -> -> -> cleanEx() -> nameEx("LMCondDistribution") -> ### * LMCondDistribution -> -> flush(stderr()); flush(stdout()) -> -> ### Name: LMCondDistribution -> ### Title: Generating function for the conditional distribution of a linear -> ### regression model. -> ### Aliases: LMCondDistribution -> ### Keywords: distribution models -> -> ### ** Examples -> -> # normal error distribution -> (D1 <- LMCondDistribution(theta = 1)) # corresponds to Norm(cond, 1) -Distribution object of class: AbscontCondDistribution - theta: 1 - intercept: 0 - scale: 1 -## cond: -name: conditioning by an Euclidean space -Range: Euclidean Space with dimension 1 -> plot(D1) -Warning in plot(D1) : - 'plot' not yet implemented for objects of class AbscontCondDistribution -> r(D1) -function (n, cond, ...) -{ - if (length(cond) != 1L) - stop("'cond' has wrong dimension") - r <- function (n) - { - rnorm(n, mean = 0, sd = 1) - } - 0 + cond %*% 1 + 1 * r(n, ...) -} - -> d(D1) -function (x, cond, log = FALSE, ...) -{ - if (length(cond) != 1L) - stop("'cond' has wrong dimension") - d <- function (x, log = FALSE) - { - dnorm(x, mean = 0, sd = 1, log = log) - } - if ("log" %in% names(formals(d))) - d0 <- d((x - 0 - as.vector(cond %*% 1))/1, log = log) - else { - d0 <- d((x - 0 - as.vector(cond %*% 1))/1) - if (log) - d0 <- log(d0) - } - if (log) - d0 <- d0 - log(1) - else d0 <- d0/1 - return(d0) -} - -> p(D1) -function (q, cond, lower.tail = TRUE, log.p = FALSE, ...) -{ - if (length(cond) != 1L) - stop("'cond' has wrong dimension") - p <- function (q, lower.tail = TRUE, log.p = FALSE) - { - pnorm(q, mean = 0, sd = 1, lower.tail = lower.tail, log.p = log.p) - } - argList <- alist((q - 0 - as.vector(cond %*% 1))/1) - if ("lower.tail" %in% names(formals(p))) - argList <- c(argList, lower.tail = lower.tail) - if ("log.p" %in% names(formals(p))) - argList <- c(argList, log.p = log.p) - dots <- alist(...) - if (length(dots)) - argList <- c(argList, dots) - p0 <- do.call(p, argList) - if (!("lower.tail" %in% names(formals(p)))) - if (!lower.tail) - p0 <- 1 - p0 - if (!("log.p" %in% names(formals(p)))) - if (log.p) - p0 <- log(p0) - return(p0) -} - -> q(D1) -function (p, cond, lower.tail = TRUE, log.p = FALSE, ...) -{ - if (length(cond) != 1L) - stop("'cond' has wrong dimension") - q <- function (p, lower.tail = TRUE, log.p = FALSE) - { - qnorm(p, mean = 0, sd = 1, lower.tail = lower.tail, log.p = log.p) - } - argList <- alist(p) - if ("lower.tail" %in% names(formals(q))) - argList <- c(argList, lower.tail = lower.tail) - else if (log.p) - p <- exp(p) - if ("log.p" %in% names(formals(q))) - argList <- c(argList, log.p = log.p) - else if (!lower.tail) - p <- 1 - p - dots <- alist(...) - if (length(dots)) - argList <- c(argList, dots) - 1 * do.call(q, argList) + 0 + as.vector(cond %*% 1) -} - -> param(D1) -name: parameter of a linear regression model -theta: 1 -intercept: 0 -scale: 1 -> cond(D1) -name: conditioning by an Euclidean space -Range: Euclidean Space with dimension 1 -> -> d(D1)(0, cond = 1) -[1] 0.2419707 -> d(Norm(mean=1))(0) -[1] 0.2419707 -> -> E(D1, cond = 1) -[1] 0.9999998 -> E(D1, function(x){x^2}, cond = 2) -[1] 4.999993 -> E(Norm(mean=2), function(x){x^2}) -[1] 4.999993 -> -> -> -> cleanEx() -> nameEx("LMParameter-class") -> ### * LMParameter-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: LMParameter-class -> ### Title: Parameter of a linear regression model -> ### Aliases: LMParameter-class show,LMParameter-method -> ### Keywords: distribution -> -> ### ** Examples -> -> new("LMParameter") -name: parameter of a linear regression model -theta: 0 -intercept: 0 -scale: 1 -> -> -> -> cleanEx() -> nameEx("LMParameter") -> ### * LMParameter -> -> flush(stderr()); flush(stdout()) -> -> ### Name: LMParameter -> ### Title: Generating function for LMParameter-class -> ### Aliases: LMParameter -> ### Keywords: models -> -> ### ** Examples -> -> LMParameter(theta = c(1,1), intercept = 2, scale = 0.5) -name: parameter of a linear regression model -theta: 1 - theta: 1 -intercept: 2 -scale: 0.5 -> -> ## The function is currently defined as -> function(theta = 0, intercept = 0, scale = 1){ -+ new("LMParameter", theta = theta, intercept = intercept, scale = 1) -+ } -function (theta = 0, intercept = 0, scale = 1) -{ - new("LMParameter", theta = theta, intercept = intercept, - scale = 1) -} -> -> -> -> cleanEx() -> nameEx("MultivariateDistribution-class") -> ### * MultivariateDistribution-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: MultivariateDistribution-class -> ### Title: Multivariate Distributions -> ### Aliases: MultivariateDistribution-class -> ### show,MultivariateDistribution-method [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 1090 From noreply at r-forge.r-project.org Sat Apr 23 14:09:37 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 14:09:37 +0200 (CEST) Subject: [Distr-commits] r1091 - in pkg/distrSim: . man tests/Examples Message-ID: <20160423120937.145BC187E7E@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 14:09:36 +0200 (Sat, 23 Apr 2016) New Revision: 1091 Modified: pkg/distrSim/DESCRIPTION pkg/distrSim/man/0distrSim-package.Rd pkg/distrSim/tests/Examples/distrSim-Ex.Rout.save Log: distrSim-2.6 is on CRAN Modified: pkg/distrSim/DESCRIPTION =================================================================== --- pkg/distrSim/DESCRIPTION 2016-04-23 12:00:02 UTC (rev 1090) +++ pkg/distrSim/DESCRIPTION 2016-04-23 12:09:36 UTC (rev 1091) @@ -1,6 +1,6 @@ Package: distrSim Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Simulation Classes Based on Package 'distr' Description: S4-classes for setting up a coherent framework for simulation within the distr family of packages. @@ -18,4 +18,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1090 Modified: pkg/distrSim/man/0distrSim-package.Rd =================================================================== --- pkg/distrSim/man/0distrSim-package.Rd 2016-04-23 12:00:02 UTC (rev 1090) +++ pkg/distrSim/man/0distrSim-package.Rd 2016-04-23 12:09:36 UTC (rev 1091) @@ -14,14 +14,14 @@ \tabular{ll}{ Package: \tab distrSim \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.14.0), methods, graphics, setRNG(>= 2006.2-1), distr(>= 2.5.2) \cr Suggests: \tab distrEx(>= 2.2) \cr Imports: \tab startupmsg, stats, grDevices \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1090 \cr } } \section{Classes}{ Modified: pkg/distrSim/tests/Examples/distrSim-Ex.Rout.save =================================================================== --- pkg/distrSim/tests/Examples/distrSim-Ex.Rout.save 2016-04-23 12:00:02 UTC (rev 1090) +++ pkg/distrSim/tests/Examples/distrSim-Ex.Rout.save 2016-04-23 12:09:36 UTC (rev 1091) @@ -1,7 +1,7 @@ -R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) +R Under development (unstable) (2016-04-22 r70532) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing +Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -20,11 +20,12 @@ > pkgname <- "distrSim" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) +> options(pager = "console") > library('distrSim') Loading required package: setRNG Loading required package: distr Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) +:startupmsg> Utilities for Start-Up Messages (version 0.9.2) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") @@ -59,9 +60,9 @@ :SweaveListingUtils> vignette("ExampleSweaveListingUtils"). -Attaching package: ?SweaveListingUtils? +Attaching package: 'SweaveListingUtils' -The following objects are masked from ?package:base?: +The following objects are masked from 'package:base': library, require @@ -85,13 +86,13 @@ :distr> vignette("distr"). -Attaching package: ?distr? +Attaching package: 'distr' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': df, qqplot, sd -:distrSim> Simulation Classes Based on Package distr (version +:distrSim> Simulation Classes Based on Package 'distr' (version :distrSim> 2.6) :distrSim> :distrSim> Some functions from package 'stats' are intentionally @@ -106,13 +107,13 @@ :distrSim> vignette("distr"). -Attaching package: ?distrSim? +Attaching package: 'distrSim' -The following object is masked from ?package:stats?: +The following object is masked from 'package:stats': simulate -The following object is masked from ?package:base?: +The following object is masked from 'package:base': rbind @@ -854,7 +855,6 @@ we intentionally mask the base function "rbind" however "rbind" may still be used in exactly the same way as before masking. - > > > @@ -939,7 +939,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 1.016 0.02 1.039 0 0.003 +Time elapsed: 1.13 0.11 1.28 NA NA > grDevices::dev.off() null device 1 From noreply at r-forge.r-project.org Sat Apr 23 14:44:43 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 14:44:43 +0200 (CEST) Subject: [Distr-commits] r1092 - in pkg: SweaveListingUtils startupmsg Message-ID: <20160423124443.870FB187E82@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 14:44:43 +0200 (Sat, 23 Apr 2016) New Revision: 1092 Modified: pkg/SweaveListingUtils/DESCRIPTION pkg/startupmsg/DESCRIPTION Log: fixed a minor thing in DESCRIPTION after mail by U. Ligges Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 12:09:36 UTC (rev 1091) +++ pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 12:44:43 UTC (rev 1092) @@ -1,10 +1,10 @@ Package: SweaveListingUtils Title: Utilities for Sweave Together with TeX 'listings' Package -Description: Package SweaveListingUtils provides utilities for defining R / Rd as "language" - for Tex-package-listings and for 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. -Version: 0.7 +Description: Provides utilities for defining R / Rd as "language" for Tex-package-listings + and for 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. +Version: 0.7.1 Encoding: latin1 Date: 2016-04-23 Depends: R(>= 2.14.0), startupmsg Modified: pkg/startupmsg/DESCRIPTION =================================================================== --- pkg/startupmsg/DESCRIPTION 2016-04-23 12:09:36 UTC (rev 1091) +++ pkg/startupmsg/DESCRIPTION 2016-04-23 12:44:43 UTC (rev 1092) @@ -1,9 +1,9 @@ Package: startupmsg Encoding: latin1 -Version: 0.9.2 +Version: 0.9.3 Date: 2016-04-23 Title: Utilities for Start-Up Messages -Description: Package startupmsg provides utilities to create or suppress start-up messages. +Description: Provides utilities to create or suppress start-up messages. Authors at R: person("Peter", "Ruckdeschel", role=c("cre", "cph"), email="peter.ruckdeschel at uni-oldenburg.de") Depends: R(>= 1.8.0) From noreply at r-forge.r-project.org Sat Apr 23 14:45:24 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 14:45:24 +0200 (CEST) Subject: [Distr-commits] r1093 - in pkg/distrTEst: . man tests/Examples Message-ID: <20160423124525.4BFBB187653@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 14:45:24 +0200 (Sat, 23 Apr 2016) New Revision: 1093 Modified: pkg/distrTEst/DESCRIPTION pkg/distrTEst/man/0distrTEst-package.Rd pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save Log: distrTEst-2.6 is on CRAN Modified: pkg/distrTEst/DESCRIPTION =================================================================== --- pkg/distrTEst/DESCRIPTION 2016-04-23 12:44:43 UTC (rev 1092) +++ pkg/distrTEst/DESCRIPTION 2016-04-23 12:45:24 UTC (rev 1093) @@ -1,6 +1,6 @@ Package: distrTEst Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Estimation and Testing Classes Based on Package 'distr' Description: Evaluation (S4-)classes based on package distr for evaluating procedures (estimators/tests) at data/simulation in a unified way. @@ -18,4 +18,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1091 Modified: pkg/distrTEst/man/0distrTEst-package.Rd =================================================================== --- pkg/distrTEst/man/0distrTEst-package.Rd 2016-04-23 12:44:43 UTC (rev 1092) +++ pkg/distrTEst/man/0distrTEst-package.Rd 2016-04-23 12:45:24 UTC (rev 1093) @@ -16,14 +16,14 @@ \tabular{ll}{ Package: \tab distrTEst \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.6.0), methods, graphics, setRNG(>= 2006.2-1), distrSim(>= 2.2) \cr Imports: \tab startupmsg, utils\cr Suggests: \tab distrEx(>= 2.2)\cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1091 \cr }} \section{Classes}{ \preformatted{ Modified: pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save =================================================================== --- pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save 2016-04-23 12:44:43 UTC (rev 1092) +++ pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save 2016-04-23 12:45:24 UTC (rev 1093) @@ -1,7 +1,7 @@ -R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) +R Under development (unstable) (2016-04-22 r70532) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing +Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -20,12 +20,13 @@ > pkgname <- "distrTEst" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) +> options(pager = "console") > library('distrTEst') Loading required package: setRNG Loading required package: distrSim Loading required package: distr Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) +:startupmsg> Utilities for Start-Up Messages (version 0.9.2) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") @@ -60,9 +61,9 @@ :SweaveListingUtils> vignette("ExampleSweaveListingUtils"). -Attaching package: ?SweaveListingUtils? +Attaching package: 'SweaveListingUtils' -The following objects are masked from ?package:base?: +The following objects are masked from 'package:base': library, require @@ -86,9 +87,9 @@ :distr> vignette("distr"). -Attaching package: ?distr? +Attaching package: 'distr' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': df, qqplot, sd @@ -107,13 +108,13 @@ :distrSim> vignette("distr"). -Attaching package: ?distrSim? +Attaching package: 'distrSim' -The following object is masked from ?package:stats?: +The following object is masked from 'package:stats': simulate -The following object is masked from ?package:base?: +The following object is masked from 'package:base': rbind @@ -495,7 +496,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 1.333 0.022 1.356 0 0 +Time elapsed: 1.57 0.11 1.73 NA NA > grDevices::dev.off() null device 1 From noreply at r-forge.r-project.org Sat Apr 23 14:53:23 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 14:53:23 +0200 (CEST) Subject: [Distr-commits] r1094 - in pkg/distrTeach: . man Message-ID: <20160423125323.E4A04187653@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 14:53:23 +0200 (Sat, 23 Apr 2016) New Revision: 1094 Modified: pkg/distrTeach/DESCRIPTION pkg/distrTeach/man/0distrTeach-package.Rd Log: distrTeach-2.6 is on CRAN Modified: pkg/distrTeach/DESCRIPTION =================================================================== --- pkg/distrTeach/DESCRIPTION 2016-04-23 12:45:24 UTC (rev 1093) +++ pkg/distrTeach/DESCRIPTION 2016-04-23 12:53:23 UTC (rev 1094) @@ -1,6 +1,6 @@ Package: distrTeach Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Extensions of Package 'distr' for Teaching Stochastics/Statistics in Secondary School Description: Provides flexible examples of LLN and CLT for teaching purposes in secondary school. @@ -19,4 +19,4 @@ Packaged: Fri Jun 8 00:12:57 2007; Peter LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1091 Modified: pkg/distrTeach/man/0distrTeach-package.Rd =================================================================== --- pkg/distrTeach/man/0distrTeach-package.Rd 2016-04-23 12:45:24 UTC (rev 1093) +++ pkg/distrTeach/man/0distrTeach-package.Rd 2016-04-23 12:53:23 UTC (rev 1094) @@ -21,14 +21,14 @@ \tabular{ll}{ Package: \tab distrTeach \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.2.0), methods, distr(>= 2.2), distrEx(>= 2.2) \cr Suggests: \tab tcltk\cr Imports: \tab startupmsg, grDevices, graphics, stats\cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1091 \cr } } \section{Classes}{ From noreply at r-forge.r-project.org Sat Apr 23 15:47:33 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 15:47:33 +0200 (CEST) Subject: [Distr-commits] r1095 - in pkg/SweaveListingUtils: . tests/Examples Message-ID: <20160423134733.D2362187C0D@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 15:47:33 +0200 (Sat, 23 Apr 2016) New Revision: 1095 Modified: pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save Log: [SweaveListingUtils] yet another fix for Uwe Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 12:53:23 UTC (rev 1094) +++ pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 13:47:33 UTC (rev 1095) @@ -1,10 +1,10 @@ Package: SweaveListingUtils Title: Utilities for Sweave Together with TeX 'listings' Package -Description: Provides utilities for defining R / Rd as "language" for Tex-package-listings - and for including R / Rd source file (sniplets) copied from R-forge in its most - recent version (or another url) thereby avoiding inconsistencies between vignette +Description: Provides utilities for defining R / Rd as "language" for TeX-package "listings" + and for including R / Rd source file (snippets) copied from R-forge in its most + recent version (or another URL) thereby avoiding inconsistencies between vignette and documented source code. -Version: 0.7.1 +Version: 0.7.2 Encoding: latin1 Date: 2016-04-23 Depends: R(>= 2.14.0), startupmsg Modified: pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save =================================================================== --- pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-23 12:53:23 UTC (rev 1094) +++ pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-23 13:47:33 UTC (rev 1095) @@ -30,7 +30,7 @@ :SweaveListingUtils> Utilities for Sweave Together with :SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7) +:SweaveListingUtils> 0.7.2) :SweaveListingUtils> :SweaveListingUtils> NOTE: Support for this package :SweaveListingUtils> will stop soon. @@ -3334,7 +3334,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 1.24 0.28 6.36 NA NA +Time elapsed: 1.29 0.33 4.95 NA NA > grDevices::dev.off() null device 1 From noreply at r-forge.r-project.org Sat Apr 23 16:08:44 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 16:08:44 +0200 (CEST) Subject: [Distr-commits] r1096 - in pkg/distrTeach: . tests/Examples Message-ID: <20160423140844.AB248187C0D@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 16:08:44 +0200 (Sat, 23 Apr 2016) New Revision: 1096 Modified: pkg/distrTeach/DESCRIPTION pkg/distrTeach/tests/Examples/distrTeach-Ex.Rout.save Log: kleine ?