From noreply at r-forge.r-project.org Thu Apr 20 22:45:25 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 20 Apr 2017 22:45:25 +0200 (CEST) Subject: [Distr-commits] r1131 - branches/distr-2.7/pkg/distr branches/distr-2.7/pkg/distr/R branches/distr-2.7/pkg/distr/demo branches/distr-2.7/pkg/distr/man branches/distr-2.7/pkg/distr/src branches/distr-2.7/pkg/distr/vignettes branches/distr-2.7/pkg/distrDoc/vignettes branches/distr-2.7/pkg/distrEllipse/man branches/distr-2.7/pkg/distrEx branches/distr-2.7/pkg/distrEx/R branches/distr-2.7/pkg/distrEx/man branches/distr-2.7/pkg/distrEx/src branches/distr-2.7/pkg/distrMod/man branches/distr-2.7/pkg/distrMod/vignettes branches/distr-2.7/pkg/distrRmetrics/man branches/distr-2.7/pkg/distrSim/man branches/distr-2.7/pkg/distrTeach/man branches/distr-2.7/pkg/utils pkg/distr pkg/distr/R pkg/distr/demo pkg/distr/man pkg/distr/src pkg/distr/vignettes Message-ID: <20170420204525.DACF6188D4F@r-forge.r-project.org> Author: ruckdeschel Date: 2017-04-20 22:45:25 +0200 (Thu, 20 Apr 2017) New Revision: 1131 Added: branches/distr-2.7/pkg/distr/src/distr.h branches/distr-2.7/pkg/distr/src/init.c pkg/distr/src/distr.h pkg/distr/src/init.c Modified: branches/distr-2.7/pkg/distr/NAMESPACE branches/distr-2.7/pkg/distr/R/Convpow.R branches/distr-2.7/pkg/distr/R/flat.R branches/distr-2.7/pkg/distr/R/internals-qqplot.R branches/distr-2.7/pkg/distr/demo/nFoldConvolution.R branches/distr-2.7/pkg/distr/man/0distr-package.Rd branches/distr-2.7/pkg/distr/man/sqrt-methods.Rd branches/distr-2.7/pkg/distr/src/ks.c branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd branches/distr-2.7/pkg/distrEx/NAMESPACE branches/distr-2.7/pkg/distrEx/R/distrExIntegrate.R branches/distr-2.7/pkg/distrEx/man/0distrEx-package.Rd branches/distr-2.7/pkg/distrEx/src/GLaw.c branches/distr-2.7/pkg/distrMod/man/0distrMod-package.Rd branches/distr-2.7/pkg/distrMod/man/returnlevelplot.Rd branches/distr-2.7/pkg/distrMod/vignettes/distrMod.Rnw branches/distr-2.7/pkg/distrRmetrics/man/0distrRmetrics-package.Rd branches/distr-2.7/pkg/distrSim/man/0distrSim-package.Rd branches/distr-2.7/pkg/distrTeach/man/0distrTeach-package.Rd branches/distr-2.7/pkg/utils/finde.R pkg/distr/DESCRIPTION pkg/distr/R/Convpow.R pkg/distr/R/flat.R pkg/distr/R/internals-qqplot.R pkg/distr/demo/nFoldConvolution.R pkg/distr/man/0distr-package.Rd pkg/distr/man/sqrt-methods.Rd pkg/distr/src/ks.c pkg/distr/vignettes/newDistributions.Rnw Log: some fixes after a mail by K. Hornik: distr (in branch and in trunk): registered native code; fixed usage issue with sqrt, fixed http(s)-warning; fixed [[]] issue in flat.R distrEx (in branch only): registered native code; all (in branch only) fixed http(s) code Modified: branches/distr-2.7/pkg/distr/NAMESPACE =================================================================== --- branches/distr-2.7/pkg/distr/NAMESPACE 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/NAMESPACE 2017-04-20 20:45:25 UTC (rev 1131) @@ -1,4 +1,4 @@ -useDynLib("distr") +useDynLib("distr", .registration = TRUE, .fixes = "C_") import("methods") import("stats") importFrom("grDevices", "dev.list", "dev.new", "xy.coords") Modified: branches/distr-2.7/pkg/distr/R/Convpow.R =================================================================== --- branches/distr-2.7/pkg/distr/R/Convpow.R 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/R/Convpow.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -4,14 +4,9 @@ ########################################################## ##implentation of Algorithm 3.4. of -# Kohl, M., Ruckdeschel, P., Stabla, T. (2005): -# General purpose convolution algorithm for distributions -# in S4-Classes by means of FFT. -# Technical report, Feb. 2005. Also available in -# http://www.uni-bayreuth.de/departments/math/org/mathe7/ -# /RUCKDESCHEL/pubs/comp.pdf +#P. Ruckdeschel, M. Kohl (2014): General Purpose Convolution Algorithm for +# Distributions in S4 Classes by Means of FFT. J. Statist. Softw. 59(4), 1-25. - setMethod("convpow", signature(D1 = "AbscontDistribution"), function(D1, N){ Modified: branches/distr-2.7/pkg/distr/R/flat.R =================================================================== --- branches/distr-2.7/pkg/distr/R/flat.R 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/R/flat.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -95,8 +95,8 @@ for(i in seq(length(mixDistr))) {if ( is(mixDistr[[i]],"UnivarMixingDistribution") && !is(mixDistr[[i]],"UnivarLebDecDistribution")) - mixDistr2[i] <- flat.mix(mixDistr[[i]]) - else mixDistr2[i] <- as(mixDistr[[i]],"UnivarLebDecDistribution") + mixDistr2[[i]] <- flat.mix(mixDistr[[i]]) + else mixDistr2[[i]] <- as(mixDistr[[i]],"UnivarLebDecDistribution") } erg <- do.call(flat.LCD, c(mixDistr2, alist(mixCoeff = mixCoeff))) simplifyD(erg) Modified: branches/distr-2.7/pkg/distr/R/internals-qqplot.R =================================================================== --- branches/distr-2.7/pkg/distr/R/internals-qqplot.R 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/R/internals-qqplot.