\195?\132nderung Modified: pkg/distrTeach/DESCRIPTION =================================================================== --- pkg/distrTeach/DESCRIPTION 2016-04-23 13:47:33 UTC (rev 1095) +++ pkg/distrTeach/DESCRIPTION 2016-04-23 14:08:44 UTC (rev 1096) @@ -1,5 +1,5 @@ Package: distrTeach -Version: 2.6 +Version: 2.6.1 Date: 2016-04-23 Title: Extensions of Package 'distr' for Teaching Stochastics/Statistics in Secondary School Description: Provides flexible examples of LLN and CLT for teaching purposes in secondary @@ -16,7 +16,6 @@ License: LGPL-3 Encoding: latin1 URL: http://distr.r-forge.r-project.org/ -Packaged: Fri Jun 8 00:12:57 2007; Peter LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1091 +SVNRevision: 1094 Modified: pkg/distrTeach/tests/Examples/distrTeach-Ex.Rout.save =================================================================== --- pkg/distrTeach/tests/Examples/distrTeach-Ex.Rout.save 2016-04-23 13:47:33 UTC (rev 1095) +++ pkg/distrTeach/tests/Examples/distrTeach-Ex.Rout.save 2016-04-23 14:08:44 UTC (rev 1096) @@ -1,7 +1,7 @@ -R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) +R Under development (unstable) (2016-04-22 r70532) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing +Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -20,10 +20,11 @@ > pkgname <- "distrTeach" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) +> options(pager = "console") > library('distrTeach') Loading required package: distr Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) +:startupmsg> Utilities for Start-Up Messages (version 0.9.2) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") @@ -58,9 +59,9 @@ :SweaveListingUtils> vignette("ExampleSweaveListingUtils"). -Attaching package: ?SweaveListingUtils? +Attaching package: 'SweaveListingUtils' -The following objects are masked from ?package:base?: +The following objects are masked from 'package:base': library, require @@ -84,9 +85,9 @@ :distr> vignette("distr"). -Attaching package: ?distr? +Attaching package: 'distr' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': df, qqplot, sd @@ -108,9 +109,9 @@ :distrEx> vignette("distr"). -Attaching package: ?distrEx? +Attaching package: 'distrEx' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': IQR, mad, median, var @@ -196,7 +197,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 5.786 0.084 5.869 0 0 +Time elapsed: 7.78 0.51 8.32 NA NA > grDevices::dev.off() null device 1 From noreply at r-forge.r-project.org Sat Apr 23 16:13:23 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 16:13:23 +0200 (CEST) Subject: [Distr-commits] r1097 - in pkg/distrRmetrics: . man tests/Examples Message-ID: <20160423141323.8C9C8187608@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 16:13:23 +0200 (Sat, 23 Apr 2016) New Revision: 1097 Modified: pkg/distrRmetrics/DESCRIPTION pkg/distrRmetrics/man/0distrRmetrics-package.Rd pkg/distrRmetrics/tests/Examples/distrRmetrics-Ex.Rout.save Log: distrRmetrics-2.6 is on CRAN Modified: pkg/distrRmetrics/DESCRIPTION =================================================================== --- pkg/distrRmetrics/DESCRIPTION 2016-04-23 14:08:44 UTC (rev 1096) +++ pkg/distrRmetrics/DESCRIPTION 2016-04-23 14:13:23 UTC (rev 1097) @@ -1,6 +1,6 @@ Package: distrRmetrics Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Distribution Classes for Distributions from Rmetrics Description: S4-distribution classes based on package distr for distributions from packages 'fBasics' and 'fGarch'. @@ -15,4 +15,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate: 2011-11-18 13:15:04 +0100 (Fr, 18 Nov 2011) $} LastChangedRevision: {$LastChangedRevision: 758 $} -SVNRevision: 1080 +SVNRevision: 1095 Modified: pkg/distrRmetrics/man/0distrRmetrics-package.Rd =================================================================== --- pkg/distrRmetrics/man/0distrRmetrics-package.Rd 2016-04-23 14:08:44 UTC (rev 1096) +++ pkg/distrRmetrics/man/0distrRmetrics-package.Rd 2016-04-23 14:13:23 UTC (rev 1097) @@ -14,14 +14,14 @@ \tabular{ll}{ Package: \tab distrRmetrics \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.6.0), methods, distr(>= 2.4), fBasics(>= 270.73), fGarch(>= 270.73) \cr Suggests: \tab distrEx(>= 2.4), distrMod(>= 2.4) \cr Imports: startupmsg \cr ByteCompile: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1095 \cr } } \section{Classes}{ Modified: pkg/distrRmetrics/tests/Examples/distrRmetrics-Ex.Rout.save =================================================================== --- pkg/distrRmetrics/tests/Examples/distrRmetrics-Ex.Rout.save 2016-04-23 14:08:44 UTC (rev 1096) +++ pkg/distrRmetrics/tests/Examples/distrRmetrics-Ex.Rout.save 2016-04-23 14:13:23 UTC (rev 1097) @@ -1,7 +1,7 @@ -R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) +R Under development (unstable) (2016-04-22 r70532) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing +Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -20,10 +20,11 @@ > pkgname <- "distrRmetrics" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) +> options(pager = "console") > library('distrRmetrics') Loading required package: distr Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) +:startupmsg> Utilities for Start-Up Messages (version 0.9.2) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") @@ -58,9 +59,9 @@ :SweaveListingUtils> vignette("ExampleSweaveListingUtils"). -Attaching package: ?SweaveListingUtils? +Attaching package: 'SweaveListingUtils' -The following objects are masked from ?package:base?: +The following objects are masked from 'package:base': library, require @@ -84,9 +85,9 @@ :distr> vignette("distr"). -Attaching package: ?distr? +Attaching package: 'distr' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': df, qqplot, sd @@ -342,7 +343,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 1.495 0.02 1.515 0 0 +Time elapsed: 1.59 0.08 1.71 NA NA > grDevices::dev.off() null device 1 From noreply at r-forge.r-project.org Sat Apr 23 16:27:43 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 16:27:43 +0200 (CEST) Subject: [Distr-commits] r1098 - in pkg/distrEllipse: . man tests/Examples Message-ID: <20160423142744.0C754187C0D@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 16:27:43 +0200 (Sat, 23 Apr 2016) New Revision: 1098 Modified: pkg/distrEllipse/DESCRIPTION pkg/distrEllipse/man/0distrEllipse-package.Rd pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save Log: distrEllipse-2.6 is on CRAN Modified: pkg/distrEllipse/DESCRIPTION =================================================================== --- pkg/distrEllipse/DESCRIPTION 2016-04-23 14:13:23 UTC (rev 1097) +++ pkg/distrEllipse/DESCRIPTION 2016-04-23 14:27:43 UTC (rev 1098) @@ -1,6 +1,6 @@ Package: distrEllipse Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: S4 Classes for Elliptically Contoured Distributions Description: Distribution (S4-)classes for elliptically contoured distributions (based on package 'distr'). @@ -16,4 +16,4 @@ Encoding: latin1 LastChangedDate: {$LastChangedDate: 2009-03-31 15:31:30 +0200 (Di, 31 Mrz 2009) $} LastChangedRevision: {$LastChangedRevision: 447 $} -SVNRevision: 1080 +SVNRevision: 1096 Modified: pkg/distrEllipse/man/0distrEllipse-package.Rd =================================================================== --- pkg/distrEllipse/man/0distrEllipse-package.Rd 2016-04-23 14:13:23 UTC (rev 1097) +++ pkg/distrEllipse/man/0distrEllipse-package.Rd 2016-04-23 14:27:43 UTC (rev 1098) @@ -13,7 +13,7 @@ \tabular{ll}{ Package: \tab distrEllipse \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-1), distr(>= 2.2), distrEx(>= 2.2), distrSim(>= 2.2)\cr Suggests: \tab distrMod(>= 2.2), distrTEst(>= 2.2)\cr @@ -21,7 +21,7 @@ ByteCompile: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1096 \cr } } \section{Classes}{ Modified: pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save =================================================================== --- pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2016-04-23 14:13:23 UTC (rev 1097) +++ pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2016-04-23 14:27:43 UTC (rev 1098) @@ -1,7 +1,7 @@ -R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) +R Under development (unstable) (2016-04-22 r70532) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing +Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -20,12 +20,13 @@ > pkgname <- "distrEllipse" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) +> options(pager = "console") > library('distrEllipse') Loading required package: mvtnorm Loading required package: setRNG Loading required package: distr Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) +:startupmsg> Utilities for Start-Up Messages (version 0.9.2) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") @@ -60,9 +61,9 @@ :SweaveListingUtils> vignette("ExampleSweaveListingUtils"). -Attaching package: ?SweaveListingUtils? +Attaching package: 'SweaveListingUtils' -The following objects are masked from ?package:base?: +The following objects are masked from 'package:base': library, require @@ -86,9 +87,9 @@ :distr> vignette("distr"). -Attaching package: ?distr? +Attaching package: 'distr' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': df, qqplot, sd @@ -110,9 +111,9 @@ :distrEx> vignette("distr"). -Attaching package: ?distrEx? +Attaching package: 'distrEx' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': IQR, mad, median, var @@ -132,13 +133,13 @@ :distrSim> vignette("distr"). -Attaching package: ?distrSim? +Attaching package: 'distrSim' -The following object is masked from ?package:stats?: +The following object is masked from 'package:stats': simulate -The following object is masked from ?package:base?: +The following object is masked from 'package:base': rbind @@ -595,8 +596,18 @@ > > mylist <- MultivarMixingDistribution(Binom(3,.3), Dirac(2), Norm(), + mixCoeff=c(1/4,1/5,11/20)) +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated > mylist2 <- MultivarMixingDistribution(Binom(3,.3), mylist, + mixCoeff=c(.3,.7)) +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated > mylist2 An object of class "UnivarLebDecDistribution" --- a Lebesgue decomposed distribution: @@ -775,6 +786,12 @@ > > mylist <- MultivarMixingDistribution(Binom(3,.3), Dirac(2), Norm(), + mixCoeff=c(1/4,1/5,11/20)) +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated > > > @@ -869,7 +886,6 @@ *** intentional masking: *** - > > > @@ -937,7 +953,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 4.3 0.024 4.327 0 0.006 +Time elapsed: 5.11 0.17 5.28 NA NA > grDevices::dev.off() null device 1 From noreply at r-forge.r-project.org Sat Apr 23 17:16:30 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 17:16:30 +0200 (CEST) Subject: [Distr-commits] r1099 - in pkg: SweaveListingUtils SweaveListingUtils/tests/Examples utils Message-ID: <20160423151631.0B754186E55@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 17:16:30 +0200 (Sat, 23 Apr 2016) New Revision: 1099 Modified: pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save pkg/utils/finde.R Log: yet another fix for SweaveListingUtils for Uwe ... Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 14:27:43 UTC (rev 1098) +++ pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 15:16:30 UTC (rev 1099) @@ -4,7 +4,7 @@ and for including R / Rd source file (snippets) copied from R-forge in its most recent version (or another URL) thereby avoiding inconsistencies between vignette and documented source code. -Version: 0.7.2 +Version: 0.7.3 Encoding: latin1 Date: 2016-04-23 Depends: R(>= 2.14.0), startupmsg Modified: pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save =================================================================== --- pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-23 14:27:43 UTC (rev 1098) +++ pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-23 15:16:30 UTC (rev 1099) @@ -23,14 +23,14 @@ > options(pager = "console") > library('SweaveListingUtils') Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.2) +:startupmsg> Utilities for Start-Up Messages (version 0.9.3) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") :SweaveListingUtils> Utilities for Sweave Together with :SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7.2) +:SweaveListingUtils> 0.7.3) :SweaveListingUtils> :SweaveListingUtils> NOTE: Support for this package :SweaveListingUtils> will stop soon. @@ -3334,7 +3334,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 1.29 0.33 4.95 NA NA +Time elapsed: 1.16 0.22 3.03 NA NA > grDevices::dev.off() null device 1 Modified: pkg/utils/finde.R =================================================================== --- pkg/utils/finde.R 2016-04-23 14:27:43 UTC (rev 1098) +++ pkg/utils/finde.R 2016-04-23 15:16:30 UTC (rev 1099) @@ -23,6 +23,7 @@ #finde(x="Wow6432Node", dir ="C:/R/devel/src/gnuwin32", rec=TRUE, ext="") #finde(x="getPos", dir ="C:/rtest/distr/branches/distr-2.4/pkg/distrMod/", rec=TRUE) +finde(x="updatePackageHelp", dir ="C:/rtest/distr/pkg/utils", rec=TRUE) finde(x="roptest\\(", dir ="C:/rtest/robast/branches/robast-0.9/pkg/ROptEst/", rec=TRUE) finde(x="getSlots\\(", dir ="C:/rtest/distr/branches/distr-2.4/pkg/distrMod/", rec=TRUE) finde(x="\"loc\"", dir ="C:/rtest/distr/branches/distr-2.4/pkg/distrEx/", rec=TRUE) From noreply at r-forge.r-project.org Sat Apr 23 17:34:53 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 17:34:53 +0200 (CEST) Subject: [Distr-commits] r1100 - pkg/distrDoc/vignettes Message-ID: <20160423153453.49707187608@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 17:34:52 +0200 (Sat, 23 Apr 2016) New Revision: 1100 Modified: pkg/distrDoc/vignettes/distr.Rnw Log: [distr] updated vignette distr.Rnw Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2016-04-23 15:16:30 UTC (rev 1099) +++ pkg/distrDoc/vignettes/distr.Rnw 2016-04-23 15:34:52 UTC (rev 1100) @@ -83,8 +83,8 @@ @ % % ------------------------------------------------------------------------------- -\renewcommand{\pkgversion}{{\tt 2.5}} -\newcommand{\pkgExversion}{{\tt 2.5}} +\renewcommand{\pkgversion}{{\tt 2.6}} +\newcommand{\pkgExversion}{{\tt 2.6}} \newcommand{\Reals}{\mathbb{R}} \newcommand{\R}{\mathbb{R}} \newcommand{\N}{\mathbb{N}} @@ -105,7 +105,7 @@ \pkg{distrTEst}, \pkg{distrTeach}, version \pkgversion} %,version \pkgExversion} -\author{\small Peter Ruckdeschel\thanks{Fraunhofer ITWM, Kaiserslautern} +\author{\small Peter Ruckdeschel\thanks{Carl von Ossietzky Universit\"at Oldenburg} \\[-.5ex] \small Matthias Kohl\thanks{FH Furtwangen} \\[-.5ex] @@ -113,9 +113,10 @@ \\[-.5ex] \small Florian Camphausen\thanks{West-LB, London} \smallskip\\ -\small Fraunhofer ITWM\\[-.5ex] -\small Fraunhofer Platz 1\\[-.5ex] -\small 67663 Kaiserslautern\\[-.5ex] +\small Institute for Mathematics\\[-.5ex] +\small School of Mathematics and Science\\[-.5ex] +\small PO box 25 03\\[-.5ex] +\small 26111 Oldenburg (Oldb.)