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -86,13 +86,16 @@ .C("pkolmogorov2x", p = as.double(p0), as.integer(n), PACKAGE = "stats")$p }else function(p0,n){ - .Call("pKolmogorov2x", p0, n) #, PACKAGE = "stats") + .Call(C_pKolmogorov2x, #"pKolmogorov2x", + p0, n) #, PACKAGE = "stats") } .pks2 <- if(getRversion()<"2.16.0") function(x, tol){ - .C("pkstwo", as.integer(1), + .C("pkstwo", + as.integer(1), p = as.double(x), as.double(tol), PACKAGE = "stats")$p }else function(x, tol){ - .Call("pKS2", p = x, tol) #, PACKAGE = "stats") + .Call(C_pKS2, #"pKS2", + p = x, tol) #, PACKAGE = "stats") } Modified: branches/distr-2.7/pkg/distr/demo/nFoldConvolution.R =================================================================== --- branches/distr-2.7/pkg/distr/demo/nFoldConvolution.R 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/demo/nFoldConvolution.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -17,13 +17,9 @@ ## -- absolute continuous distribution -- ########################################################## -##implentation of Algorithm 3.4. of -# Kohl, M., Ruckdeschel, P., Stabla, T. (2005): -# General purpose convolution algorithm for distributions -# in S4-Classes by means of FFT. -# Technical report, Feb. 2005. Also available in -# http://www.uni-bayreuth.de/departments/math/org/mathe7/ -# /RUCKDESCHEL/pubs/comp.pdf +##implentation of Algorithm 3.4. of +#P. Ruckdeschel, M. Kohl (2014): General Purpose Convolution Algorithm for +# Distributions in S4 Classes by Means of FFT. J. Statist. Softw. 59(4), 1-25. setMethod("convpow", Modified: branches/distr-2.7/pkg/distr/man/0distr-package.Rd =================================================================== --- branches/distr-2.7/pkg/distr/man/0distr-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/man/0distr-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -3,7 +3,7 @@ \alias{distr} \docType{package} \title{ -distr -- Object Orientated Implementation of Distributions +distr -- Object Oriented Implementation of Distributions } \description{ \pkg{distr} provides a conceptual treatment of distributions by means of S4 @@ -335,7 +335,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} P. Ruckdeschel and M. Kohl (2014): General purpose convolution algorithm for distributions Modified: branches/distr-2.7/pkg/distr/man/sqrt-methods.Rd =================================================================== --- branches/distr-2.7/pkg/distr/man/sqrt-methods.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/man/sqrt-methods.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -6,7 +6,7 @@ \title{ Methods for Function sqrt in Package `distr' } \description{sqrt-methods using generalized inverses for p.s.d. matrices} -\usage{sqrt(x) +\usage{ \S4method{sqrt}{PosSemDefSymmMatrix}(x) } \arguments{ @@ -18,7 +18,7 @@ }} \author{Peter Ruckdeschel \email{peter.ruckdeschel at uni-oldenburg.de}} \seealso{ -\code{\link{solve}} } +\code{\link{solve}}} \keyword{algebra} \keyword{array} \concept{pseudo inverse} Added: branches/distr-2.7/pkg/distr/src/distr.h =================================================================== --- branches/distr-2.7/pkg/distr/src/distr.h (rev 0) +++ branches/distr-2.7/pkg/distr/src/distr.h 2017-04-20 20:45:25 UTC (rev 1131) @@ -0,0 +1,30 @@ +/* + * taken from R Core: /src/library/stats/src/init.c rev72233 + * with slight modifications by P. Ruckdeschel 2017-04-20 + */ + +/* + * R : A Computer Language for Statistical Data Analysis + * Copyright (C) 2012 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, a copy is available at + * https://www.R-project.org/Licenses/ + */ + +#include +#include + +SEXP pSmirnov2x(SEXP statistic, SEXP snx, SEXP sny); +SEXP pKolmogorov2x(SEXP statistic, SEXP sn); +SEXP pKS2(SEXP sn, SEXP stol); Added: branches/distr-2.7/pkg/distr/src/init.c =================================================================== --- branches/distr-2.7/pkg/distr/src/init.c (rev 0) +++ branches/distr-2.7/pkg/distr/src/init.c 2017-04-20 20:45:25 UTC (rev 1131) @@ -0,0 +1,46 @@ +/* + * taken from R Core: /src/library/stats/src/init.c rev72233 + * with slight modifications by P. Ruckdeschel 2017-04-20 + */ + + /* + * R : A Computer Language for Statistical Data Analysis + * Copyright (C) 2001-2017 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, a copy is available at + * https://www.R-project.org/Licenses/ + */ + +#include +#include +#include +#include "distr.h" + +#define CALLDEF(name, n) {#name, (DL_FUNC) &name, n} + + +static const R_CallMethodDef R_CallDef[] = { + CALLDEF(pSmirnov2x, 3), + CALLDEF(pKolmogorov2x, 2), + CALLDEF(pKS2, 2), + {NULL, NULL, 0} +}; + +void attribute_visible R_init_distr(DllInfo *dll) +{ + R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL); + R_useDynamicSymbols(dll, FALSE); + R_forceSymbols(dll, TRUE); + +} Modified: branches/distr-2.7/pkg/distr/src/ks.c =================================================================== --- branches/distr-2.7/pkg/distr/src/ks.c 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/src/ks.c 2017-04-20 20:45:25 UTC (rev 1131) @@ -29,6 +29,7 @@ #include #include #include /* constants */ +#include static double K(int n, double d); static void m_multiply(double *A, double *B, double *C, int m); @@ -245,7 +246,7 @@ } /* Two-sided two-sample */ -SEXP pSmirnov2x(SEXP statistic, SEXP snx, SEXP sny) +SEXP attribute_hidden pSmirnov2x(SEXP statistic, SEXP snx, SEXP sny) { int nx = asInteger(snx), ny = asInteger(sny); double st = asReal(statistic); @@ -253,7 +254,7 @@ } /* Two-sample two-sided asymptotic distribution */ -SEXP pKS2(SEXP statistic, SEXP stol) +SEXP attribute_hidden pKS2(SEXP statistic, SEXP stol) { int n = LENGTH(statistic); double tol = asReal(stol); @@ -264,7 +265,7 @@ /* The two-sided one-sample 'exact' distribution */ -SEXP pKolmogorov2x(SEXP statistic, SEXP sn) +SEXP attribute_hidden pKolmogorov2x(SEXP statistic, SEXP sn) { int n = asInteger(sn); double st = asReal(statistic), p; Modified: branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw =================================================================== --- branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw 2017-04-20 20:45:25 UTC (rev 1131) @@ -203,7 +203,7 @@ If you would like to create new parametric distributions, using already implemented {\tt r}, {\tt d}, {\tt p}, and {\tt q} functions (e.g.