\\[-.5ex] \small Germany\\ \small e-Mail: {\small \tt peter.ruckdeschel at uni-oldenburg.de}\medskip\\ \parbox[t]{5cm}{ @@ -248,6 +249,16 @@ @ \par \begin{small} +Due to a non-conformal implementation of function \code{q} in \texttt{RStudio}, +our approach to overload function \code{q} by method dispatch does not work +from an \texttt{RStudio} console (it does work, though within a function +environment). To overcome this, from version 2.6 on, we have aliases +\code{p.r} and \code{q.l} for functions \code{p} and \code{q}, alluding to +the right (resp. left) continous form of the cdf and the quantile function. +these two aliases (in particular \code{q.l}) do work in \texttt{RStudio}. +\end{small} +\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 From noreply at r-forge.r-project.org Sat Apr 23 17:39:49 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 17:39:49 +0200 (CEST) Subject: [Distr-commits] r1101 - in pkg/distrEllipse: . R inst man tests/Examples Message-ID: <20160423153949.2971C187608@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 17:39:48 +0200 (Sat, 23 Apr 2016) New Revision: 1101 Modified: pkg/distrEllipse/DESCRIPTION pkg/distrEllipse/NAMESPACE pkg/distrEllipse/R/AllGenerics.R pkg/distrEllipse/R/SphericalDistribution.R pkg/distrEllipse/inst/NEWS pkg/distrEllipse/man/SphericalDistribution-class.Rd pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save Log: revised distrEllipse for S3 methods plot.Rd (and r.rd, d.rd, p.rd, q.rd) against S3 method dispatch clashes -> aliases plot.Rd (and rRd, dRd, pRd, qRd) Modified: pkg/distrEllipse/DESCRIPTION =================================================================== --- pkg/distrEllipse/DESCRIPTION 2016-04-23 15:34:52 UTC (rev 1100) +++ pkg/distrEllipse/DESCRIPTION 2016-04-23 15:39:48 UTC (rev 1101) @@ -1,5 +1,5 @@ Package: distrEllipse -Version: 2.6 +Version: 2.6.1 Date: 2016-04-23 Title: S4 Classes for Elliptically Contoured Distributions Description: Distribution (S4-)classes for elliptically contoured distributions (based on Modified: pkg/distrEllipse/NAMESPACE =================================================================== --- pkg/distrEllipse/NAMESPACE 2016-04-23 15:34:52 UTC (rev 1100) +++ pkg/distrEllipse/NAMESPACE 2016-04-23 15:39:48 UTC (rev 1101) @@ -21,6 +21,7 @@ exportMethods("dimension", "radDistr", "scale", "location", "dim", "radDistr<-", "scale<-", "location<-", "plot.rd", "r.rd", "d.rd", "p.rd", "q.rd", + "plotRd", "rRd", "dRd", "pRd", "qRd", "E", "var", "mean", "sigma","mixCoeff", "mixDistr") exportMethods("plot", "show", "showobj", "Symmetry") exportMethods("+", "*", "%*%") Modified: pkg/distrEllipse/R/AllGenerics.R =================================================================== --- pkg/distrEllipse/R/AllGenerics.R 2016-04-23 15:34:52 UTC (rev 1100) +++ pkg/distrEllipse/R/AllGenerics.R 2016-04-23 15:39:48 UTC (rev 1101) @@ -24,3 +24,14 @@ setGeneric("plot.rd", function(x, ...) standardGeneric("plot.rd")) +if(!isGeneric("rRd")) + setGeneric("rRd", function(object) standardGeneric("rRd")) +if(!isGeneric("dRd")) + setGeneric("dRd", function(object) standardGeneric("dRd")) +if(!isGeneric("pRd")) + setGeneric("pRd", function(object) standardGeneric("pRd")) +if(!isGeneric("qRd")) + setGeneric("qRd", function(object) standardGeneric("qRd")) +if(!isGeneric("plotRd")) + setGeneric("plotRd", function(x, ...) standardGeneric("plotRd")) + Modified: pkg/distrEllipse/R/SphericalDistribution.R =================================================================== --- pkg/distrEllipse/R/SphericalDistribution.R 2016-04-23 15:34:52 UTC (rev 1100) +++ pkg/distrEllipse/R/SphericalDistribution.R 2016-04-23 15:39:48 UTC (rev 1101) @@ -49,6 +49,13 @@ setMethod("p.rd", "SphericalDistribution", function(object) p(object at radDistr)) setMethod("q.rd", "SphericalDistribution", function(object) q(object at radDistr)) +setMethod("plotRd", "SphericalDistribution", + function(x, ... ) plot(x at radDistr,...)) +setMethod("rRd", "SphericalDistribution", function(object) r(object at radDistr)) +setMethod("dRd", "SphericalDistribution", function(object) d(object at radDistr)) +setMethod("pRd", "SphericalDistribution", function(object) p(object at radDistr)) +setMethod("qRd", "SphericalDistribution", function(object) q(object at radDistr)) + ## functionals: setMethod("E", signature(object = "SphericalDistribution", Modified: pkg/distrEllipse/inst/NEWS =================================================================== --- pkg/distrEllipse/inst/NEWS 2016-04-23 15:34:52 UTC (rev 1100) +++ pkg/distrEllipse/inst/NEWS 2016-04-23 15:39:48 UTC (rev 1101) @@ -13,6 +13,8 @@ user-visible CHANGES: + title changed to title style / capitalization ++ new synonyma plotRd, rRd, dRd, pRd, and qRd for plot.rd, r.rd, d.rd, p.rd, and q.rd + to substitute the old ones on the long run (to avoid clashes with S3 inheritance) under the hood: Modified: pkg/distrEllipse/man/SphericalDistribution-class.Rd =================================================================== --- pkg/distrEllipse/man/SphericalDistribution-class.Rd 2016-04-23 15:34:52 UTC (rev 1100) +++ pkg/distrEllipse/man/SphericalDistribution-class.Rd 2016-04-23 15:39:48 UTC (rev 1101) @@ -7,6 +7,11 @@ \alias{dim,SphericalDistribution-method} \alias{radDistr,SphericalDistribution-method} \alias{radDistr<-,SphericalDistribution-method} +\alias{plotRd,SphericalDistribution-method} +\alias{rRd,SphericalDistribution-method} +\alias{dRd,SphericalDistribution-method} +\alias{pRd,SphericalDistribution-method} +\alias{qRd,SphericalDistribution-method} \alias{plot.rd,SphericalDistribution-method} \alias{r.rd,SphericalDistribution-method} \alias{d.rd,SphericalDistribution-method} @@ -19,6 +24,11 @@ \alias{d.rd} \alias{p.rd} \alias{q.rd} +\alias{plotRd} +\alias{rRd} +\alias{dRd} +\alias{pRd} +\alias{qRd} \alias{E,SphericalDistribution,missing,missing-method} \alias{var,SphericalDistribution-method} \alias{coerce,SphericalDistribution,EllipticalDistribution-method} @@ -103,18 +113,26 @@ \item{radDistr}{\code{signature(object = "SphericalDistribution")}: access method for slot \code{radDistr}. } \item{r.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{r} of slot \code{radDistr}. } + slot \code{r} of slot \code{radDistr}. From version 2.6 on, an alias \code{rRd} is + introduced to replace \code{r.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{d.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{d} of slot \code{radDistr}. } + slot \code{d} of slot \code{radDistr}. From version 2.6 on, an alias \code{dRd} is + introduced to replace \code{d.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{p.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{p} of slot \code{radDistr}. } + slot \code{p} of slot \code{radDistr}. From version 2.6 on, an alias \code{pRd} is + introduced to replace \code{p.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{q.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{q} of slot \code{radDistr}. } + slot \code{q} of slot \code{radDistr}. From version 2.6 on, an alias \code{qRd} is + introduced to replace \code{q.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{plot.rd}{\code{signature(x = "SphericalDistribution")}: utility; calls \code{plot} - for slot \code{radDistr}. } + for slot \code{radDistr}. From version 2.6 on, an alias \code{plotRd} is introduced + to replace \code{plot.rd} on the long run in order to avoid clashes with S3-method inheritance.} \item{plot}{\code{signature(x = "SphericalDistribution", y = "missing")}: - plot for an spherically symmetric distribution; see \code{\link{plot-methods}}. - } + plot for an spherically symmetric distribution; see \code{\link{plot-methods}}. } \item{show}{\code{signature(object = "SphericalDistribution")}: \code{show} method for spherically symmetric distributions. } Modified: pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save =================================================================== --- pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2016-04-23 15:34:52 UTC (rev 1100) +++ pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2016-04-23 15:39:48 UTC (rev 1101) @@ -26,7 +26,7 @@ Loading required package: setRNG Loading required package: distr Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.2) +:startupmsg> Utilities for Start-Up Messages (version 0.9.3) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") @@ -35,7 +35,7 @@ Loading required package: SweaveListingUtils :SweaveListingUtils> Utilities for Sweave Together with :SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7) +:SweaveListingUtils> 0.7.3) :SweaveListingUtils> :SweaveListingUtils> NOTE: Support for this package :SweaveListingUtils> will stop soon. @@ -144,7 +144,7 @@ rbind :distrEllipse> S4 Classes for Elliptically Contoured -:distrEllipse> Distributions (version 2.6) +:distrEllipse> Distributions (version 2.6.1) :distrEllipse> :distrEllipse> Some functions from package 'stats' are :distrEllipse> intentionally masked ---see @@ -809,11 +809,13 @@ > ### dim,SphericalDistribution-method > ### radDistr,SphericalDistribution-method > ### radDistr<-,SphericalDistribution-method -> ### plot.rd,SphericalDistribution-method +> ### plotRd,SphericalDistribution-method rRd,SphericalDistribution-method +> ### dRd,SphericalDistribution-method pRd,SphericalDistribution-method +> ### qRd,SphericalDistribution-method plot.rd,SphericalDistribution-method > ### r.rd,SphericalDistribution-method d.rd,SphericalDistribution-method > ### p.rd,SphericalDistribution-method q.rd,SphericalDistribution-method -> ### radDistr radDistr<- plot.rd r.rd d.rd p.rd q.rd -> ### E,SphericalDistribution,missing,missing-method +> ### radDistr radDistr<- plot.rd r.rd d.rd p.rd q.rd plotRd rRd dRd pRd +> ### qRd E,SphericalDistribution,missing,missing-method > ### var,SphericalDistribution-method > ### coerce,SphericalDistribution,EllipticalDistribution-method > ### show,SphericalDistribution-method @@ -953,7 +955,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 5.11 0.17 5.28 NA NA +Time elapsed: 4.68 0.13 4.8 NA NA > grDevices::dev.off() null device 1 From noreply at r-forge.r-project.org Sat Apr 23 18:16:00 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 18:16:00 +0200 (CEST) Subject: [Distr-commits] r1102 - pkg/utils Message-ID: <20160423161600.F2BC3187608@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 18:16:00 +0200 (Sat, 23 Apr 2016) New Revision: 1102 Added: pkg/utils/updateTo2_6.R Modified: pkg/utils/getRevNr.R pkg/utils/showsvnlog.R Log: further update of utils for distr Modified: pkg/utils/getRevNr.R =================================================================== --- pkg/utils/getRevNr.R 2016-04-23 15:39:48 UTC (rev 1101) +++ pkg/utils/getRevNr.R 2016-04-23 16:16:00 UTC (rev 1102) @@ -16,6 +16,7 @@ toRev <- "HEAD" if(inRforge) pathRepo <- paste("svn://svn.r-forge.r-project.org/svnroot/",pathRepo,sep="") + print(pathRepo) inQuotes <- function(x) paste("\"",x,"\"", sep="") comd <- paste(inQuotes(PathToBash), ifelse(withlogin,"--login",""), inQuotes(paste(PathToUtils, "readsvnlog.sh", sep="/")), Modified: pkg/utils/showsvnlog.R =================================================================== --- pkg/utils/showsvnlog.R 2016-04-23 15:39:48 UTC (rev 1101) +++ pkg/utils/showsvnlog.R 2016-04-23 16:16:00 UTC (rev 1102) @@ -40,6 +40,7 @@ myline <- paste(rep("-",length.out=72),collapse="",sep="") if(inRforge) pathRepo <- paste("svn://svn.r-forge.r-project.org/svnroot/",pathRepo,sep="") + inQuotes <- function(x) paste("\"",x,"\"", sep="") comd <- paste(inQuotes(PathToBash), ifelse(withlogin,"--login",""), @@ -69,5 +70,7 @@ showsvnlog("robast",from=1,to=Inf,limit=1000,con="C:/rtest/svnlog-robast.txt") showsvnlog(from=580,to=Inf,limit=1000) showsvnlog("robast",from=220,to=Inf,limit=1000,con="C:/rtest/svnlog-robast-ex.txt") +showsvnlog("robast",from=220,to=Inf,limit=1000) +getRevNr("C:/rtest/RobASt/", pathRepo="robast", inRforge=TRUE, withlogin=TRUE, PathToBash="C:/cygwin64/bin/bash", "C:/rtest/distr/branches/distr-2.4/pkg/utils")[[1]] } Added: pkg/utils/updateTo2_6.R =================================================================== --- pkg/utils/updateTo2_6.R (rev 0) +++ pkg/utils/updateTo2_6.R 2016-04-23 16:16:00 UTC (rev 1102) @@ -0,0 +1,90 @@ +Pkgs <- c("SweaveListingUtils", "distr", "distrEx", "distrDoc", + "distrMod", "distrTeach", "distrSim", "distrTEst", + "distrEllipse") +Names <- c("Version","Date","SVNRevision") +Values <- matrix(c("2.0.2", format(Sys.time(), format="%Y-%m-%d"),1),3,length(Pkgs)) +colnames(Values) <- Pkgs +rownames(Values) <- Names +Values["Version",] <- c("0.5", rep("2.3", 8)) +changeDescription(startDir = "C:/rtest/distr/",names=Names, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("0.9.2",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "startupmsg" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("0.7",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "SweaveListingUtils" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distr" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrEx" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrSim" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrTEst" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrTeach" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrRmetrics" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrEllipse" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrDoc" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) From noreply at r-forge.r-project.org Sat Apr 23 18:26:36 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 18:26:36 +0200 (CEST) Subject: [Distr-commits] r1103 - in pkg/distrDoc: . inst man vignettes Message-ID: <20160423162636.46D16187F21@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 18:26:35 +0200 (Sat, 23 Apr 2016) New Revision: 1103 Modified: pkg/distrDoc/DESCRIPTION pkg/distrDoc/inst/NEWS pkg/distrDoc/man/0distrDoc-package.Rd pkg/distrDoc/vignettes/distr.Rnw Log: distrDoc-2.6 is on CRAN Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2016-04-23 16:16:00 UTC (rev 1102) +++ pkg/distrDoc/DESCRIPTION 2016-04-23 16:26:35 UTC (rev 1103) @@ -1,9 +1,9 @@ Package: distrDoc Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Documentation for 'distr' Family of R Packages -Description: Provides documentation in form of a common vignette to packages distr, distrEx, - distrMod, distrSim, distrTEst, distrTeach, and distrEllipse. +Description: Provides documentation in form of a common vignette to packages 'distr', 'distrEx', + 'distrMod', 'distrSim', 'distrTEst', 'distrTeach', and 'distrEllipse'. Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the documented packages in the initial phase --2005"), person("Matthias", "Kohl", role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "cph"), @@ -21,4 +21,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1097 Modified: pkg/distrDoc/inst/NEWS =================================================================== --- pkg/distrDoc/inst/NEWS 2016-04-23 16:16:00 UTC (rev 1102) +++ pkg/distrDoc/inst/NEWS 2016-04-23 16:26:35 UTC (rev 1103) @@ -18,6 +18,7 @@ + updated references in vignette distr.Rnw + mention that pattern substitution can now be switched on and off in all plot functions according to argument withSubst ++ mention aliases p.r and q.l for RStudio under the hood + fixed \VignetteKeyword issue detected as in mail by K. Hornik 2015-02-03 Modified: pkg/distrDoc/man/0distrDoc-package.Rd =================================================================== --- pkg/distrDoc/man/0distrDoc-package.Rd 2016-04-23 16:16:00 UTC (rev 1102) +++ pkg/distrDoc/man/0distrDoc-package.Rd 2016-04-23 16:26:35 UTC (rev 1103) @@ -14,7 +14,7 @@ \tabular{ll}{ Package: \tab distrDoc \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.14.0) \cr Imports: \tab distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0), distrTeach(>= 2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods, @@ -23,7 +23,7 @@ ByteCompile: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1097 \cr }} Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2016-04-23 16:16:00 UTC (rev 1102) +++ pkg/distrDoc/vignettes/distr.Rnw 2016-04-23 16:26:35 UTC (rev 1103) @@ -251,11 +251,11 @@ \begin{small} Due to a non-conformal implementation of function \code{q} in \texttt{RStudio}, our approach to overload function \code{q} by method dispatch does not work -from an \texttt{RStudio} console (it does work, though within a function +from an \texttt{RStudio} console (it does work, though, within a function environment). To overcome this, from version 2.6 on, we have aliases -\code{p.r} and \code{q.l} for functions \code{p} and \code{q}, alluding to -the right (resp. left) continous form of the cdf and the quantile function. -these two aliases (in particular \code{q.l}) do work in \texttt{RStudio}. +\code{p.r} and \code{q.l} for functions \code{p} and \code{q}, respectively, +alluding to the right (resp. left) continous form of the cdf and the quantile +function. These two aliases (in particular \code{q.l}) do work in \texttt{RStudio}. \end{small} \par \begin{small} From noreply at r-forge.r-project.org Sat Apr 23 19:09:34 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 19:09:34 +0200 (CEST) Subject: [Distr-commits] r1104 - in branches/distr-2.7/pkg: SweaveListingUtils distr/R distr/inst distr/man distrDoc/vignettes distrEllipse distrEllipse/R distrEllipse/inst distrEllipse/man distrEllipse/tests/Examples startupmsg utils Message-ID: <20160423170934.734C218754D@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 19:09:34 +0200 (Sat, 23 Apr 2016) New Revision: 1104 Modified: branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION branches/distr-2.7/pkg/distr/R/qqplot.R branches/distr-2.7/pkg/distr/inst/NEWS branches/distr-2.7/pkg/distr/man/qqplot.Rd branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw branches/distr-2.7/pkg/distrEllipse/DESCRIPTION branches/distr-2.7/pkg/distrEllipse/NAMESPACE branches/distr-2.7/pkg/distrEllipse/R/AllGenerics.R branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R branches/distr-2.7/pkg/distrEllipse/inst/NEWS branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd branches/distr-2.7/pkg/distrEllipse/man/SphericalDistribution-class.Rd branches/distr-2.7/pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save branches/distr-2.7/pkg/startupmsg/DESCRIPTION branches/distr-2.7/pkg/utils/DESCRIPTIONutils.R branches/distr-2.7/pkg/utils/RCRAN.bat branches/distr-2.7/pkg/utils/RCheck.bat branches/distr-2.7/pkg/utils/getRevNr.R branches/distr-2.7/pkg/utils/showsvnlog.R Log: updated some packages in branch 2.7 Modified: branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION 2016-04-23 17:09:34 UTC (rev 1104) @@ -1,11 +1,11 @@ Package: SweaveListingUtils Title: Utilities for Sweave Together with TeX 'listings' Package -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. +Description: Provides utilities for defining R / Rd as "language" for TeX-package "listings" + and for including R / Rd source file (snippets) copied from R-forge in its most + recent version (or another URL) thereby avoiding inconsistencies between vignette + and documented source code. Encoding: latin1 -Version: 0.7.1 +Version: 0.7.4 Depends: R(>= 2.14.