\ implementing additional distributions realized in another -\href{http://cran.r-project.org}{\tt CRAN} package), +\href{https://cran.r-project.org}{\tt CRAN} package), you should probably envisage introducing new distribution {\tt S4} (sub-)classes and hence better look at the implementation of some discrete and continuous parametric distribution classes in package \pkg{distr}. @@ -399,7 +399,7 @@ Ruckdeschel P., Kohl M., Stabla T., and Camphausen F. (2006): \newblock {S4 Classes for Distributions.} \newblock {\em R-News\/}, {\bf 6}(2): 10--13. -\newblock http://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf +\newblock https://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf %\newblock See also {http://www.uni-bayreuth.de/departments/math/org/mathe7/RUCKDESCHEL/pubs/distr.pdf} \end{thebibliography} Modified: branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw 2017-04-20 20:45:25 UTC (rev 1131) @@ -178,7 +178,7 @@ \pkg{RobExtremes}. This concerns the Gumbel, Weibull, Pareto distributions. %\noindent The latter two of them require package \pkg{setRNG} by %\href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert} -%to be installed from \href{http://cran.r-project.org/mirrors.html}{\tt CRAN}. +%to be installed from \href{https://cran.r-project.org/mirrors.html}{\tt CRAN}. % \\ %\noindent Additionally, mainly contributed by \cite{MK:05}, in \pkg{distrEx} we @@ -2765,7 +2765,7 @@ In package \pkg{distrSim}, and conseqently also in package \pkg{distrTEst} we use \href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert's} package \pkg{setRNG} -to be installed from \href{http://cran.r-project.org/mirrors.html}{\tt CRAN} +to be installed from \href{https://cran.r-project.org/mirrors.html}{\tt CRAN} for the control of the seed of the random number generator in our simulation classes. More precisely, for our version $\le$ {\tt 1.6} we need his @@ -2774,7 +2774,7 @@ From package version {\tt 1.7}/{\tt 0.4-3} on, we also need package \pkg{startupmsg} by the first of the present authors, which also is available - on \href{http://cran.r-project.org/mirrors.html}{\tt CRAN}. + on \href{https://cran.r-project.org/mirrors.html}{\tt CRAN}. \subsection{License} This software is distributed under the terms of the GNU GENERAL @@ -3626,7 +3626,7 @@ Ruckdeschel P., Kohl M., Stabla T., and Camphausen F. (2006): \newblock {S4 Classes for Distributions.} \newblock {\em R-News\/}, {\bf 6}(2): 10--13. -\newblock http://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf +\newblock https://CRAN.R-project.org/doc/Rnews/Rnews\_2006-2.pdf %\newblock See also {http://www.uni-bayreuth.de/departments/math/org/mathe7/RUCKDESCHEL/pubs/distr.pdf} \end{thebibliography} Modified: branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd =================================================================== --- branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrEllipse/man/0distrEllipse-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -101,7 +101,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} A vignette for packages \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, \pkg{distrEx}, \pkg{distrTeach}, \pkg{distrMod}, and \pkg{distrEllipse} Modified: branches/distr-2.7/pkg/distrEx/NAMESPACE =================================================================== --- branches/distr-2.7/pkg/distrEx/NAMESPACE 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrEx/NAMESPACE 2017-04-20 20:45:25 UTC (rev 1131) @@ -1,4 +1,4 @@ -useDynLib("distrEx") +useDynLib("distrEx", .registration = TRUE, .fixes = "C_") importFrom("stats", "dnorm", "integrate", "optimize", "pbinom", "pchisq", "pexp", "pnorm", "ppois", "qcauchy", "qnorm", "uniroot") Modified: branches/distr-2.7/pkg/distrEx/R/distrExIntegrate.R =================================================================== --- branches/distr-2.7/pkg/distrEx/R/distrExIntegrate.R 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrEx/R/distrExIntegrate.