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines Imports: methods @@ -13,7 +13,7 @@ Authors at R: person("Peter", "Ruckdeschel", role=c("cre", "cph"), email="peter.ruckdeschel at uni-oldenburg.de") License: LGPL-3 -Date: 2015-11-07 +Date: 2016-04-23 LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} SVNRevision: 1080 Modified: branches/distr-2.7/pkg/distr/R/qqplot.R =================================================================== --- branches/distr-2.7/pkg/distr/R/qqplot.R 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distr/R/qqplot.R 2016-04-23 17:09:34 UTC (rev 1104) @@ -118,6 +118,24 @@ xy <- sort(c(xy,xy0,xy1)) } } + qqplotInfo <- list(xy.0=xy, y.0=y, + withConf.pw=withConf.pw, + withConf.sim=withConf.sim, + alpha.CI=alpha.CI , + col.pCI = col.pCI , lty.pCI = lty.pCI , + lwd.pCI = lwd.pCI , pch.pCI = pch.pCI, + cex.pCI = cex.pCI , + col.sCI = col.sCI , lty.sCI = lty.sCI , + lwd.sCI = lwd.sCI , pch.sCI = pch.sCI, + cex.sCI = cex.sCI , + n = n , + exact.sCI = exact.sCI, exact.pCI = exact.pCI, + nosym.pCI = nosym.pCI, with.legend = with.legend, + legend.bg = legend.bg, legend.pos = legend.pos, + legend.cex = legend.cex, legend.pref = legend.pref, + legend.postf = legend.postf, legend.alpha = legend.alpha, debug = debug, + args.stats.qqplot = mcl + ) if(plot.it){ qqb <- .confqq(xy, y, datax=TRUE, withConf.pw, withConf.sim, alpha.CI, col.pCI, lty.pCI, lwd.pCI, pch.pCI, cex.pCI, @@ -134,6 +152,8 @@ } } } - return(invisible(c(ret,qqb))) + qqplotInfo <- c(ret, qqplotInfo, qqb) + class(qqplotInfo) <- c("qqplotInfo","DiagnInfo") + return(invisible(qqplotInfo)) }) Modified: branches/distr-2.7/pkg/distr/inst/NEWS =================================================================== --- branches/distr-2.7/pkg/distr/inst/NEWS 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distr/inst/NEWS 2016-04-23 17:09:34 UTC (rev 1104) @@ -8,6 +8,10 @@ information) ############## +v 2.7 +############## + +############## v 2.6 ############## @@ -37,6 +41,9 @@ argument has now been enhanced in the sense that now more detailed information about which helper function was the culprit and where (uniroot/optimize) this happens + + now returns an object of S3-classes "qqplotInfo","DiagnInfo" + to be able to recover all information used to produce the plot + for later use in enhanced graphics (e.g. with ggplot) -qqbounds: + the respective helper functions .BinomCI.nosym, .BinomCI, .q2kolmogorov capsulate their calls to uniroot / optimize in Modified: branches/distr-2.7/pkg/distr/man/qqplot.Rd =================================================================== --- branches/distr-2.7/pkg/distr/man/qqplot.Rd 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distr/man/qqplot.Rd 2016-04-23 17:09:34 UTC (rev 1104) @@ -110,8 +110,12 @@ } } \value{ - As for function \code{\link[stats:qqnorm]{qqplot}} from package \pkg{stats}: a - list with components + A list of elements containing the information needed to compute the + respective QQ plot, in particular it extends the elements of the + return value of function \code{\link[stats:qqnorm]{qqplot}} + from package \pkg{stats}, i.e., a + list with components \code{x} and \code{y} for x and y coordinates + of the plotted points; more specifically it contains \item{x}{The x coordinates of the points that were/would be plotted} \item{y}{The corresponding quantiles of the second distribution, \emph{including \code{\link{NA}}s}.} @@ -120,6 +124,8 @@ \item{err}{logical vector of length 2.} (elements \code{crit} and \code{err} are taken from the return value(s) of \code{qqbounds}). + The return value allows to recover all information used to produce the plot + for later use in enhanced graphics (e.g. with ggplot). } \references{ Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) Modified: branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw 2016-04-23 17:09:34 UTC (rev 1104) @@ -83,8 +83,8 @@ @ % % ------------------------------------------------------------------------------- -\renewcommand{\pkgversion}{{\tt 2.5}} -\newcommand{\pkgExversion}{{\tt 2.5}} +\renewcommand{\pkgversion}{{\tt 2.7}} +\newcommand{\pkgExversion}{{\tt 2.7}} \newcommand{\Reals}{\mathbb{R}} \newcommand{\R}{\mathbb{R}} \newcommand{\N}{\mathbb{N}} @@ -105,7 +105,7 @@ \pkg{distrTEst}, \pkg{distrTeach}, version \pkgversion} %,version \pkgExversion} -\author{\small Peter Ruckdeschel\thanks{Fraunhofer ITWM, Kaiserslautern} +\author{\small Peter Ruckdeschel\thanks{Carl von Ossietzky Universit\"at Oldenburg} \\[-.5ex] \small Matthias Kohl\thanks{FH Furtwangen} \\[-.5ex] @@ -113,9 +113,10 @@ \\[-.5ex] \small Florian Camphausen\thanks{West-LB, London} \smallskip\\ -\small Fraunhofer ITWM\\[-.5ex] -\small Fraunhofer Platz 1\\[-.5ex] -\small 67663 Kaiserslautern\\[-.5ex] +\small Institute for Mathematics\\[-.5ex] +\small School of Mathematics and Science\\[-.5ex] +\small PO box 25 03\\[-.5ex] +\small 26111 Oldenburg (Oldb.)\\[-.5ex] \small Germany\\ \small e-Mail: {\small \tt peter.ruckdeschel at uni-oldenburg.de}\medskip\\ \parbox[t]{5cm}{ @@ -248,6 +249,16 @@ @ \par \begin{small} +Due to a non-conformal implementation of function \code{q} in \texttt{RStudio}, +our approach to overload function \code{q} by method dispatch does not work +from an \texttt{RStudio} console (it does work, though within a function +environment). To overcome this, from version 2.6 on, we have aliases +\code{p.r} and \code{q.l} for functions \code{p} and \code{q}, alluding to +the right (resp. left) continous form of the cdf and the quantile function. +these two aliases (in particular \code{q.l}) do work in \texttt{RStudio}. +\end{small} +\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 Modified: branches/distr-2.7/pkg/distrEllipse/DESCRIPTION =================================================================== --- branches/distr-2.7/pkg/distrEllipse/DESCRIPTION 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/DESCRIPTION 2016-04-23 17:09:34 UTC (rev 1104) @@ -1,6 +1,6 @@ Package: distrEllipse Version: 2.7 -Date: 2015-11-07 +Date: 2016-04-23 Title: S4 Classes for Elliptically Contoured Distributions Description: Distribution (S4-)classes for elliptically contoured distributions (based on package 'distr'). @@ -16,4 +16,4 @@ Encoding: latin1 LastChangedDate: {$LastChangedDate: 2009-03-31 15:31:30 +0200 (Di, 31 Mrz 2009) $} LastChangedRevision: {$LastChangedRevision: 447 $} -SVNRevision: 1080 +SVNRevision: 1096 Modified: branches/distr-2.7/pkg/distrEllipse/NAMESPACE =================================================================== --- branches/distr-2.7/pkg/distrEllipse/NAMESPACE 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/NAMESPACE 2016-04-23 17:09:34 UTC (rev 1104) @@ -21,6 +21,7 @@ exportMethods("dimension", "radDistr", "scale", "location", "dim", "radDistr<-", "scale<-", "location<-", "plot.rd", "r.rd", "d.rd", "p.rd", "q.rd", + "plotRd", "rRd", "dRd", "pRd", "qRd", "E", "var", "mean", "sigma","mixCoeff", "mixDistr") exportMethods("plot", "show", "showobj", "Symmetry") exportMethods("+", "*", "%*%") Modified: branches/distr-2.7/pkg/distrEllipse/R/AllGenerics.R =================================================================== --- branches/distr-2.7/pkg/distrEllipse/R/AllGenerics.R 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/R/AllGenerics.R 2016-04-23 17:09:34 UTC (rev 1104) @@ -24,3 +24,14 @@ setGeneric("plot.rd", function(x, ...) standardGeneric("plot.rd")) +if(!isGeneric("rRd")) + setGeneric("rRd", function(object) standardGeneric("rRd")) +if(!isGeneric("dRd")) + setGeneric("dRd", function(object) standardGeneric("dRd")) +if(!isGeneric("pRd")) + setGeneric("pRd", function(object) standardGeneric("pRd")) +if(!isGeneric("qRd")) + setGeneric("qRd", function(object) standardGeneric("qRd")) +if(!isGeneric("plotRd")) + setGeneric("plotRd", function(x, ...) standardGeneric("plotRd")) + Modified: branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R =================================================================== --- branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R 2016-04-23 17:09:34 UTC (rev 1104) @@ -49,6 +49,13 @@ setMethod("p.rd", "SphericalDistribution", function(object) p(object at radDistr)) setMethod("q.rd", "SphericalDistribution", function(object) q(object at radDistr)) +setMethod("plotRd", "SphericalDistribution", + function(x, ... ) plot(x at radDistr,...)) +setMethod("rRd", "SphericalDistribution", function(object) r(object at radDistr)) +setMethod("dRd", "SphericalDistribution", function(object) d(object at radDistr)) +setMethod("pRd", "SphericalDistribution", function(object) p(object at radDistr)) +setMethod("qRd", "SphericalDistribution", function(object) q(object at radDistr)) + ## functionals: setMethod("E", signature(object = "SphericalDistribution", Modified: branches/distr-2.7/pkg/distrEllipse/inst/NEWS =================================================================== --- branches/distr-2.7/pkg/distrEllipse/inst/NEWS 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/inst/NEWS 2016-04-23 17:09:34 UTC (rev 1104) @@ -13,6 +13,8 @@ user-visible CHANGES: + title changed to title style / capitalization ++ new synonyma plotRd, rRd, dRd, pRd, and qRd for plot.rd, r.rd, d.rd, p.rd, and q.rd + to substitute the old ones on the long run (to avoid clashes with S3 inheritance) under the hood: Modified: branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd =================================================================== --- branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd 2016-04-23 17:09:34 UTC (rev 1104) @@ -12,8 +12,8 @@ \details{ \tabular{ll}{ Package: \tab distrEllipse \cr -Version: \tab 2.7 \cr -Date: \tab 2015-11-07 \cr +Version: \tab 2.6 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.8.0), methods, graphics, mvtnorm, setRNG(>= 2006.2-1), distr(>= 2.2), distrEx(>= 2.2), distrSim(>= 2.2)\cr Suggests: \tab distrMod(>= 2.2), distrTEst(>= 2.2)\cr @@ -21,7 +21,7 @@ ByteCompile: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1096 \cr } } \section{Classes}{ Modified: branches/distr-2.7/pkg/distrEllipse/man/SphericalDistribution-class.Rd =================================================================== --- branches/distr-2.7/pkg/distrEllipse/man/SphericalDistribution-class.Rd 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/man/SphericalDistribution-class.Rd 2016-04-23 17:09:34 UTC (rev 1104) @@ -7,6 +7,11 @@ \alias{dim,SphericalDistribution-method} \alias{radDistr,SphericalDistribution-method} \alias{radDistr<-,SphericalDistribution-method} +\alias{plotRd,SphericalDistribution-method} +\alias{rRd,SphericalDistribution-method} +\alias{dRd,SphericalDistribution-method} +\alias{pRd,SphericalDistribution-method} +\alias{qRd,SphericalDistribution-method} \alias{plot.rd,SphericalDistribution-method} \alias{r.rd,SphericalDistribution-method} \alias{d.rd,SphericalDistribution-method} @@ -19,6 +24,11 @@ \alias{d.rd} \alias{p.rd} \alias{q.rd} +\alias{plotRd} +\alias{rRd} +\alias{dRd} +\alias{pRd} +\alias{qRd} \alias{E,SphericalDistribution,missing,missing-method} \alias{var,SphericalDistribution-method} \alias{coerce,SphericalDistribution,EllipticalDistribution-method} @@ -103,18 +113,26 @@ \item{radDistr}{\code{signature(object = "SphericalDistribution")}: access method for slot \code{radDistr}. } \item{r.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{r} of slot \code{radDistr}. } + slot \code{r} of slot \code{radDistr}. From version 2.6 on, an alias \code{rRd} is + introduced to replace \code{r.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{d.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{d} of slot \code{radDistr}. } + slot \code{d} of slot \code{radDistr}. From version 2.6 on, an alias \code{dRd} is + introduced to replace \code{d.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{p.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{p} of slot \code{radDistr}. } + slot \code{p} of slot \code{radDistr}. From version 2.6 on, an alias \code{pRd} is + introduced to replace \code{p.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{q.rd}{\code{signature(object = "SphericalDistribution")}: wrapped access method for - slot \code{q} of slot \code{radDistr}. } + slot \code{q} of slot \code{radDistr}. From version 2.6 on, an alias \code{qRd} is + introduced to replace \code{q.rd} on the long run in order to avoid clashes with + S3-method inheritance. } \item{plot.rd}{\code{signature(x = "SphericalDistribution")}: utility; calls \code{plot} - for slot \code{radDistr}. } + for slot \code{radDistr}. From version 2.6 on, an alias \code{plotRd} is introduced + to replace \code{plot.rd} on the long run in order to avoid clashes with S3-method inheritance.} \item{plot}{\code{signature(x = "SphericalDistribution", y = "missing")}: - plot for an spherically symmetric distribution; see \code{\link{plot-methods}}. - } + plot for an spherically symmetric distribution; see \code{\link{plot-methods}}. } \item{show}{\code{signature(object = "SphericalDistribution")}: \code{show} method for spherically symmetric distributions. } Modified: branches/distr-2.7/pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save =================================================================== --- branches/distr-2.7/pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save 2016-04-23 17:09:34 UTC (rev 1104) @@ -1,7 +1,7 @@ -R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) +R Under development (unstable) (2016-04-22 r70532) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing +Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -20,12 +20,13 @@ > pkgname <- "distrEllipse" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) +> options(pager = "console") > library('distrEllipse') Loading required package: mvtnorm Loading required package: setRNG Loading required package: distr Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) +:startupmsg> Utilities for Start-Up Messages (version 0.9.3) :startupmsg> :startupmsg> For more information see ?"startupmsg", :startupmsg> NEWS("startupmsg") @@ -34,7 +35,7 @@ Loading required package: SweaveListingUtils :SweaveListingUtils> Utilities for Sweave Together with :SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7) +:SweaveListingUtils> 0.7.3) :SweaveListingUtils> :SweaveListingUtils> NOTE: Support for this package :SweaveListingUtils> will stop soon. @@ -60,9 +61,9 @@ :SweaveListingUtils> vignette("ExampleSweaveListingUtils"). -Attaching package: ?SweaveListingUtils? +Attaching package: 'SweaveListingUtils' -The following objects are masked from ?package:base?: +The following objects are masked from 'package:base': library, require @@ -86,9 +87,9 @@ :distr> vignette("distr"). -Attaching package: ?distr? +Attaching package: 'distr' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': df, qqplot, sd @@ -110,9 +111,9 @@ :distrEx> vignette("distr"). -Attaching package: ?distrEx? +Attaching package: 'distrEx' -The following objects are masked from ?package:stats?: +The following objects are masked from 'package:stats': IQR, mad, median, var @@ -132,18 +133,18 @@ :distrSim> vignette("distr"). -Attaching package: ?distrSim? +Attaching package: 'distrSim' -The following object is masked from ?package:stats?: +The following object is masked from 'package:stats': simulate -The following object is masked from ?package:base?: +The following object is masked from 'package:base': rbind :distrEllipse> S4 Classes for Elliptically Contoured -:distrEllipse> Distributions (version 2.6) +:distrEllipse> Distributions (version 2.6.1) :distrEllipse> :distrEllipse> Some functions from package 'stats' are :distrEllipse> intentionally masked ---see @@ -595,8 +596,18 @@ > > mylist <- MultivarMixingDistribution(Binom(3,.3), Dirac(2), Norm(), + mixCoeff=c(1/4,1/5,11/20)) +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated > mylist2 <- MultivarMixingDistribution(Binom(3,.3), mylist, + mixCoeff=c(.3,.7)) +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated > mylist2 An object of class "UnivarLebDecDistribution" --- a Lebesgue decomposed distribution: @@ -775,6 +786,12 @@ > > mylist <- MultivarMixingDistribution(Binom(3,.3), Dirac(2), Norm(), + mixCoeff=c(1/4,1/5,11/20)) +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated +Warning in `[<-`(`*tmp*`, i, value = as(mixDistr[[i]], "UnivarLebDecDistribution")) : + implicit list embedding of S4 objects is deprecated > > > @@ -792,11 +809,13 @@ > ### dim,SphericalDistribution-method > ### radDistr,SphericalDistribution-method > ### radDistr<-,SphericalDistribution-method -> ### plot.rd,SphericalDistribution-method +> ### plotRd,SphericalDistribution-method rRd,SphericalDistribution-method +> ### dRd,SphericalDistribution-method pRd,SphericalDistribution-method +> ### qRd,SphericalDistribution-method plot.rd,SphericalDistribution-method > ### r.rd,SphericalDistribution-method d.rd,SphericalDistribution-method > ### p.rd,SphericalDistribution-method q.rd,SphericalDistribution-method -> ### radDistr radDistr<- plot.rd r.rd d.rd p.rd q.rd -> ### E,SphericalDistribution,missing,missing-method +> ### radDistr radDistr<- plot.rd r.rd d.rd p.rd q.rd plotRd rRd dRd pRd +> ### qRd E,SphericalDistribution,missing,missing-method > ### var,SphericalDistribution-method > ### coerce,SphericalDistribution,EllipticalDistribution-method > ### show,SphericalDistribution-method @@ -869,7 +888,6 @@ *** intentional masking: *** - > > > @@ -937,7 +955,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 4.3 0.024 4.327 0 0.006 +Time elapsed: 4.68 0.13 4.8 NA NA > grDevices::dev.off() null device 1 Modified: branches/distr-2.7/pkg/startupmsg/DESCRIPTION =================================================================== --- branches/distr-2.7/pkg/startupmsg/DESCRIPTION 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/startupmsg/DESCRIPTION 2016-04-23 17:09:34 UTC (rev 1104) @@ -1,7 +1,7 @@ Package: startupmsg Encoding: latin1 -Version: 0.9.2 -Date: 2015-11-07 +Version: 0.9.4 +Date: 2016-04-23 Title: Utilities for Start-Up Messages Description: Provides utilities to create or suppress start-up messages. Authors at R: person("Peter", "Ruckdeschel", role=c("cre", "cph"), Modified: branches/distr-2.7/pkg/utils/DESCRIPTIONutils.R =================================================================== --- branches/distr-2.7/pkg/utils/DESCRIPTIONutils.R 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/utils/DESCRIPTIONutils.R 2016-04-23 17:09:34 UTC (rev 1104) @@ -41,7 +41,7 @@ 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 + PathToBash = "C:/cygwin64/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 @@ -98,10 +98,15 @@ FN <- file.path("pkg",x,"DESCRIPTION") xx <- read.dcf(FN) if(verbose){ + cat("\nxx:\n---\n") print(xx) + cat("\nvalues:\n-------\n") print(values) + cat("\nnames:\n------\n") print(names) + cat("\nvalues[names,x]:\n-----------------\n") print(values[names,x]) + cat("\nxx[names,x]:\n-------------\n") print(xx[,names]) } xx[,names] <- values[names,x] Modified: branches/distr-2.7/pkg/utils/RCRAN.bat =================================================================== --- branches/distr-2.7/pkg/utils/RCRAN.bat 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/utils/RCRAN.bat 2016-04-23 17:09:34 UTC (rev 1104) @@ -1,6 +1,6 @@ @echo off if not "%2"=="" ( -call R CMD check --as-cran --outdir=%2 %1 +call R CMD check --as-cran --output=%2 %1 ) else ( call R CMD check --as-cran %1 ) Modified: branches/distr-2.7/pkg/utils/RCheck.bat =================================================================== --- branches/distr-2.7/pkg/utils/RCheck.bat 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/utils/RCheck.bat 2016-04-23 17:09:34 UTC (rev 1104) @@ -1,7 +1,7 @@ @echo off if not "%2"=="" ( -call R CMD check --multiarch --outdir=%2 --timings --install-args="--byte-compile --with-keep.source --compact-docs --resave-data --install-tests --example --html --latex --clean --preclean --compile-both" %1 +call R CMD check --multiarch --output=%2 --timings --install-args="--byte-compile --with-keep.source --compact-docs --resave-data --install-tests --example --html --latex --clean --preclean --compile-both --force-biarch" %1 ) else ( -call 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" %1 +call 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 --force-biarch" %1 ) echo on Modified: branches/distr-2.7/pkg/utils/getRevNr.R =================================================================== --- branches/distr-2.7/pkg/utils/getRevNr.R 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/utils/getRevNr.R 2016-04-23 17:09:34 UTC (rev 1104) @@ -3,7 +3,7 @@ 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 + PathToBash = "C:/cygwin64/bin/bash", ## path to bash PathToUtils="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 Modified: branches/distr-2.7/pkg/utils/showsvnlog.R =================================================================== --- branches/distr-2.7/pkg/utils/showsvnlog.R 2016-04-23 16:26:35 UTC (rev 1103) +++ branches/distr-2.7/pkg/utils/showsvnlog.R 2016-04-23 17:09:34 UTC (rev 1104) @@ -21,7 +21,7 @@ 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 + PathToBash = "C:/cygwin64/bin/bash", ## path to bash PathToUtils="C:/rtest/distr/branches/distr-2.4/pkg/utils", ### path to shell script readsvnlog.sh fromRev = 501, ## arg for svn log --- first log-listed revision From noreply at r-forge.r-project.org Sat Apr 23 20:08:55 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 20:08:55 +0200 (CEST) Subject: [Distr-commits] r1105 - in pkg/distrMod: . R man tests/Examples Message-ID: <20160423180855.69223187CDB@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 20:08:54 +0200 (Sat, 23 Apr 2016) New Revision: 1105 Removed: pkg/distrMod/man/internalmdeHelpers.Rd Modified: pkg/distrMod/DESCRIPTION pkg/distrMod/R/0distrModUtils.R pkg/distrMod/R/qqplot.R pkg/distrMod/man/0distrMod-package.Rd pkg/distrMod/man/internals.Rd pkg/distrMod/man/qqplot.Rd pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save Log: first attempt to get distrMod on CRAN Modified: pkg/distrMod/DESCRIPTION =================================================================== --- pkg/distrMod/DESCRIPTION 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/DESCRIPTION 2016-04-23 18:08:54 UTC (rev 1105) @@ -1,6 +1,6 @@ Package: distrMod Version: 2.6 -Date: 2015-11-07 +Date: 2016-04-23 Title: Object Oriented Implementation of Probability Models Description: Implements S4 classes for probability models based on packages 'distr' and 'distrEx'. @@ -17,4 +17,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1080 +SVNRevision: 1104 Modified: pkg/distrMod/R/0distrModUtils.R =================================================================== --- pkg/distrMod/R/0distrModUtils.R 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/R/0distrModUtils.R 2016-04-23 18:08:54 UTC (rev 1105) @@ -106,56 +106,66 @@ ## shift L2family to a parameter value as given in main(param) param0 <- L2Fam at param dim0 <- dimension(param0) -# print(param0) paramP <- param0 paramP at main <- main(param) paramP at trafo <- diag(dim0) -# print(paramP) L2Fam <- modifyModel(L2Fam, paramP) -# print(L2deriv(L2Fam)[[1]]@Map) distr <- L2Fam at distribution ### get a sensible integration range: - low0 <- q(distr)(TruncQuantile) - up0 <- q(distr)(TruncQuantile, lower.tail = FALSE) - m0 <- median(distr); s0 <- IQR(distr) - low1 <- m0 - IQR.fac * s0 - up1 <- m0 + IQR.fac * s0 - low <- max(low0,low1); up <- min(up0,up1) - + if(is(distr,"DiscreteDistribution")){ + x.seq0 <- x.seq <- support(distr) + low <- min(x.seq) + up <- max(x.seq) + }else{ ### get a sensible integration range: - if(missing(mu)) mu <- distr - low0.mu <- q(mu)(TruncQuantile) - up0.mu <- q(mu)(TruncQuantile, lower.tail = FALSE) - m0.mu <- median(mu); s0.mu <- IQR(mu) - low1.mu <- m0.mu - IQR.fac * s0.mu - up1.mu <- m0.mu + IQR.fac * s0.mu - low.mu <- max(low0.mu,low1.mu); up.mu <- min(up0.mu,up1.mu) + low0 <- q(distr)(TruncQuantile) + up0 <- q(distr)(TruncQuantile, lower.tail = FALSE) + m0 <- median(distr); s0 <- IQR(distr) + low1 <- m0 - IQR.fac * s0 + up1 <- m0 + IQR.fac * s0 + low <- max(low0,low1); up <- min(up0,up1) + if(is(distr,"AbscontDistribution")){ + x.seq0 <- seq(low, up, length = N1) + h0 <- x.seq0[1:2]%*%c(-1,1) + x.seq <- x.seq0[odd] + }else{ + x.seq0 <- x.seq <- seq(low,up, length = N) + } + } - - if(is(distr,"DiscreteDistribution")) - x.seq <-support(distr) - else - {if(is(distr,"AbscontDistribution")){ - x.seq0 <- seq(low, up, length = N1) - h0 <- x.seq0[1:2]%*%c(-1,1) - x.seq <- x.seq0[odd] - }else{ - x.seq <- seq(low,up, length = N) - } - } - if(is(mu,"DiscreteDistribution")) + ## similar for mu + if(missing(mu)){ + mu <- distr + low.mu <- low + up.mu <- up + x.mu.seq <- x.seq + if(is(distr,"AbscontDistribution")){ + x.mu.seq0 <- x.seq0 + h0.mu <- h0 + } + }else{ + if(is(distr,"DiscreteDistribution")){ x.mu.seq <- support(mu) - else - {if(is(mu,"AbscontDistribution")){ + low.mu <- min(x.mu.seq) + up.mu <- max(x.mu.seq) + }else{ + low0.mu <- q(mu)(TruncQuantile) + up0.mu <- q(mu)(TruncQuantile, lower.tail = FALSE) + m0.mu <- median(mu); s0.mu <- IQR(mu) + low1.mu <- m0.mu - IQR.fac * s0.mu + up1.mu <- m0.mu + IQR.fac * s0.mu + low.mu <- max(low0.mu,low1.mu); up.mu <- min(up0.mu,up1.mu) + if(is(mu,"AbscontDistribution")){ x.mu.seq0 <- seq(low.mu, up.mu, length = N1) h0.mu <- x.mu.seq0[1:2]%*%c(-1,1) x.mu.seq <- x.mu.seq0[odd] - }else{ + }else{ x.mu.seq <- seq(low.mu, up.mu, length = N) - } } + } + } L2deriv <- L2deriv(L2Fam)[[1]] # y.seq <- sapply(x.seq, function(x) evalRandVar(L2deriv, x)) @@ -178,30 +188,35 @@ d(distr)(x.seq0) Delta0 <- h0*.csimpsum(Delta0x) }else{ - L2x <- function(x,y) (x<=y)*evalRandVar(L2deriv, x) - Delta0 <- sapply(x.seq, function(Y){ fct <- function(x) L2x(x,y=Y) + if(is(distr,"DiscreteDistribution")){ + Delta0x <- sapply(x.seq0, function(x) + evalRandVar(L2deriv, x)) * + d(distr)(x.seq0) + Delta0 <- cumsum(Delta0x) + }else{ + L2x <- function(x,y) (x<=y)*evalRandVar(L2deriv, x) + Delta0 <- sapply(x.seq, function(Y){ fct <- function(x) L2x(x,y=Y) return(E(object=distr, fun = fct))}) + } } # print(Delta0) Delta1 <- approxfun(x.seq, Delta0, yleft = 0, yright = 0) if(is(distr,"DiscreteDistribution")) Delta <- function(x) Delta1(x) * (x %in% support(distr)) - else Delta <- function(x) Delta1(x) - # print(Delta(x.seq)) + else Delta <- Delta1 +# print(Delta(x.seq)) # print(Delta(rnorm(100))) ## J = Var_Ptheta Delta - J1 <- E(object=distr, fun = Delta) # print(J1) - Delta.0 <- function(x) Delta(x) - J1 # print(Delta.0(x.seq)) # print(Delta.0(r(distr)(100))^2) #J <- distrExIntegrate(function(x) d(distr)(x)*Delta.0(x)^2, lower=low, upper=up) - J <- E(object=distr, fun = function(x) Delta.0(x)^2 ) + J <- E(object=distr, fun = function(x) Delta(x)^2 ) # print(J) ### CvM-IC phi - phi <- function(x) Delta.0(x)/J + phi <- function(x) Delta(x)/J ## integrand phi x Ptheta in formula (51) [ibid] phi1 <- function(x) phi(x) * p(distr)(x) @@ -236,13 +251,14 @@ psi.01 <- function(x) psi.0(x)/E3 if(withplot) { dev.new() #windows() + plot(x.seq, psi.01(x.seq), type = if(is(distr,"DiscreteDistribution")) "p" else "l") } E4 <- E(object=distr, fun = function(x) psi.01(x)^2) psi.01 <- EuclRandVariable(Map = list(psi.01), Domain = Reals()) -# print(list(E2,E4,E2-E4)) +# print(list(E1,E2,E4,E2-E4)) }else{ @@ -380,7 +396,7 @@ B0 <- BinomFamily(size=8, prob=0.3);.CvMMDCovariance(B0,par=ParamFamParameter("",.3), withplot=TRUE) N0 <- NormLocationFamily();.CvMMDCovariance(N0,par=ParamFamParameter("",0), withplot=TRUE, N = 200) C0 <- L2LocationFamily(central=Cauchy());.CvMMDCovariance(C0,par=ParamFamParameter("",0), withplot=TRUE, N = 200) -N1 <- NormScaleFamily(); re=.CvMMDCovariance(N1,par=ParamFamParameter("",1), withICwithplot=TRUE, N = 200) +N1 <- NormScaleFamily(); re=.CvMMDCovariance(N1,par=ParamFamParameter("",1), withpreIC,withplot=TRUE, N = 200) NS <- NormLocationScaleFamily();paramP <- ParamFamParameter(name = "locscale", main = c("loc"=0,"scale"=1),trafo = diag(2)); .CvMMDCovariance(NS,par=paramP, withplot=TRUE, N = 100) cls <- CauchyLocationScaleFamily();.CvMMDCovariance(cls,par=ParamFamParameter("",0:1), withplot=TRUE, N = 200) Modified: pkg/distrMod/R/qqplot.R =================================================================== --- pkg/distrMod/R/qqplot.R 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/R/qqplot.R 2016-04-23 18:08:54 UTC (rev 1105) @@ -6,7 +6,7 @@ ## helper into distrMod -.labelprep <- function(x,y,lab.pts,col.lbl,cex.lbl,which.lbs,which.Order,order.traf){ +.labelprep <- function(x,y,lab.pts,col.lbl,cex.lbl,adj.lbl,which.lbs,which.Order,order.traf){ n <- length(x) rx <- rank(x) xys <- cbind(x,y[rx]) @@ -26,7 +26,8 @@ col.lbl <- col.lbl[rx] lab.pts <- lab.pts[rx] cex.lbl <- cex.lbl[rx] - return(list(x0=x0,y0=y0,lab=lab.pts[oN],col=col.lbl[oN],cex=cex.lbl[oN])) + adj.lbl <- adj.lbl[rx] + return(list(x0=x0,y0=y0,lab=lab.pts[oN],col=col.lbl[oN],cex=cex.lbl[oN],adj=adj.lbl[oN])) } @@ -79,7 +80,7 @@ col.pch = par("col"),## color for the plotted symbols cex.lbl = par("cex"),## magnification factor for the plotted observation labels col.lbl = par("col"),## color for the plotted observation labels - adj.lbl = NULL, ## adj parameter for the plotted observation labels + adj.lbl = par("adj"),## adj parameter for the plotted observation labels alpha.trsp = NA, ## alpha transparency to be added afterwards jit.fac = 0, ## jittering factor used for discrete distributions jit.tol = .Machine$double.eps, ## tolerance for jittering: if distance @@ -134,6 +135,7 @@ function(x,a) x else function(x,a) mapply(x,alp.t,a1=a) cex.pch <- .makeLenAndOrder(cex.pch,ord.x) cex.lbl <- .makeLenAndOrder(cex.lbl,ord.x) + adj.lbl <- .makeLenAndOrder(adj.lbl,ord.x) col.pch <- alp.f(.makeLenAndOrder(col.pch,ord.x),alp.v) col.lbl <- alp.f(.makeLenAndOrder(col.lbl,ord.x),alp.v) @@ -190,14 +192,14 @@ if(mfColRow) opar1 <- par(mfrow = c(1,1), no.readonly = TRUE) ret <- do.call(stats::qqplot, args=mcl) - + lbprep <- NULL if(withLab&& plot.it){ lbprep <- .labelprep(xj,yc,lab.pts, - col.lbl,cex.lbl,which.lbs,which.Order,order.traf) + col.lbl,cex.lbl, adj.lbl,which.lbs,which.Order,order.traf) xlb0 <- if(datax) lbprep$x0 else lbprep$y0 ylb0 <- if(datax) lbprep$y0 else lbprep$x0 text(x = xlb0, y = ylb0, labels = lbprep$lab, - cex = lbprep$cex, col = lbprep$col, adj = adj.lbl) + cex = lbprep$cex, col = lbprep$col, adj = lbprep$adj) } qqb <- NULL @@ -232,6 +234,27 @@ } } + qqplotInfo <- list(xy.0=xy, y.0=y, datax = datax, + withConf.pw=withConf.pw, + withConf.sim=withConf.sim, + alpha.CI=alpha.CI , + col.pCI = col.pCI , lty.pCI = lty.pCI , + lwd.pCI = lwd.pCI , pch.pCI = pch.pCI, + cex.pCI = cex.pCI , + col.sCI = col.sCI , lty.sCI = lty.sCI , + lwd.sCI = lwd.sCI , pch.sCI = pch.sCI, + cex.sCI = cex.sCI , + n = n , + exact.sCI = exact.sCI, exact.pCI = exact.pCI, + nosym.pCI = nosym.pCI, with.legend = with.legend, + legend.bg = legend.bg, legend.pos = legend.pos, + legend.cex = legend.cex, legend.pref = legend.pref, + legend.postf = legend.postf, legend.alpha = legend.alpha, + debug = debug, + args.stats.qqplot = mcl, + withLab = withLab, + lbprep = lbprep + ) if(plot.it){ qqb <- .confqq(xy, y, datax=datax, withConf.pw, withConf.sim, alpha.CI, col.pCI, lty.pCI, lwd.pCI, pch.pCI, cex.pCI, @@ -247,7 +270,9 @@ } } } - return(invisible(c(ret,qqb))) + qqplotInfo <- c(ret, qqplotInfo, qqb) + class(qqplotInfo) <- c("qqplotInfo","DiagnInfo") + return(invisible(qqplotInfo)) }) ## into distrMod Modified: pkg/distrMod/man/0distrMod-package.Rd =================================================================== --- pkg/distrMod/man/0distrMod-package.Rd 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/man/0distrMod-package.Rd 2016-04-23 18:08:54 UTC (rev 1105) @@ -16,7 +16,7 @@ \tabular{ll}{ Package: \tab distrMod \cr Version: \tab 2.6 \cr -Date: \tab 2015-11-07 \cr +Date: \tab 2016-04-23 \cr Depends: \tab R(>= 2.14.0), distr(>= 2.5.2), distrEx(>= 2.4), RandVar(>= 0.6.3), MASS, stats4, methods \cr Imports: \tab startupmsg, sfsmisc, graphics, stats, grDevices \cr @@ -24,7 +24,7 @@ ByteCompile: \tab yes \cr License: \tab LGPL-3 \cr URL: \tab http://distr.r-forge.r-project.org/\cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1104 \cr }} \section{Classes}{ Deleted: pkg/distrMod/man/internalmdeHelpers.Rd =================================================================== --- pkg/distrMod/man/internalmdeHelpers.Rd 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/man/internalmdeHelpers.Rd 2016-04-23 18:08:54 UTC (rev 1105) @@ -1,61 +0,0 @@ -\name{internal_mdehelpers_for_distrMod} -\alias{internal_mdehelpers_for_distrMod} -\alias{.CvMMDCovariance} - -\title{Internal helper functions for treating MDEstimators in package distrMod} - -\description{ -These functions are used internally by function \code{MDEstimator} in -package ``distrMod''.