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -40,9 +40,10 @@ W <- numeric(n) # mm<-dyn.load("G:/rtest/GLaw.dll") - erg<-.C("gauleg",n = as.integer(n),eps = as.double(.Machine$double.eps), - A = as.double(A),W = as.double(W), PACKAGE = "distrEx") + erg<-.C(C_gauleg,n = as.integer(n),eps = as.double(.Machine$double.eps), + A = as.double(A),W = as.double(W)) #, PACKAGE = "distrEx") ### PACKAGE ARGUMENT added P.R. 270507 + #### removed again 200417 / used registered symbol instead # dyn.unload("G:/rtest/GLaw.dll") # # P.R. 20140810: .Call interface instead of .C interface Modified: branches/distr-2.7/pkg/distrEx/man/0distrEx-package.Rd =================================================================== --- branches/distr-2.7/pkg/distrEx/man/0distrEx-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrEx/man/0distrEx-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -222,7 +222,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} %a more detailed manual for \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, and \pkg{distrEx} may be downloaded from %\url{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/distr.pdf}\cr Modified: branches/distr-2.7/pkg/distrEx/src/GLaw.c =================================================================== --- branches/distr-2.7/pkg/distrEx/src/GLaw.c 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrEx/src/GLaw.c 2017-04-20 20:45:25 UTC (rev 1131) @@ -3,8 +3,12 @@ #include #include #include /* constants */ +#include +#include -void gauleg(int *n, double *eps, double *A, double *W) +#define C_DEF(name, n) {#name, (DL_FUNC) &name, n} + +void attribute_hidden gauleg(int *n, double *eps, double *A, double *W) { int i,j, m=((*n)+1)/2; double z1,z,pp,p1,p2,p3; for(i=1;i<=m;i++){ z=cos(PI*(i-0.25)/((*n)+0.5)); @@ -26,6 +30,21 @@ } } +/* P.R. 20170427: register routine */ + +static const R_CMethodDef R_CDef[] = { + C_DEF(gauleg, 4), + {NULL, NULL, 0} +}; + +void attribute_visible R_init_distrEx(DllInfo *dll) +{ + R_registerRoutines(dll, R_CDef, NULL, NULL, NULL); + R_useDynamicSymbols(dll, FALSE); + R_forceSymbols(dll, TRUE); + +} + /* P.R. 20140810: Yet to be tested: preparation for .Call - interface SEXP Gauleg(SEXP nFromR, SEXP epsFromR) Modified: branches/distr-2.7/pkg/distrMod/man/0distrMod-package.Rd =================================================================== --- branches/distr-2.7/pkg/distrMod/man/0distrMod-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrMod/man/0distrMod-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -297,7 +297,7 @@ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} A vignette for packages \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, and \pkg{distrEx} is included into the mere documentation package \pkg{distrDoc} Modified: branches/distr-2.7/pkg/distrMod/man/returnlevelplot.Rd =================================================================== --- branches/distr-2.7/pkg/distrMod/man/returnlevelplot.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrMod/man/returnlevelplot.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -201,7 +201,7 @@ } \references{ ismev: An Introduction to Statistical Modeling of Extreme Values. R package - version 1.39. http://CRAN.R-project.org/package=ismev; original S functions + version 1.39. https://CRAN.R-project.org/package=ismev; original S functions written by Janet E. Heffernan with R port and R documentation provided by Alec G. Stephenson. (2012). Modified: branches/distr-2.7/pkg/distrMod/vignettes/distrMod.Rnw =================================================================== --- branches/distr-2.7/pkg/distrMod/vignettes/distrMod.Rnw 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrMod/vignettes/distrMod.Rnw 2017-04-20 20:45:25 UTC (rev 1131) @@ -160,7 +160,7 @@ \textbf{Availability } The current version of package~\pkg{distrMod} is 2.2 and can be found on the Comprehensive \proglang{R} Archive Network at -\url{http://CRAN.R-project.org/package=distrMod}. The development version of the distr-family is located at R-Forge; +\url{https://CRAN.R-project.org/package=distrMod}. The development version of the distr-family is located at R-Forge; see~\citet{RForge}. % ----------------------------------------------------------------------------- \subsection{Running examples}\label{examples} @@ -350,7 +350,7 @@ \textbf{Packages \pkg{distr} and \pkg{distrEx} } Much of our infrastructure relies on our \proglang{R} packages \pkg{distr} and \pkg{distrEx} available on -\href{http://cran.r-project.org/}{\tt CRAN}. +\href{https://cran.r-project.org/}{\tt CRAN}. Package \pkg{distr}, see~\citet{distr,distrTeach}, aims to provide a conceptual treatment of distributions by means of \proglang{S}4 classes. A mother class \code{Distribution} is introduced with slots for a parameter and for functions Modified: branches/distr-2.7/pkg/distrRmetrics/man/0distrRmetrics-package.Rd =================================================================== --- branches/distr-2.7/pkg/distrRmetrics/man/0distrRmetrics-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrRmetrics/man/0distrRmetrics-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -88,7 +88,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} A vignette for packages \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, \pkg{distrEx}, \pkg{distrTeach}, \pkg{distrMod}, and \pkg{distrRmetrics} Modified: branches/distr-2.7/pkg/distrSim/man/0distrSim-package.Rd =================================================================== --- branches/distr-2.7/pkg/distrSim/man/0distrSim-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrSim/man/0distrSim-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -117,7 +117,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} A vignette for packages \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, and \pkg{distrEx} is included into the mere documentation package \pkg{distrDoc} and may be called by Modified: branches/distr-2.7/pkg/distrTeach/man/0distrTeach-package.Rd =================================================================== --- branches/distr-2.7/pkg/distrTeach/man/0distrTeach-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/distrTeach/man/0distrTeach-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -103,7 +103,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} %a more detailed manual for \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, and \pkg{distrTeach} may be downloaded from %\url{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/distr.pdf}\cr Modified: branches/distr-2.7/pkg/utils/finde.R =================================================================== --- branches/distr-2.7/pkg/utils/finde.R 2016-10-24 17:40:00 UTC (rev 1130) +++ branches/distr-2.7/pkg/utils/finde.