} - -\usage{ -.CvMMDCovariance<- function(L2Fam, param, mu = distribution(L2Fam), - withplot = FALSE, withpreIC = FALSE, - N = getdistrOption("DefaultNrGridPoints")+1, - rel.tol=.Machine$double.eps^0.3, - TruncQuantile = getdistrOption("TruncQuantile"), - IQR.fac = 15, - ...) -} - - -\arguments{ - \item{L2Fam}{an object of class \code{L2ParamFamily}; - the parametric family at which to evaluate the MCE} - \item{param}{an object of class \code{ParamFamParameter}; - contains the parameter value at which to evaluate the - variance} - \item{mu}{an object of class \code{UnivariateDistribution}; - the distribution on the reals at which to integrate the squared - distance of the cdf's in the CvM-distance} - \item{withplot}{logical; defaults to \code{FALSE}; if \code{TRUE} for diagnostic - purposes plots the influence function of the CvM-MDE} - \item{withpreIC}{logical; should corresponding IC of the CvM-MDE be returned?} - \item{\dots}{currently not used} - \item{N}{integer; the number of grid points at which to evaluate the antiderivative - in case of an absolutely continuous distribution; more precisely, internally - this becomes \eqn{2N+1}} - \item{rel.tol}{numeric; relative tolerance; currently not used} - \item{TruncQuantile}{numeric in (0,1); in case of an unbounded support of the - distribution the quantile level at which to cut the distribution} - \item{IQR.fac}{a positive numeric; a factor by which to multiply the IQR of the distribution - to obtain a sensible cut of point for the integration bounds} - } - -\details{ -\code{.CvMMDCovariance} computes the asymptotic covariance of the CvM-MDE according to -H. Rieder (1994) "Robust Asymptotic Statistics". - } - -\value{ -\item{.CvMMDCovariance}{if argument \code{withpreIC} is \code{TRUE}, then -a list with elements the IC of the CvM-MDE and its covariance is returned, otherwise -just the covariance} -} - -\author{ - Peter Ruckdeschel \email{peter.ruckdeschel at uni-oldenburg.de} -} - -\keyword{internal} -\concept{utilities} Modified: pkg/distrMod/man/internals.Rd =================================================================== --- pkg/distrMod/man/internals.Rd 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/man/internals.Rd 2016-04-23 18:08:54 UTC (rev 1105) @@ -18,7 +18,7 @@ .isUnitMatrix(m) .csimpsum(fx) .validTrafo(trafo, dimension, dimensionwithN) -.CvMMDCovariance(L2Fam, param, mu = distribution(L2Fam), +.CvMMDCovariance(L2Fam, param, mu = distribution(L2Fam), withplot = FALSE, withpreIC = FALSE, N = getdistrOption("DefaultNrGridPoints")+1, rel.tol=.Machine$double.eps^0.3, @@ -42,29 +42,30 @@ \item{trafo}{an object of class \code{MatrixorFunction}} \item{dimension}{a numeric --- length of main part of the parameter} \item{dimensionwithN}{a numeric --- length of main and nuisance part of the parameter} + \item{L2Fam}{an object of class \code{L2ParamFamily} --- for which we want to determine the IC resp. the as. [co]variance of the corresponding Minimum CvM estimator} - \item{param}{an object of class \code{ParamFamParameter}, the parameter value - at which we want to determine the IC resp. the as. [co]variance of the corresponding - Minimum CvM estimator} \item{mu}{an object of class \code{UnivariateDistribution}: integration measure (resp. distribution) for CvM distance} - \item{rel.tol}{relative tolerance for \code{distrExIntegrate}.} - \item{TruncQuantile}{quantile for quantile based integration range.} - \item{lowerTruncQuantile}{lower quantile for quantile based integration range.} - \item{upperTruncQuantile}{upper quantile for quantile based integration range.} - \item{IQR.fac}{factor for scale based integration range (i.e.; - median of the distribution \eqn{\pm}{+-}\code{IQR.fac}\eqn{\times}{*}IQR).} - \item{withplot}{logical: shall we plot corresponding ICs?} + \item{withplot}{logical; defaults to \code{FALSE}; if \code{TRUE} for diagnostic + purposes plots the influence function of the CvM-MDE} \item{withpreIC}{logical: shall we return a list with components \code{preIC} and \code{var} or just \code{var}; here \code{var} is the corresponding asymptotic variance and \code{preIC} the corresponding \code{EuclRandVarList} featuring as argument \code{Curve} in \code{IC}s of package \pkg{RobAStBase}} - \item{N}{a numeric: the number of gridpoints for constructing the - \eqn{\mu}{mu}- resp. \eqn{P_\theta}{P_theta}-``primitive'' - function} + \item{\dots}{currently not used} + \item{N}{integer; the number of grid points at which to evaluate the antiderivative + in case of an absolutely continuous distribution; more precisely, internally + this becomes \eqn{2N+1}} + \item{rel.tol}{relative tolerance for \code{distrExIntegrate}.} + \item{TruncQuantile}{numeric in (0,1); in case of an unbounded support of the + distribution the quantile level at which to cut the distribution} + \item{IQR.fac}{a positive numeric; a factor by which to multiply the IQR of the distribution + to obtain a sensible cut of point for the integration bounds} + \item{lowerTruncQuantile}{lower quantile for quantile based integration range.} + \item{upperTruncQuantile}{upper quantile for quantile based integration range.} \item{fx}{a vector of function evaluations multiplied by the gridwidth} \item{distr}{an object of class \code{AbscontDistribution}} \item{\dots}{further argument to be passed through --- so @@ -87,9 +88,8 @@ \code{.validTrafo} checks whether the argument is a valid transformation. -\code{.CvMMDCovariance} determines the IC resp. the as. [co]variance of - the corresponding Minimum CvM estimator. Still some checking / optimization / - improvement needed. +\code{.CvMMDCovariance} computes the asymptotic covariance of the CvM-MDE +according to H. Rieder (1994) "Robust Asymptotic Statistics". \code{.show.with.sd} is code borrowed from \code{print.fitdistr} in package \pkg{MASS} by B.D. Ripley. It pretty-prints estimates with corresponding @@ -115,6 +115,9 @@ \code{preIC} and \code{var} ---see above} \item{.show.with.sd}{\code{invisible()}} \item{.deleteDim}{vector \code{x} without \code{dim} attribute} +\item{.CvMMDCovariance}{if argument \code{withpreIC} is \code{TRUE}, then +a list with elements the IC of the CvM-MDE and its covariance is returned, otherwise +just the covariance} } \author{ Modified: pkg/distrMod/man/qqplot.Rd =================================================================== --- pkg/distrMod/man/qqplot.Rd 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/man/qqplot.Rd 2016-04-23 18:08:54 UTC (rev 1105) @@ -239,9 +239,9 @@ } \examples{ set.seed(123) -x <- rnorm(40,mean=15,sd=30) -qqplot(x, Chisq(df=15)) -NF <- NormLocationScaleFamily(mean=15, sd=30) +x <- rnorm(40,mean=5,sd=sqrt(10)) +qqplot(x, Chisq(df=5)) +NF <- NormLocationScaleFamily(mean=5, sd=30^.5) qqplot(x, NF) mlE <- MLEstimator(x, NF) qqplot(x, mlE) Modified: pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save =================================================================== --- pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2016-04-23 17:09:34 UTC (rev 1104) +++ pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2016-04-23 18:08:54 UTC (rev 1105) @@ -1,3179 +1,3178 @@ - -R version 3.2.2 Patched (2015-11-06 r69612) -- "Fire Safety" -Copyright (C) 2015 The R Foundation for Statistical Computing -Platform: x86_64-pc-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> pkgname <- "distrMod" -> source(file.path(R.home("share"), "R", "examples-header.R")) -> options(warn = 1) -> library('distrMod') -Loading required package: distr -Loading required package: startupmsg -:startupmsg> Utilities for Start-Up Messages (version 0.9.1) -:startupmsg> -:startupmsg> For more information see ?"startupmsg", -:startupmsg> NEWS("startupmsg") - -Loading required package: sfsmisc -Loading required package: SweaveListingUtils -:SweaveListingUtils> Utilities for Sweave Together with -:SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7) -:SweaveListingUtils> -:SweaveListingUtils> NOTE: Support for this package -:SweaveListingUtils> will stop soon. -:SweaveListingUtils> -:SweaveListingUtils> Package 'knitr' is providing the -:SweaveListingUtils> same functionality in a better -:SweaveListingUtils> way. -: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 objects are masked from ?package:base?: - - library, require - -:distr> Object Oriented Implementation of Distributions (version -:distr> 2.6) -:distr> -:distr> Attention: Arithmetics on distribution objects are -:distr> understood as operations on corresponding random variables -: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 objects are masked from ?package:stats?: - - df, qqplot, sd - -Loading required package: distrEx -:distrEx> Extensions of Package 'distr' (version 2.6) -: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 objects are masked from ?package:stats?: - - IQR, mad, median, var - -Loading required package: RandVar -:RandVar> Implementation of random variables (version 0.9.2) -: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 2.6) -: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 is masked from ?package:stats4?: - - confint - -The following object is masked from ?package:stats?: - - confint - -The following object is masked from ?package:base?: - - norm - -> -> base::assign(".oldSearch", base::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 -precision of Fisher information - relativ error [%]: - shape1 shape2 -shape1 -0.0018510679 -0.0002555806 -shape2 -0.0002555806 -0.0018510679 -condition of Fisher information: -[1] 5.277691 -$maximum.deviation -[1] 3.963591e-05 - -> -> -> -> cleanEx() -> nameEx("BiasType-class") -> ### * BiasType-class -> -> flush(stderr()); flush(stdout()) -> -> ### Name: BiasType-class -> ### Title: Bias Type -> ### Aliases: BiasType-class name,BiasType-method name<-,BiasType-method -> ### Keywords: classes -> -> ### ** Examples -> -> aB <- positiveBias() -> name(aB) -[1] "positive Bias" -> -> -> -> cleanEx() -> nameEx("BinomFamily") -> ### * BinomFamily -> -> flush(stderr()); flush(stdout()) -> -> ### Name: BinomFamily -> ### Title: Generating function for Binomial families -> ### Aliases: BinomFamily -> ### Keywords: models -> -> ### ** Examples -> -> (B1 <- BinomFamily(size = 25, prob = 0.25)) -An object of class "BinomFamily" -### name: Binomial family - -### distribution: Distribution Object of Class: Binom - size: 25 - prob: 0.25 - -### param: An object of class "ParamFamParameter" -name: probability of success -prob: 0.25 -fixed part of param.: - size: 25 -trafo: - prob -prob 1 - -### props: -[1] "The Binomial family is symmetric with respect to prob = 0.5;" -[2] "i.e., d(Binom(size, prob))(k)=d(Binom(size,1-prob))(size-k)" -> plot(B1) -> FisherInfo(B1) -An object of class "PosSemDefSymmMatrix" - prob -prob 133.3333 -> checkL2deriv(B1) -precision of centering: -1.099042e-15 -precision of Fisher information: - prob -prob 2.842171e-14 -precision of Fisher information - relativ error [%]: - prob -prob 2.131628e-14 -condition of Fisher information: -[1] 1 -$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 -precision of Fisher information - relativ error [%]: - loc scale -loc -0.006275047 NaN -scale NaN -4.236286 -condition of Fisher information: -[1] 1 -$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 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 1105 From noreply at r-forge.r-project.org Sat Apr 23 21:46:24 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 23 Apr 2016 21:46:24 +0200 (CEST) Subject: [Distr-commits] r1106 - branches/distr-2.7/pkg/distrMod/R Message-ID: <20160423194625.02024187E11@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-23 21:46:24 +0200 (Sat, 23 Apr 2016) New Revision: 1106 Modified: branches/distr-2.7/pkg/distrMod/R/qqplot.R Log: [distrMod] branch minor backfix in qqplot (from trunk) Modified: branches/distr-2.7/pkg/distrMod/R/qqplot.R =================================================================== --- branches/distr-2.7/pkg/distrMod/R/qqplot.R 2016-04-23 18:08:54 UTC (rev 1105) +++ branches/distr-2.7/pkg/distrMod/R/qqplot.R 2016-04-23 19:46:24 UTC (rev 1106) @@ -6,7 +6,7 @@ ## helper into distrMod -.labelprep <- function(x,y,lab.pts,col.lbl,cex.lbl,which.lbs,which.Order,order.traf){ +.labelprep <- function(x,y,lab.pts,col.lbl,cex.lbl,adj.lbl,which.lbs,which.Order,order.traf){ n <- length(x) rx <- rank(x) xys <- cbind(x,y[rx]) @@ -26,7 +26,8 @@ col.lbl <- col.lbl[rx] lab.pts <- lab.pts[rx] cex.lbl <- cex.lbl[rx] - return(list(x0=x0,y0=y0,lab=lab.pts[oN],col=col.lbl[oN],cex=cex.lbl[oN])) + adj.lbl <- adj.lbl[rx] + return(list(x0=x0,y0=y0,lab=lab.pts[oN],col=col.lbl[oN],cex=cex.lbl[oN],adj=adj.lbl[oN])) } @@ -79,7 +80,7 @@ col.pch = par("col"),## color for the plotted symbols cex.lbl = par("cex"),## magnification factor for the plotted observation labels col.lbl = par("col"),## color for the plotted observation labels - adj.lbl = NULL, ## adj parameter for the plotted observation labels + adj.lbl = par("adj"),## adj parameter for the plotted observation labels alpha.trsp = NA, ## alpha transparency to be added afterwards jit.fac = 0, ## jittering factor used for discrete distributions jit.tol = .Machine$double.eps, ## tolerance for jittering: if distance @@ -134,6 +135,7 @@ function(x,a) x else function(x,a) mapply(x,alp.t,a1=a) cex.pch <- .makeLenAndOrder(cex.pch,ord.x) cex.lbl <- .makeLenAndOrder(cex.lbl,ord.x) + adj.lbl <- .makeLenAndOrder(adj.lbl,ord.x) col.pch <- alp.f(.makeLenAndOrder(col.pch,ord.x),alp.v) col.lbl <- alp.f(.makeLenAndOrder(col.lbl,ord.x),alp.v) @@ -190,14 +192,14 @@ if(mfColRow) opar1 <- par(mfrow = c(1,1), no.readonly = TRUE) ret <- do.call(stats::qqplot, args=mcl) - + lbprep <- NULL if(withLab&& plot.it){ lbprep <- .labelprep(xj,yc,lab.pts, - col.lbl,cex.lbl,which.lbs,which.Order,order.traf) + col.lbl,cex.lbl, adj.lbl,which.lbs,which.Order,order.traf) xlb0 <- if(datax) lbprep$x0 else lbprep$y0 ylb0 <- if(datax) lbprep$y0 else lbprep$x0 text(x = xlb0, y = ylb0, labels = lbprep$lab, - cex = lbprep$cex, col = lbprep$col, adj = adj.lbl) + cex = lbprep$cex, col = lbprep$col, adj = lbprep$adj) } qqb <- NULL @@ -232,6 +234,27 @@ } } + qqplotInfo <- list(xy.0=xy, y.0=y, datax = datax, + withConf.pw=withConf.pw, + withConf.sim=withConf.sim, + alpha.CI=alpha.CI , + col.pCI = col.pCI , lty.pCI = lty.pCI , + lwd.pCI = lwd.pCI , pch.pCI = pch.pCI, + cex.pCI = cex.pCI , + col.sCI = col.sCI , lty.sCI = lty.sCI , + lwd.sCI = lwd.sCI , pch.sCI = pch.sCI, + cex.sCI = cex.sCI , + n = n , + exact.sCI = exact.sCI, exact.pCI = exact.pCI, + nosym.pCI = nosym.pCI, with.legend = with.legend, + legend.bg = legend.bg, legend.pos = legend.pos, + legend.cex = legend.cex, legend.pref = legend.pref, + legend.postf = legend.postf, legend.alpha = legend.alpha, + debug = debug, + args.stats.qqplot = mcl, + withLab = withLab, + lbprep = lbprep + ) if(plot.it){ qqb <- .confqq(xy, y, datax=datax, withConf.pw, withConf.sim, alpha.CI, col.pCI, lty.pCI, lwd.pCI, pch.pCI, cex.pCI, @@ -247,7 +270,9 @@ } } } - return(invisible(c(ret,qqb))) + qqplotInfo <- c(ret, qqplotInfo, qqb) + class(qqplotInfo) <- c("qqplotInfo","DiagnInfo") + return(invisible(qqplotInfo)) }) ## into distrMod From noreply at r-forge.r-project.org Mon Apr 25 14:07:28 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Apr 2016 14:07:28 +0200 (CEST) Subject: [Distr-commits] r1107 - branches/distr-2.7/pkg/distrEllipse/inst Message-ID: <20160425120728.32977187AEA@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-25 14:07:27 +0200 (Mon, 25 Apr 2016) New Revision: 1107 Modified: branches/distr-2.7/pkg/distrEllipse/inst/NEWS Log: backport branch 2.7 Modified: branches/distr-2.7/pkg/distrEllipse/inst/NEWS =================================================================== --- branches/distr-2.7/pkg/distrEllipse/inst/NEWS 2016-04-23 19:46:24 UTC (rev 1106) +++ branches/distr-2.7/pkg/distrEllipse/inst/NEWS 2016-04-25 12:07:27 UTC (rev 1107) @@ -16,6 +16,8 @@ + new synonyma plotRd, rRd, dRd, pRd, and qRd for plot.rd, r.rd, d.rd, p.rd, and q.rd to substitute the old ones on the long run (to avoid clashes with S3 inheritance) +deprecated: ++ plot.rd, r.rd, d.rd, p.rd, and q.rd will soon be replaced by the upper aliases under the hood: + removed ::: internal dependencies (within distr-Fam of pkgs) by copying From noreply at r-forge.r-project.org Mon Apr 25 14:08:39 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Apr 2016 14:08:39 +0200 (CEST) Subject: [Distr-commits] r1108 - in pkg: distrEllipse/inst utils Message-ID: <20160425120839.7E37A187CAA@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-25 14:08:39 +0200 (Mon, 25 Apr 2016) New Revision: 1108 Modified: pkg/distrEllipse/inst/NEWS pkg/utils/updateTo2_6.R Log: minor thing in distEllipse as to deprecation Modified: pkg/distrEllipse/inst/NEWS =================================================================== --- pkg/distrEllipse/inst/NEWS 2016-04-25 12:07:27 UTC (rev 1107) +++ pkg/distrEllipse/inst/NEWS 2016-04-25 12:08:39 UTC (rev 1108) @@ -16,6 +16,9 @@ + new synonyma plotRd, rRd, dRd, pRd, and qRd for plot.rd, r.rd, d.rd, p.rd, and q.rd to substitute the old ones on the long run (to avoid clashes with S3 inheritance) +deprecated: ++ plot.rd, r.rd, d.rd, p.rd, and q.rd will soon be replaced by the upper aliases + under the hood: + removed ::: internal dependencies (within distr-Fam of pkgs) by copying Modified: pkg/utils/updateTo2_6.R =================================================================== --- pkg/utils/updateTo2_6.R 2016-04-25 12:07:27 UTC (rev 1107) +++ pkg/utils/updateTo2_6.R 2016-04-25 12:08:39 UTC (rev 1108) @@ -88,3 +88,43 @@ rownames(Values) <- Names changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, pkgs=Pkgs, values=Values) + +Values <- matrix(c("0.9.4",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "RandVar" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/RobASt/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values, pathRepo="robast") + +Values <- matrix(c("2.6",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "distrMod" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/distr/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values) + +Values <- matrix(c("1.0",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "RandVar" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/RobASt/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values, pathRepo="robast") + +Values <- matrix(c("1.0",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "RobAStRDA" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/RobASt/",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values, pathRepo="robast") + +Values <- matrix(c("1.0",format(Sys.time(), format="%Y-%m-%d")),2,1) +Pkgs <- "RobAStBase" +Names <- c("Version","Date") +colnames(Values) <- Pkgs +rownames(Values) <- Names +changeDescription(startDir = "C:/rtest/RobASt/branches/robast-1.0",names=Names, verbose=TRUE, + pkgs=Pkgs, values=Values, pathRepo="robast") From noreply at r-forge.r-project.org Mon Apr 25 16:33:58 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Apr 2016 16:33:58 +0200 (CEST) Subject: [Distr-commits] r1109 - branches/distr-2.7/pkg/SweaveListingUtils/man branches/distr-2.7/pkg/distrEllipse/R pkg/SweaveListingUtils pkg/SweaveListingUtils/man pkg/SweaveListingUtils/tests/Examples Message-ID: <20160425143358.95C9D187A36@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-25 16:33:58 +0200 (Mon, 25 Apr 2016) New Revision: 1109 Modified: branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd branches/distr-2.7/pkg/SweaveListingUtils/man/copySourceFromRForge.Rd branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd pkg/SweaveListingUtils/man/changeKeywordstyles.Rd pkg/SweaveListingUtils/man/copySourceFromRForge.Rd pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save Log: SweaveListingUtils next try: moved some examples into \donttest so that CRAN does not see fuzzy diffs Modified: branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 12:08:39 UTC (rev 1108) +++ branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 14:33:58 UTC (rev 1109) @@ -127,9 +127,9 @@ \author{Peter Ruckdeschel \email{peter.ruckdeschel at uni-oldenburg.de}} \examples{ -SweaveListingPreparations() +\donttest{SweaveListingPreparations() SweaveListingPreparations(pkv="2.1") -} +}} \keyword{utilities} Modified: branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 12:08:39 UTC (rev 1108) +++ branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 14:33:58 UTC (rev 1109) @@ -63,12 +63,13 @@ % \examples{ require(MASS) +\donttest{ lstsetLanguage(pkgs = c("MASS","stats"), keywordstyles = paste("\\\\bfseries\\\\color{",c("blue","red"),"}", sep="", collapse="")) changeKeywordstyles(pkgs = c("distr","distrEx"), keywordstyles = paste("\\\\bfseries\\\\color{",c("green","blue"),"}", collapse="", sep = "")) -} +}} % \keyword{utilities} Modified: branches/distr-2.7/pkg/SweaveListingUtils/man/copySourceFromRForge.Rd =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/man/copySourceFromRForge.Rd 2016-04-25 12:08:39 UTC (rev 1108) +++ branches/distr-2.7/pkg/SweaveListingUtils/man/copySourceFromRForge.Rd 2016-04-25 14:33:58 UTC (rev 1109) @@ -58,9 +58,11 @@ \examples{ copySourceFromRForge("distr","R","AllClasses.R","distr", from =2, to =3, offset.after=2) +\donttest{ copySourceFromRForge("distr","R","AllClasses.R","distr", from ="setClass", to ="\\\\}") } +} \keyword{utilities} Modified: branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R =================================================================== --- branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R 2016-04-25 12:08:39 UTC (rev 1108) +++ branches/distr-2.7/pkg/distrEllipse/R/SphericalDistribution.R 2016-04-25 14:33:58 UTC (rev 1109) @@ -43,11 +43,30 @@ ## wrappers: setMethod("plot.rd", "SphericalDistribution", - function(x, ... ) plot(x at radDistr,...)) -setMethod("r.rd", "SphericalDistribution", function(object) r(object at radDistr)) -setMethod("d.rd", "SphericalDistribution", function(object) d(object at radDistr)) -setMethod("p.rd", "SphericalDistribution", function(object) p(object at radDistr)) -setMethod("q.rd", "SphericalDistribution", function(object) q(object at radDistr)) + function(x, ... ){ .Deprecated("plotRd", package="distrEllipse", + msg = gettext("To avoid clashes with S3 method dispatch, + this function will soon be replaced by 'plotRd'")) + plot(x at radDistr,...)}) +setMethod("r.rd", "SphericalDistribution", function(object){ +.Deprecated("rRd", package="distrEllipse", + msg = gettext("To avoid clashes with S3 method dispatch, + this function will soon be replaced by 'rRd'")) + r(object at radDistr)}) +setMethod("d.rd", "SphericalDistribution", function(object){ +.Deprecated("dRd", package="distrEllipse", + msg = gettext("To avoid clashes with S3 method dispatch, + this function will soon be replaced by 'dRd'")) +d(object at radDistr)}) +setMethod("p.rd", "SphericalDistribution", function(object){ +.Deprecated("pRd", package="distrEllipse", + msg = gettext("To avoid clashes with S3 method dispatch, + this function will soon be replaced by 'pRd'")) + p(object at radDistr)}) +setMethod("q.rd", "SphericalDistribution", function(object){ +.Deprecated("qRd", package="distrEllipse", + msg = gettext("To avoid clashes with S3 method dispatch, + this function will soon be replaced by 'qRd'")) + q(object at radDistr)}) setMethod("plotRd", "SphericalDistribution", function(x, ... ) plot(x at radDistr,...)) Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2016-04-25 12:08:39 UTC (rev 1108) +++ pkg/SweaveListingUtils/DESCRIPTION 2016-04-25 14:33:58 UTC (rev 1109) @@ -4,9 +4,9 @@ and for including R / Rd source file (snippets) copied from R-forge in its most recent version (or another URL) thereby avoiding inconsistencies between vignette and documented source code. -Version: 0.7.3 +Version: 0.7.4 Encoding: latin1 -Date: 2016-04-23 +Date: 2016-04-25 Depends: R(>= 2.14.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines Imports: methods @@ -16,4 +16,4 @@ License: LGPL-3 LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1087 +SVNRevision: 1108 \ No newline at end of file Modified: pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd =================================================================== --- pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 12:08:39 UTC (rev 1108) +++ pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 14:33:58 UTC (rev 1109) @@ -127,9 +127,9 @@ \author{Peter Ruckdeschel \email{peter.ruckdeschel at uni-oldenburg.de}} \examples{ -SweaveListingPreparations() +\donttest{SweaveListingPreparations() SweaveListingPreparations(pkv="2.1") -} +}} \keyword{utilities} Modified: pkg/SweaveListingUtils/man/changeKeywordstyles.Rd =================================================================== --- pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 12:08:39 UTC (rev 1108) +++ pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 14:33:58 UTC (rev 1109) @@ -63,12 +63,13 @@ % \examples{ require(MASS) +\donttest{ lstsetLanguage(pkgs = c("MASS","stats"), keywordstyles = paste("\\\\bfseries\\\\color{",c("blue","red"),"}", sep="", collapse="")) changeKeywordstyles(pkgs = c("distr","distrEx"), keywordstyles = paste("\\\\bfseries\\\\color{",c("green","blue"),"}", collapse="", sep = "")) -} +}} % \keyword{utilities} Modified: pkg/SweaveListingUtils/man/copySourceFromRForge.Rd =================================================================== --- pkg/SweaveListingUtils/man/copySourceFromRForge.Rd 2016-04-25 12:08:39 UTC (rev 1108) +++ pkg/SweaveListingUtils/man/copySourceFromRForge.Rd 2016-04-25 14:33:58 UTC (rev 1109) @@ -58,9 +58,11 @@ \examples{ copySourceFromRForge("distr","R","AllClasses.R","distr", from =2, to =3, offset.after=2) +\donttest{ copySourceFromRForge("distr","R","AllClasses.R","distr", from ="setClass", to ="\\\\}") } +} \keyword{utilities} Modified: pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save =================================================================== --- pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-25 12:08:39 UTC (rev 1108) +++ pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-25 14:33:58 UTC (rev 1109) @@ -30,7 +30,7 @@ :SweaveListingUtils> Utilities for Sweave Together with :SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7.3) +:SweaveListingUtils> 0.7.4) :SweaveListingUtils> :SweaveListingUtils> NOTE: Support for this package :SweaveListingUtils> will stop soon. @@ -315,680 +315,8 @@ > > ### ** Examples > -> SweaveListingPreparations() -%------------------------------------------------------------------------------% -%Preparations for Sweave and Listings -%------------------------------------------------------------------------------% -% -\RequirePackage{color} -\definecolor{Rcolor}{rgb}{0, 0.5, 0.5} -\definecolor{RRecomdcolor}{rgb}{0, 0.6, 0.4} -\definecolor{Rbcolor}{rgb}{0, 0.6, 0.6} -\definecolor{Routcolor}{rgb}{0.461, 0.039, 0.102} -\definecolor{Rcommentcolor}{rgb}{0.101, 0.043, 0.432} -%------------------------------------------------------------------------------% -\lstdefinelanguage{Rd}[common]{TeX}% -{moretexcs={acronym,alias,arguments,author,bold,cite,% - code,command,concept,cr,deqn,describe,% - description,details,dfn,doctype,dots,% - dontrun,dontshow,donttest,dQuote,% - email,emph,enc,encoding,enumerate,env,eqn,% - examples,file,format,if,ifelse,item,itemize,kbd,keyword,% - ldots,link,linkS4class,method,name,note,% - option,out,pkg,preformatted,R,Rdopts,Rdversion,% - references,S3method,S4method,Sexpr,samp,section,% - seealso,source,sp,special,sQuote,strong,% - subsection,synopsis,tab,tabular,testonly,% - title,url,usage,value,var,verb}, - sensitive=true,% - morecomment=[l]\%% 2008/9 Peter Ruckdeschel -}[keywords,comments]%% -%------------------------------------------------------------------------------% - -%---------------- -\lstdefinestyle{RstyleO1}{fancyvrb=true,escapechar=`,extendedchars=false,% - language=R,% - basicstyle={\color{Rcolor}\small},% - keywordstyle={\bf\color{Rcolor}},%Warning in print.taglist(taglist, LineLength = LineLength, offset.start = nchar(startS), : - Some elements of taglist are too long - - commentstyle={\color{Rcommentcolor}\ttfamily\itshape},% - literate={"}{\texttt{"}}1{<-}{{$\leftarrow$}}2{<<-}{{$\twoheadleftarrow$}}2{~}{{$\sim$}}1{<=}{{$\leq$}}2{>=}{{$\geq$}}2{^}{{$\scriptstyle\wedge$}}1,% - alsoother={$},% - alsoletter={.<-},% - otherkeywords={!,!=,~,$,*,\&,\%/\%,\%*\%,\%\%,<-,<<-,/},% - escapeinside={(*}{*)}}% -%---------------- -\lstdefinestyle{Rstyle}{style=RstyleO1} - -%---------------- -\lstdefinestyle{Rdstyle}{fancyvrb=true,language=Rd,keywordstyle={\bf},% - basicstyle={\color{black}\footnotesize},% - commentstyle={\ttfamily\itshape},% - alsolanguage=R}% -%---------------- -%------------------------------------------------------------------------------% -\global\def\Rlstset{\lstset{style=Rstyle}}% -\global\def\Rdlstset{\lstset{style=Rdstyle}}% -%------------------------------------------------------------------------------% -\global\def\Rinlstset{\lstset{style=Rinstyle}}% -\global\def\Routlstset{\lstset{style=Routstyle}}% -\global\def\Rcodelstset{\lstset{style=Rcodestyle}}% -%------------------------------------------------------------------------------% -\Rlstset -%------------------------------------------------------------------------------% -%copying relevant parts of Sweave.sty -%------------------------------------------------------------------------------% -% -\RequirePackage{graphicx,fancyvrb}% -\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}% - -\RequirePackage{ifthen}% -\newboolean{Sweave at gin}% -\setboolean{Sweave at gin}{true}% -\setkeys{Gin}{width=0.8\textwidth}% -\newboolean{Sweave at ae} -\setboolean{Sweave at ae}{true}% -\RequirePackage[T1]{fontenc} -\RequirePackage{ae} -% -\newenvironment{Schunk}{}{} - -\newcommand{\Sconcordance}[1]{% -\ifx\pdfoutput\undefined% -\csname newcount\endcsname\pdfoutput\fi% -\ifcase\pdfoutput\special{#1}% -\else\immediate\pdfobj{#1}\fi} - -%------------------------------------------------------------------------------% -% ---- end of parts of Sweave.sty -%------------------------------------------------------------------------------% -% -% ---- input -\lstdefinestyle{RinstyleO}{style=Rstyle,fancyvrb=true,% - basicstyle=\color{Rcolor}\small}% -\lstdefinestyle{Rinstyle}{style=RinstyleO} -\lstnewenvironment{Sinput}{\Rinlstset}{\Rlstset} -% -% ---- output -\lstdefinestyle{RoutstyleO}{ -V1=0,V2=1,V3=0}% -\lstdefinestyle{Routstyle}{style=RoutstyleO} -\lstnewenvironment{Soutput}{\Routlstset}{\Rlstset} -% -% ---- code -\lstdefinestyle{RcodestyleO}{style=Rstyle,fancyvrb=true,fontshape=sl,% - basicstyle=\color{Rcolor}}% -\lstdefinestyle{Rcodestyle}{style=RcodestyleO} -\lstnewenvironment{Scode}{\Rcodelstset}{\Rlstset} -% -%------------------------------------------------------------------------------% -\let\code\lstinline -\def\Code#1{{\tt\color{Rcolor} #1}} -\def\file#1{{\tt #1}} -\def\pkg#1{{\tt "#1"}} -\newcommand{\pkgversion}{{\tt 2.6}} -%------------------------------------------------------------------------------% -Warning in setBaseOrRecommended(pkgs = pkgs) : - number of items to replace is not a multiple of replacement length - -\lstdefinestyle{RstyleO2}{style=RstyleO1,% -% -------------------------- -% Registration of package SweaveListingUtils -% -------------------------- -morekeywords={[2]taglist,setToBeDefinedPkgs,setBaseOrRecommended,readSourceFromRForge,readPkgVersion,% -lstsetRout,lstsetRin,lstsetRd,lstsetRcode,lstsetRall,% -lstsetR,lstsetLanguage,lstset,lstinputSourceFromRForge,lstdefRstyle,% -isBaseOrRecommended,getSweaveListingOption,copySourceFromRForge,changeKeywordstyles,SweaveListingoptions,% -SweaveListingPreparations,SweaveListingOptions,SweaveListingMASK% -},% -keywordstyle={[2]{\bf}},% -% -% -------------------------- -% Registration of package startupmsg -% -------------------------- -morekeywords={[3]suppressStartupMessages,startupType,startupPackage,startupMessage,startupEndline,% -readVersionInformation,readURLInformation,pointertoNEWS,onlytypeStartupMessages,mystartupMessage,% -mySMHandler,infoShow,buildStartupMessage,TOBEDONE,StartupMessage,% -NEWS% -},% -keywordstyle={[3]{\bf}},% -% -% -------------------------- -% Registration of package stats [recommended or