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -20,7 +20,9 @@ } infind(dir) } +finde(x="http\\:/", dir ="C:/rtest/distr/branches/distr-2.7/pkg/distr/", rec=TRUE) #finde(x="Wow6432Node", dir ="C:/R/devel/src/gnuwin32", rec=TRUE, ext="") +finde(x="omega", dir ="C:/rtest/distr/branches/distr-2.7/pkg/distrMod/", rec=TRUE) #finde(x="getPos", dir ="C:/rtest/distr/branches/distr-2.4/pkg/distrMod/", rec=TRUE) finde(x="roptest\\(", dir ="C:/rtest/robast/branches/robast-0.9/pkg/ROptEst/", rec=TRUE) Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2016-10-24 17:40:00 UTC (rev 1130) +++ pkg/distr/DESCRIPTION 2017-04-20 20:45:25 UTC (rev 1131) @@ -1,6 +1,6 @@ Package: distr -Version: 2.6 -Date: 2016-04-23 +Version: 2.6.1 +Date: 2017-04-21 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 Modified: pkg/distr/R/Convpow.R =================================================================== --- pkg/distr/R/Convpow.R 2016-10-24 17:40:00 UTC (rev 1130) +++ pkg/distr/R/Convpow.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -4,14 +4,9 @@ ########################################################## ##implentation of Algorithm 3.4. of -# Kohl, M., Ruckdeschel, P., Stabla, T. (2005): -# General purpose convolution algorithm for distributions -# in S4-Classes by means of FFT. -# Technical report, Feb. 2005. Also available in -# http://www.uni-bayreuth.de/departments/math/org/mathe7/ -# /RUCKDESCHEL/pubs/comp.pdf +#P. Ruckdeschel, M. Kohl (2014): General Purpose Convolution Algorithm for +# Distributions in S4 Classes by Means of FFT. J. Statist. Softw. 59(4), 1-25. - setMethod("convpow", signature(D1 = "AbscontDistribution"), function(D1, N){ Modified: pkg/distr/R/flat.R =================================================================== --- pkg/distr/R/flat.R 2016-10-24 17:40:00 UTC (rev 1130) +++ pkg/distr/R/flat.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -95,8 +95,8 @@ for(i in seq(length(mixDistr))) {if ( is(mixDistr[[i]],"UnivarMixingDistribution") && !is(mixDistr[[i]],"UnivarLebDecDistribution")) - mixDistr2[i] <- flat.mix(mixDistr[[i]]) - else mixDistr2[i] <- as(mixDistr[[i]],"UnivarLebDecDistribution") + mixDistr2[[i]] <- flat.mix(mixDistr[[i]]) + else mixDistr2[[i]] <- as(mixDistr[[i]],"UnivarLebDecDistribution") } erg <- do.call(flat.LCD, c(mixDistr2, alist(mixCoeff = mixCoeff))) simplifyD(erg) Modified: pkg/distr/R/internals-qqplot.R =================================================================== --- pkg/distr/R/internals-qqplot.R 2016-10-24 17:40:00 UTC (rev 1130) +++ pkg/distr/R/internals-qqplot.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -86,13 +86,16 @@ .C("pkolmogorov2x", p = as.double(p0), as.integer(n), PACKAGE = "stats")$p }else function(p0,n){ - .Call("pKolmogorov2x", p0, n) #, PACKAGE = "stats") + .Call(C_pKolmogorov2x, #"pKolmogorov2x", + p0, n) #, PACKAGE = "stats") } .pks2 <- if(getRversion()<"2.16.0") function(x, tol){ - .C("pkstwo", as.integer(1), + .C("pkstwo", + as.integer(1), p = as.double(x), as.double(tol), PACKAGE = "stats")$p }else function(x, tol){ - .Call("pKS2", p = x, tol) #, PACKAGE = "stats") + .Call(C_pKS2, #"pKS2", + p = x, tol) #, PACKAGE = "stats") } Modified: pkg/distr/demo/nFoldConvolution.R =================================================================== --- pkg/distr/demo/nFoldConvolution.R 2016-10-24 17:40:00 UTC (rev 1130) +++ pkg/distr/demo/nFoldConvolution.R 2017-04-20 20:45:25 UTC (rev 1131) @@ -17,13 +17,9 @@ ## -- absolute continuous distribution -- ########################################################## -##implentation of Algorithm 3.4. of -# Kohl, M., Ruckdeschel, P., Stabla, T. (2005): -# General purpose convolution algorithm for distributions -# in S4-Classes by means of FFT. -# Technical report, Feb. 2005. Also available in -# http://www.uni-bayreuth.de/departments/math/org/mathe7/ -# /RUCKDESCHEL/pubs/comp.pdf +##implentation of Algorithm 3.4. of +#P. Ruckdeschel, M. Kohl (2014): General Purpose Convolution Algorithm for +# Distributions in S4 Classes by Means of FFT. J. Statist. Softw. 59(4), 1-25. setMethod("convpow", Modified: pkg/distr/man/0distr-package.Rd =================================================================== --- pkg/distr/man/0distr-package.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ pkg/distr/man/0distr-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -3,7 +3,7 @@ \alias{distr} \docType{package} \title{ -distr -- Object Orientated Implementation of Distributions +distr -- Object Oriented Implementation of Distributions } \description{ \pkg{distr} provides a conceptual treatment of distributions by means of S4 @@ -43,15 +43,15 @@ \details{ \tabular{ll}{ Package: \tab distr \cr -Version: \tab 2.6 \cr -Date: \tab 2016-04-23 \cr +Version: \tab 2.7 \cr +Date: \tab 2015-11-07 \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 1088 \cr +SVNRevision: \tab 1080 \cr }} @@ -335,7 +335,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} P. Ruckdeschel and M. Kohl (2014): General purpose convolution algorithm for distributions Modified: pkg/distr/man/sqrt-methods.Rd =================================================================== --- pkg/distr/man/sqrt-methods.Rd 2016-10-24 17:40:00 UTC (rev 1130) +++ pkg/distr/man/sqrt-methods.Rd 2017-04-20 20:45:25 UTC (rev 1131) @@ -6,7 +6,7 @@ \title{ Methods for Function sqrt in Package `distr' } \description{sqrt-methods using generalized inverses for p.s.d. matrices} -\usage{sqrt(x) +\usage{ \S4method{sqrt}{PosSemDefSymmMatrix}(x) } \arguments{ @@ -18,7 +18,7 @@ }} \author{Peter Ruckdeschel \email{peter.ruckdeschel at uni-oldenburg.de}} \seealso{ -\code{\link{solve}} } +\code{\link{solve}}} \keyword{algebra} \keyword{array} \concept{pseudo inverse} Added: pkg/distr/src/distr.h =================================================================== --- pkg/distr/src/distr.h (rev 0) +++ pkg/distr/src/distr.h 2017-04-20 20:45:25 UTC (rev 1131) @@ -0,0 +1,30 @@ +/* + * taken from R Core: /src/library/stats/src/init.c rev72233 + * with slight modifications by P. Ruckdeschel 2017-04-20 + */ + +/* + * R : A Computer Language for Statistical Data Analysis + * Copyright (C) 2012 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, a copy is available at + * https://www.R-project.org/Licenses/ + */ + +#include +#include + +SEXP pSmirnov2x(SEXP statistic, SEXP snx, SEXP sny); +SEXP pKolmogorov2x(SEXP statistic, SEXP sn); +SEXP pKS2(SEXP sn, SEXP stol); Added: pkg/distr/src/init.c =================================================================== --- pkg/distr/src/init.c (rev 0) +++ pkg/distr/src/init.c 2017-04-20 20:45:25 UTC (rev 1131) @@ -0,0 +1,46 @@ +/* + * taken from R Core: /src/library/stats/src/init.c rev72233 + * with slight modifications by P. Ruckdeschel 2017-04-20 + */ + + /* + * R : A Computer Language for Statistical Data Analysis + * Copyright (C) 2001-2017 The R Core Team. + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, a copy is available at + * https://www.R-project.org/Licenses/ + */ + +#include +#include +#include +#include "distr.h" + +#define CALLDEF(name, n) {#name, (DL_FUNC) &name, n} + + +static const R_CallMethodDef R_CallDef[] = { + CALLDEF(pSmirnov2x, 3), + CALLDEF(pKolmogorov2x, 2), + CALLDEF(pKS2, 2), + {NULL, NULL, 0} +}; + +void attribute_visible R_init_distr(DllInfo *dll) +{ + R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL); + R_useDynamicSymbols(dll, FALSE); + R_forceSymbols(dll, TRUE); + +} Modified: pkg/distr/src/ks.c =================================================================== [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/distr -r 1131 From noreply at r-forge.r-project.org Fri Apr 21 17:56:02 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 21 Apr 2017 17:56:02 +0200 (CEST) Subject: [Distr-commits] r1132 - branches/distr-2.7/pkg/SweaveListingUtils/vignettes branches/distr-2.7/pkg/distr branches/distr-2.7/pkg/distr/vignettes branches/distr-2.7/pkg/distrDoc/vignettes pkg/SweaveListingUtils pkg/SweaveListingUtils/vignettes pkg/distr pkg/distr/inst pkg/distr/man pkg/distr/vignettes pkg/distrDoc pkg/distrDoc/vignettes pkg/distrEx pkg/distrEx/R pkg/distrEx/inst pkg/distrEx/man pkg/distrEx/src Message-ID: <20170421155602.798F41883D1@r-forge.r-project.org> Author: ruckdeschel Date: 2017-04-21 17:56:01 +0200 (Fri, 21 Apr 2017) New Revision: 1132 Modified: branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw branches/distr-2.7/pkg/distr/NAMESPACE branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw pkg/distr/DESCRIPTION pkg/distr/NAMESPACE pkg/distr/inst/NEWS pkg/distr/man/0distr-package.Rd pkg/distr/vignettes/newDistributions.Rnw pkg/distrDoc/DESCRIPTION pkg/distrDoc/vignettes/distr.Rnw pkg/distrEx/DESCRIPTION pkg/distrEx/NAMESPACE pkg/distrEx/R/distrExIntegrate.R pkg/distrEx/inst/NEWS pkg/distrEx/man/0distrEx-package.Rd pkg/distrEx/src/GLaw.c Log: + [distr/Trunk] included new useDynLib directive in DESCRIPTION + updated NEWS files + registration of native routines in distrEx + updated address (Oldenburg) in several vignettes Modified: branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-20 20:45:25 UTC (rev 1131) +++ branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-21 15:56:01 UTC (rev 1132) @@ -96,9 +96,11 @@ %,version \pkgExversion} \author{\small Peter Ruckdeschel\thanks{Fraunhofer ITWM, Kaiserslautern} \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 Oldenburg University\\[-.5ex] +\small PO box 25 03\\[-.5ex] +\small 26111 Oldenburg (Oldb.)