base] -% -------------------------- -morekeywords={[4]xtabs,write.ftable,window<-,wilcox.test,weighted.residuals,% -weighted.mean,vcov,varimax,variable.names,var.test,% -update.formula,update.default,tsp<-,tsdiag,tsSmooth,% -ts.union,ts.plot,ts.intersect,toeplitz,terms.formula,% -termplot,t.test,supsmu,summary.stepfun,summary.manova,% -summary.lm,summary.glm,summary.aov,stl,stepfun,% -stat.anova,splinefunH,spectrum,spec.taper,spec.pgram,% -spec.ar,sortedXyData,smoothEnds,smooth.spline,smooth,% -simulate,sigma,shapiro.test,setNames,selfStart,% -se.contrast,screeplot,scatter.smooth,runmed,rmultinom,% -residuals.lm,residuals.glm,reshape,reorder,rect.hclust,% -read.ftable,rWishart,r2dtable,quasipoisson,quasibinomial,% -quade.test,qbirthday,prop.trend.test,prop.test,promax,% -printCoefmat,princomp,predict.lm,predict.glm,prcomp,% -ppr,power.t.test,power.prop.test,power.anova.test,polym,% -poisson.test,plot.ts,plot.stepfun,plot.spec.phase,plot.spec.coherency,% -plot.ecdf,plclust,pbirthday,pairwise.wilcox.test,pairwise.table,% -pairwise.t.test,pairwise.prop.test,pacf,p.adjust.methods,p.adjust,% -order.dendrogram,optimHess,oneway.test,numericDeriv,nobs,% -nls.control,nls,nlminb,naresid,naprint,% -napredict,na.pass,na.omit,na.fail,na.exclude,% -na.contiguous,na.action,mood.test,monthplot,model.weights,% -model.tables,model.response,model.offset,model.matrix.lm,model.matrix.default,% -model.matrix,model.frame.default,model.frame,model.extract,medpolish,% -median.default,mcnemar.test,mauchly.test,mantelhaen.test,manova,% -makepredictcall,makeARIMA,make.link,ls.print,ls.diag,% -logLik,loess.smooth,loess.control,loess,loadings,% -lm.wfit,lm.influence,lm.fit,line,lag.plot,% -lag,ksmooth,ks.test,kruskal.test,knots,% -kmeans,kernel,kernapply,isoreg,is.tskernel,% -is.ts,is.stepfun,is.mts,is.leaf,is.empty.model,% -inverse.gaussian,interaction.plot,integrate,influence.measures,heatmap,% -hclust,hatvalues,glm.fit,glm.control,get_all_vars,% -getInitial,getCall,friedman.test,fligner.test,fitted.values,% -fisher.test,filter,factor.scope,factanal,expand.model.frame,% -estVar,embed,eff.aovlist,ecdf,dummy.coef.lm,% -dummy.coef,drop.terms,drop.scope,dmultinom,dist,% -diffinv,dfbeta,df.residual,df.kernel,deriv3,% -density.default,dendrapply,delete.response,decompose,cutree,% -cpgram,cov2cor,cov.wt,cor.test,cophenetic,% -cooks.distance,contrasts<-,contr.treatment,contr.sum,contr.poly,% -contr.helmert,contr.SAS,constrOptim,confint.lm,confint.default,% -confint,complete.cases,cmdscale,chisq.test,ccf,% -case.names,cancor,bw.ucv,bw.nrd0,bw.nrd,% -bw.bcv,bw.SJ,biplot,binom.test,bartlett.test,% -bandwidth.kernel,asOneSidedFormula,as.ts,as.stepfun,as.hclust,% -as.formula,as.dist,as.dendrogram,arima0.diag,arima0,% -arima.sim,arima,ar.yw,ar.ols,ar.mle,% -ar.burg,ar,ansari.test,aggregate.ts,aggregate.data.frame,% -addmargins,add.scope,acf2AR,acf,TukeyHSD,% -StructTS,SSweibull,SSmicmen,SSlogis,SSgompertz,% -SSfpl,SSfol,SSbiexp,SSasympOrig,SSasympOff,% -SSasymp,SSD,PP.test,NLSstRtAsymptote,NLSstLfAsymptote,% -NLSstClosestX,NLSstAsymptotic,KalmanSmooth,KalmanRun,KalmanLike,% -KalmanForecast,HoltWinters,Box.test,BIC,ARMAtoMA,% -ARMAacf,AIC% -},% -keywordstyle={[4]{\bf\color{RRecomdcolor}}},% -% -% -------------------------- -% Registration of package graphics [recommended or base] -% -------------------------- -morekeywords={[5]xspline,text.default,stripchart,strheight,split.screen,% -spineplot,smoothScatter,rasterImage,polypath,points.default,% -plot.xy,plot.window,plot.new,plot.function,plot.design,% -plot.default,pie,panel.smooth,pairs.default,lines.default,% -layout.show,image.default,hist.default,grconvertY,grconvertX,% -fourfoldplot,filled.contour,erase.screen,dotchart,contour.default,% -co.intervals,close.screen,clip,cdplot,boxplot.matrix,% -boxplot.default,barplot.default,axis.POSIXct,axis.Date,axTicks,% -assocplot,Axis% -},% -keywordstyle={[5]{\bf\color{RRecomdcolor}}},% -% -% -------------------------- -% Registration of package grDevices [recommended or base] -% -------------------------- -morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,windowsFonts,% -windowsFont,windows.options,windows,win.print,win.metafile,% -win.graph,trans3d,topo.colors,tiff,terrain.colors,% -svg,setPS,setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,% -savePlot,rgb2hsv,replayPlot,recordPlot,recordGraphics,% -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,grSoftVersion,% -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}}},% -% -% -------------------------- -% Registration of package utils [recommended or base] -% -------------------------- -morekeywords={[7]zip.unpack,writeClipboard,write.table,write.socket,write.csv2,% -write.csv,winProgressBar,winMenuNames,winMenuItems,winMenuDelItem,% -winMenuDel,winMenuAddItem,winMenuAdd,winDialogString,winDialog,% -win.version,vignette,url.show,upgrade,update.packages,% -update.packageStatus,unzip,untar,unstack,undebugcall,% -type.convert,txtProgressBar,toLatex,toBibtex,timestamp,% -tar,tail.matrix,tail,suppressForeignCheck,summaryRprof,% -strcapture,strOptions,str,stack,shortPathName,% -setWindowTitle,setWinProgressBar,setTxtProgressBar,setStatusBar,setRepositories,% -setInternet2,setBreakpoint,sessionInfo,select.list,savehistory,% -rtags,removeSource,remove.packages,relist,recover,% -readRegistry,readClipboard,readCitationFile,read.table,read.socket,% -read.fwf,read.fortran,read.delim2,read.delim,read.csv2,% -read.csv,read.DIF,rc.status,rc.settings,rc.options,% -rc.getOption,promptPackage,promptImport,promptData,process.events,% -personList,person,packageVersion,packageStatus,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,% -isS3stdGeneric,isS3method,is.relistable,installed.packages,install.packages,% -hsearch_db_keywords,hsearch_db_concepts,hsearch_db,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,fileSnapshot,% -file.edit,dump.frames,download.packages,download.file,debugcall,% -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,changedFiles,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}}},% -% -% -------------------------- -% Registration of package datasets [recommended or base] -% -------------------------- -morekeywords={[8]women,warpbreaks,volcano,uspop,trees,% -treering,swiss,sunspots,sunspot.year,sunspot.month,% -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,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,UScitiesD,% -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}}},% -% -% -------------------------- -% Registration of package methods [recommended or base] -% -------------------------- -morekeywords={[9]validSlotNames,validObject,unRematchDefinition,tryNew,traceOn,% -traceOff,testVirtual,testInheritedMethods,superClassDepth,substituteFunctionArgs,% -substituteDirect,slotsFromS3,slotNames,slot<-,slot,% -signature,sigToEnv,showMlist,showMethods,showExtends,% -showDefault,showClass,setValidity,setReplaceMethod,setRefClass,% -setPrimitiveMethods,setPackageName,setOldClass,setMethod,setLoadActions,% -setLoadAction,setIs,setGroupGeneric,setGenericImplicit,setGeneric,% -setDataPart,setClassUnion,setClass,setAs,selectSuperClasses,% -selectMethod,seemsS4Object,sealClass,resetGeneric,resetClass,% -requireMethods,representation,removeMethodsObject,removeMethods,removeMethod,% -removeGeneric,removeClass,rematchDefinition,registerImplicitGenerics,reconcilePropertiesAndPrototype,% -rbind2,prototype,promptMethods,promptClass,prohibitGeneric,% -possibleExtends,packageSlot<-,packageSlot,newEmptyObject,newClassRepresentation,% -newBasic,multipleClasses,mlistMetaName,missingArg,methodsPackageMetaName,% -methodSignatureMatrix,method.skeleton,metaNameUndo,mergeMethods,matchSignature,% -makeStandardGeneric,makePrototypeFromClassDef,makeMethodsList,makeGeneric,makeExtends,% -makeClassRepresentation,loadMethod,listFromMlist,listFromMethods,linearizeMlist,% -languageEl<-,languageEl,isXS3Class,isVirtualClass,isSealedMethod,% -isSealedClass,isRematched,isGroup,isGrammarSymbol,isGeneric,% -isClassUnion,isClassDef,isClass,insertSource,insertMethod,% -insertClassMethods,initialize,initRefFields,initFieldArgs,inheritedSlotNames,% -implicitGeneric,hasMethods,hasMethod,hasLoadAction,hasArg,% -getVirtual,getValidity,getSubclasses,getSlots,getRefClass,% -getPrototype,getProperties,getPackageName,getMethodsMetaData,getMethodsForDispatch,% -getMethods,getMethod,getLoadActions,getGroupMembers,getGroup,% -getGenerics,getGeneric,getFunction,getExtends,getDataPart,% -getClasses,getClassPackage,getClassName,getClassDef,getClass,% -getAllSuperClasses,getAllMethods,getAccess,generic.skeleton,functionBody<-,% -functionBody,formalArgs,fixPre1.8,findUnique,findMethods,% -findMethodSignatures,findMethod,findFunction,findClass,finalDefaultMethod,% -externalRefMethod,extends,existsMethod,existsFunction,evalqOnLoad,% -evalSource,evalOnLoad,emptyMethodsList,empty.dump,elNamed<-,% -elNamed,el<-,el,dumpMethods,dumpMethod,% -doPrimitiveMethod,defaultPrototype,defaultDumpName,conformMethod,completeSubclasses,% -completeExtends,completeClassDefinition,coerce<-,coerce,classesToAM,% -className,classMetaName,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}}},% -% -% -------------------------- -% Registration of package base [recommended or base] -% -------------------------- -morekeywords={[10]xzfile,xtfrm.numeric_version,xtfrm.factor,xtfrm.difftime,xtfrm.default,% -xtfrm.Surv,xtfrm.POSIXlt,xtfrm.POSIXct,xtfrm.Date,xtfrm.AsIs,% -xtfrm,xpdrows.data.frame,xor.octmode,xor.hexmode,writeLines,% -writeChar,writeBin,write.dcf,within.list,within.data.frame,% -within,withVisible,withRestarts,withCallingHandlers,with.default,% -with,which.min,which.max,weekdays.POSIXt,weekdays.Date,% -weekdays,version,vapply,validUTF8,validEnc,% -utf8ToInt,upper.tri,unz,untracemem,unsplit,% -unserialize,unlockBinding,unloadNamespace,unix.time,units<-.difftime,% -units<-,units.difftime,units,unique.warnings,unique.numeric_version,% -unique.matrix,unique.default,unique.data.frame,unique.array,unique.POSIXlt,% -tryCatch,truncate.connection,truncate,trunc.POSIXt,trunc.Date,% -trimws,transform.default,transform.data.frame,tracingState,tracemem,% -toupper,topenv,tolower,toString.default,toString,% -textConnectionValue,textConnection,testPlatformEquivalence,tempdir,tcrossprod,% -taskCallbackManager,tanpi,t.default,t.data.frame,system2,% -system.time,system.file,sys.status,sys.source,sys.save.image,% -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.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,strrep,strptime,% -strftime,storage.mode<-,storage.mode,stopifnot,stdout,% -stdin,stderr,startsWith,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,% -sinpi,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,% -returnValue,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.eigen,% -print.difftime,print.default,print.data.frame,print.connection,print.condition,% -print.by,print.POSIXlt,print.POSIXct,print.NativeRoutineList,print.Dlist,% -print.Date,print.DLLRegisteredRoutines,print.DLLInfoList,print.DLLInfo,print.AsIs,% -prettyNum,pretty.default,pos.to.env,pmin.int,pmax.int,% -pipe,pi,pcre_config,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,makeActiveBinding,% -make.unique,make.names,lower.tri,logb,lockEnvironment,% -lockBinding,loadingNamespaceInfo,loadedNamespaces,loadNamespace,list2env,% -list.files,list.dirs,library.dynam.unload,library.dynam,libcurlVersion,% -lfactorial,levels<-.factor,levels<-,levels.default,letters,% -lengths,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,isNamespaceLoaded,% -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<-.numeric_version,% -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,icuGetCollate,iconvlist,iconv,% -gzfile,gzcon,grouping,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,% [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 1109 From noreply at r-forge.r-project.org Mon Apr 25 17:37:46 2016 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Apr 2016 17:37:46 +0200 (CEST) Subject: [Distr-commits] r1110 - branches/distr-2.7/pkg/SweaveListingUtils/inst branches/distr-2.7/pkg/SweaveListingUtils/man pkg/SweaveListingUtils pkg/SweaveListingUtils/inst pkg/SweaveListingUtils/man pkg/SweaveListingUtils/tests/Examples Message-ID: <20160425153746.B837E186959@r-forge.r-project.org> Author: ruckdeschel Date: 2016-04-25 17:37:46 +0200 (Mon, 25 Apr 2016) New Revision: 1110 Modified: branches/distr-2.7/pkg/SweaveListingUtils/inst/MASKING branches/distr-2.7/pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/inst/MASKING pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd pkg/SweaveListingUtils/man/changeKeywordstyles.Rd pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save Log: SweaveListingUTils --- now I think I missed a trailing \n ... Modified: branches/distr-2.7/pkg/SweaveListingUtils/inst/MASKING =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/inst/MASKING 2016-04-25 14:33:58 UTC (rev 1109) +++ branches/distr-2.7/pkg/SweaveListingUtils/inst/MASKING 2016-04-25 15:37:46 UTC (rev 1110) @@ -26,4 +26,4 @@ *** non-intentional masking: *** -... nothing discovered so far ... \ No newline at end of file +... nothing discovered so far ... Modified: branches/distr-2.7/pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2016-04-25 14:33:58 UTC (rev 1109) +++ branches/distr-2.7/pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2016-04-25 15:37:46 UTC (rev 1110) @@ -15,14 +15,14 @@ \details{ \tabular{ll}{ Package: \tab SweaveListingUtils \cr -Version: \tab 0.7.1 \cr -Date: \tab 2015-11-07 \cr +Version: \tab 0.7.5 \cr +Date: \tab 2016-04-25 \cr Depends: \tab R(>= 2.14.0), startupmsg \cr Suggests: \tab distr, MASS, survival, distrEx, Matrix, splines \cr Imports: \tab methods \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr -SVNRevision: \tab 1080 \cr +SVNRevision: \tab 1110 \cr } TeX-package \file{listings}, confer \url{http://www.ctan.org/tex-archive/macros/latex/contrib/listings/}, Modified: branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 14:33:58 UTC (rev 1109) +++ branches/distr-2.7/pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 15:37:46 UTC (rev 1110) @@ -129,7 +129,8 @@ \examples{ \donttest{SweaveListingPreparations() SweaveListingPreparations(pkv="2.1") -}} +} +} \keyword{utilities} Modified: branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 14:33:58 UTC (rev 1109) +++ branches/distr-2.7/pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 15:37:46 UTC (rev 1110) @@ -70,6 +70,7 @@ changeKeywordstyles(pkgs = c("distr","distrEx"), keywordstyles = paste("\\\\bfseries\\\\color{",c("green","blue"),"}", collapse="", sep = "")) -}} +} +} % \keyword{utilities} Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2016-04-25 14:33:58 UTC (rev 1109) +++ pkg/SweaveListingUtils/DESCRIPTION 2016-04-25 15:37:46 UTC (rev 1110) @@ -4,7 +4,7 @@ and for including R / Rd source file (snippets) copied from R-forge in its most recent version (or another URL) thereby avoiding inconsistencies between vignette and documented source code. -Version: 0.7.4 +Version: 0.7.5 Encoding: latin1 Date: 2016-04-25 Depends: R(>= 2.14.0), startupmsg Modified: pkg/SweaveListingUtils/inst/MASKING =================================================================== --- pkg/SweaveListingUtils/inst/MASKING 2016-04-25 14:33:58 UTC (rev 1109) +++ pkg/SweaveListingUtils/inst/MASKING 2016-04-25 15:37:46 UTC (rev 1110) @@ -26,4 +26,4 @@ *** non-intentional masking: *** -... nothing discovered so far ... \ No newline at end of file +... nothing discovered so far ... Modified: pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd =================================================================== --- pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2016-04-25 14:33:58 UTC (rev 1109) +++ pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2016-04-25 15:37:46 UTC (rev 1110) @@ -15,14 +15,14 @@ \details{ \tabular{ll}{ Package: \tab SweaveListingUtils \cr -Version: \tab 0.7 \cr -Date: \tab 2016-04-23 \cr +Version: \tab 0.7.5 \cr +Date: \tab 2016-04-25 \cr Depends: \tab R(>= 2.14.0), startupmsg \cr Suggests: \tab distr, MASS, survival, distrEx, Matrix, splines \cr Imports: \tab methods \cr LazyLoad: \tab yes \cr License: \tab LGPL-3 \cr -SVNRevision: \tab 1087 \cr +SVNRevision: \tab 1110 \cr } TeX-package \file{listings}, confer \url{http://www.ctan.org/tex-archive/macros/latex/contrib/listings/}, Modified: pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd =================================================================== --- pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 14:33:58 UTC (rev 1109) +++ pkg/SweaveListingUtils/man/SweaveListingPreparations.Rd 2016-04-25 15:37:46 UTC (rev 1110) @@ -129,7 +129,8 @@ \examples{ \donttest{SweaveListingPreparations() SweaveListingPreparations(pkv="2.1") -}} +} +} \keyword{utilities} Modified: pkg/SweaveListingUtils/man/changeKeywordstyles.Rd =================================================================== --- pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 14:33:58 UTC (rev 1109) +++ pkg/SweaveListingUtils/man/changeKeywordstyles.Rd 2016-04-25 15:37:46 UTC (rev 1110) @@ -70,6 +70,7 @@ changeKeywordstyles(pkgs = c("distr","distrEx"), keywordstyles = paste("\\\\bfseries\\\\color{",c("green","blue"),"}", collapse="", sep = "")) -}} +} +} % \keyword{utilities} Modified: pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save =================================================================== --- pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-25 14:33:58 UTC (rev 1109) +++ pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2016-04-25 15:37:46 UTC (rev 1110) @@ -30,7 +30,7 @@ :SweaveListingUtils> Utilities for Sweave Together with :SweaveListingUtils> TeX 'listings' Package (version -:SweaveListingUtils> 0.7.4) +:SweaveListingUtils> 0.7.5) :SweaveListingUtils> :SweaveListingUtils> NOTE: Support for this package :SweaveListingUtils> will stop soon. @@ -106,9 +106,10 @@ *** non-intentional masking: *** -... nothing discovered so far ...> +... nothing discovered so far ... > > +> > cleanEx() > nameEx("SweaveListingOptions") > ### * SweaveListingOptions @@ -317,6 +318,7 @@ > > > +> > cleanEx() > nameEx("changeKeywordstyles") > ### * changeKeywordstyles @@ -334,6 +336,7 @@ Loading required package: MASS > > +> > cleanEx() detaching 'package:MASS' @@ -2400,7 +2403,7 @@ > ### > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 1.23 0.21 2.83 NA NA +Time elapsed: 1.23 0.27 2.86 NA NA > grDevices::dev.off() null device 1