\\[-.5ex] \small Germany\\ \small e-Mail: \href{mailto:peter.ruckdeschel at uni-oldenburg.de}% {\small \tt {peter.ruckdeschel at uni-oldenburg.de}}\medskip\\ Modified: branches/distr-2.7/pkg/distr/NAMESPACE =================================================================== --- branches/distr-2.7/pkg/distr/NAMESPACE 2017-04-20 20:45:25 UTC (rev 1131) +++ branches/distr-2.7/pkg/distr/NAMESPACE 2017-04-21 15:56:01 UTC (rev 1132) @@ -1,4 +1,4 @@ -useDynLib("distr", .registration = TRUE, .fixes = "C_") +useDynLib(distr, .registration = TRUE, .fixes = "C_") import("methods") import("stats") importFrom("grDevices", "dev.list", "dev.new", "xy.coords") Modified: branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw =================================================================== --- branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw 2017-04-20 20:45:25 UTC (rev 1131) +++ branches/distr-2.7/pkg/distr/vignettes/newDistributions.Rnw 2017-04-21 15:56:01 UTC (rev 1132) @@ -85,13 +85,15 @@ % ------------------------------------------------------------------------------- \title{How to generate new distributions in packages \pkg{distr}, \pkg{distrEx}} %,version \pkgExversion} -\author{\small Peter Ruckdeschel\thanks{Fraunhofer ITWM, Kaiserslautern} +\author{\small Peter Ruckdeschel\thanks{Universit\"at Oldenburg, Oldenburg} \\[-.5ex] \small Matthias Kohl\thanks{FH Furtwangen} \smallskip\\ -\small Fraunhofer ITWM\\[-.5ex] -\small Fraunhofer Platz 1\\[-.5ex] -\small 67663 Kaiserslautern\\[-.5ex] +\small Institut f\"ur Mathematik\\[-0.5ex] +\small Fakult\"at V - Mathematik und Naturwissenschaften\\[-.5ex] +\small Carl von Ossietzky Universit\"at Oldenburg\\[-0.5ex] +\small PObox 2503\\[-.5ex] +\small 26111 Oldenburg (Oldb)\\[-.5ex] \small Germany\\ \small e-Mail: {\small \tt peter.ruckdeschel at uni-oldenburg.de}\medskip\\ \parbox[t]{5cm}{ Modified: branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw 2017-04-20 20:45:25 UTC (rev 1131) +++ branches/distr-2.7/pkg/distrDoc/vignettes/distr.Rnw 2017-04-21 15:56:01 UTC (rev 1132) @@ -115,6 +115,7 @@ \smallskip\\ \small Institute for Mathematics\\[-.5ex] \small School of Mathematics and Science\\[-.5ex] +\small Oldenburg University\\[-.5ex] \small PO box 25 03\\[-.5ex] \small 26111 Oldenburg (Oldb.)\\[-.5ex] \small Germany\\ Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/SweaveListingUtils/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) @@ -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: 0.7.5 +Version: 0.7.6 Encoding: latin1 -Date: 2016-04-25 +Date: 2017-04-21 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: 1108 \ No newline at end of file +SVNRevision: 1133 \ No newline at end of file Modified: pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw =================================================================== --- pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-21 15:56:01 UTC (rev 1132) @@ -96,9 +96,11 @@ %,version \pkgExversion} \author{\small Peter Ruckdeschel\thanks{Fraunhofer ITWM, Kaiserslautern} \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 Oldenburg University\\[-.5ex] +\small PO box 25 03\\[-.5ex] +\small 26111 Oldenburg (Oldb.)\\[-.5ex] \small Germany\\ \small e-Mail: \href{mailto:peter.ruckdeschel at uni-oldenburg.de}% {\small \tt {peter.ruckdeschel at uni-oldenburg.de}}\medskip\\ Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distr/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) @@ -1,5 +1,5 @@ Package: distr -Version: 2.6.1 +Version: 2.6.2 Date: 2017-04-21 Title: Object Oriented Implementation of Distributions Description: S4-classes and methods for distributions. @@ -19,4 +19,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1088 +SVNRevision: 1132 Modified: pkg/distr/NAMESPACE =================================================================== --- pkg/distr/NAMESPACE 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distr/NAMESPACE 2017-04-21 15:56:01 UTC (rev 1132) @@ -1,4 +1,4 @@ -useDynLib("distr") +useDynLib(distr, .registration = TRUE, .fixes = "C_") import("methods") import("stats") importFrom("grDevices", "dev.list", "dev.new", "xy.coords") Modified: pkg/distr/inst/NEWS =================================================================== --- pkg/distr/inst/NEWS 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distr/inst/NEWS 2017-04-21 15:56:01 UTC (rev 1132) @@ -8,6 +8,13 @@ information) ############## +v 2.6.2 +############## ++ fixed internals as triggered by mail "CRAN package distr" + by Kurt Hornik from Apr 07 2017; most importantly, we + registered native code and took out some usage example of sqrt(). + +############## v 2.6 ############## Modified: pkg/distr/man/0distr-package.Rd =================================================================== --- pkg/distr/man/0distr-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distr/man/0distr-package.Rd 2017-04-21 15:56:01 UTC (rev 1132) @@ -43,15 +43,15 @@ \details{ \tabular{ll}{ Package: \tab distr \cr -Version: \tab 2.7 \cr -Date: \tab 2015-11-07 \cr +Version: \tab 2.6.2 \cr +Date: \tab 2017-04-21 \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 1132 \cr }} Modified: pkg/distr/vignettes/newDistributions.Rnw =================================================================== --- pkg/distr/vignettes/newDistributions.Rnw 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distr/vignettes/newDistributions.Rnw 2017-04-21 15:56:01 UTC (rev 1132) @@ -85,13 +85,15 @@ % ------------------------------------------------------------------------------- \title{How to generate new distributions in packages \pkg{distr}, \pkg{distrEx}} %,version \pkgExversion} -\author{\small Peter Ruckdeschel\thanks{Fraunhofer ITWM, Kaiserslautern} +\author{\small Peter Ruckdeschel\thanks{Universit\"at Oldenburg, Oldenburg} \\[-.5ex] \small Matthias Kohl\thanks{FH Furtwangen} \smallskip\\ -\small Fraunhofer ITWM\\[-.5ex] -\small Fraunhofer Platz 1\\[-.5ex] -\small 67663 Kaiserslautern\\[-.5ex] +\small Institut f\"ur Mathematik\\[-0.5ex] +\small Fakult\"at V - Mathematik und Naturwissenschaften\\[-.5ex] +\small Carl von Ossietzky Universit\"at Oldenburg\\[-0.5ex] +\small PObox 2503\\[-.5ex] +\small 26111 Oldenburg (Oldb)\\[-.5ex] \small Germany\\ \small e-Mail: {\small \tt peter.ruckdeschel at uni-oldenburg.de}\medskip\\ \parbox[t]{5cm}{ Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrDoc/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) @@ -1,6 +1,6 @@ Package: distrDoc -Version: 2.6 -Date: 2016-04-23 +Version: 2.6.1 +Date: 2017-04-21 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'. @@ -21,4 +21,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1097 +SVNRevision: 1132 Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrDoc/vignettes/distr.Rnw 2017-04-21 15:56:01 UTC (rev 1132) @@ -115,6 +115,7 @@ \smallskip\\ \small Institute for Mathematics\\[-.5ex] \small School of Mathematics and Science\\[-.5ex] +\small Oldenburg University\\[-.5ex] \small PO box 25 03\\[-.5ex] \small 26111 Oldenburg (Oldb.)\\[-.5ex] \small Germany\\ Modified: pkg/distrEx/DESCRIPTION =================================================================== --- pkg/distrEx/DESCRIPTION 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrEx/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) @@ -1,6 +1,6 @@ Package: distrEx -Version: 2.6 -Date: 2016-04-23 +Version: 2.6.1 +Date: 2017-04-21 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: 1089 +SVNRevision: 1133 Modified: pkg/distrEx/NAMESPACE =================================================================== --- pkg/distrEx/NAMESPACE 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrEx/NAMESPACE 2017-04-21 15:56:01 UTC (rev 1132) @@ -1,4 +1,4 @@ -useDynLib("distrEx") +useDynLib("distrEx", .registration = TRUE, .fixes = "C_") importFrom("stats", "dnorm", "integrate", "optimize", "pbinom", "pchisq", "pexp", "pnorm", "ppois", "qcauchy", "qnorm", "uniroot") Modified: pkg/distrEx/R/distrExIntegrate.R =================================================================== --- pkg/distrEx/R/distrExIntegrate.R 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrEx/R/distrExIntegrate.R 2017-04-21 15:56:01 UTC (rev 1132) @@ -40,9 +40,10 @@ W <- numeric(n) # mm<-dyn.load("G:/rtest/GLaw.dll") - erg<-.C("gauleg",n = as.integer(n),eps = as.double(.Machine$double.eps), - A = as.double(A),W = as.double(W), PACKAGE = "distrEx") + erg<-.C(C_gauleg,n = as.integer(n),eps = as.double(.Machine$double.eps), + A = as.double(A),W = as.double(W)) #, PACKAGE = "distrEx") ### PACKAGE ARGUMENT added P.R. 270507 + #### removed again 200417 / used registered symbol instead # dyn.unload("G:/rtest/GLaw.dll") # # P.R. 20140810: .Call interface instead of .C interface Modified: pkg/distrEx/inst/NEWS =================================================================== --- pkg/distrEx/inst/NEWS 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrEx/inst/NEWS 2017-04-21 15:56:01 UTC (rev 1132) @@ -8,6 +8,13 @@ information) ############## +v 2.6.1 +############## ++ fixed internals as triggered by mail "CRAN package distr" + by Kurt Hornik from Apr 07 2017; most importantly, we + registered native code + +############## v 2.6 ############## Modified: pkg/distrEx/man/0distrEx-package.Rd =================================================================== --- pkg/distrEx/man/0distrEx-package.Rd 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrEx/man/0distrEx-package.Rd 2017-04-21 15:56:01 UTC (rev 1132) @@ -27,15 +27,15 @@ \details{ \tabular{ll}{ Package: \tab distrEx \cr -Version: \tab 2.6 \cr -Date: \tab 2016-04-23 \cr +Version: \tab 2.6.1 \cr +Date: \tab 2017-04-21 \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 1089 \cr +SVNRevision: \tab 1132 \cr } } \section{Classes}{ @@ -222,7 +222,7 @@ \references{ P. Ruckdeschel, M. Kohl, T. Stabla, F. Camphausen (2006): S4 Classes for Distributions, \emph{R News}, \emph{6}(2), 2-6. -\url{http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} +\url{https://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf} %a more detailed manual for \pkg{distr}, \pkg{distrSim}, \pkg{distrTEst}, and \pkg{distrEx} may be downloaded from %\url{http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/distr.pdf}\cr Modified: pkg/distrEx/src/GLaw.c =================================================================== --- pkg/distrEx/src/GLaw.c 2017-04-20 20:45:25 UTC (rev 1131) +++ pkg/distrEx/src/GLaw.c 2017-04-21 15:56:01 UTC (rev 1132) @@ -3,8 +3,12 @@ #include #include #include /* constants */ +#include +#include -void gauleg(int *n, double *eps, double *A, double *W) +#define C_DEF(name, n) {#name, (DL_FUNC) &name, n} + +void attribute_hidden gauleg(int *n, double *eps, double *A, double *W) { int i,j, m=((*n)+1)/2; double z1,z,pp,p1,p2,p3; for(i=1;i<=m;i++){ z=cos(PI*(i-0.25)/((*n)+0.5)); @@ -26,6 +30,21 @@ } } +/* P.R. 20170427: register routine */ + +static const R_CMethodDef R_CDef[] = { + C_DEF(gauleg, 4), + {NULL, NULL, 0} +}; + +void attribute_visible R_init_distrEx(DllInfo *dll) +{ + R_registerRoutines(dll, R_CDef, NULL, NULL, NULL); + R_useDynamicSymbols(dll, FALSE); + R_forceSymbols(dll, TRUE); + +} + /* P.R. 20140810: Yet to be tested: preparation for .Call - interface SEXP Gauleg(SEXP nFromR, SEXP epsFromR) From noreply at r-forge.r-project.org Sat Apr 22 12:23:45 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 22 Apr 2017 12:23:45 +0200 (CEST) Subject: [Distr-commits] r1133 - branches/distr-2.7/pkg/SweaveListingUtils branches/distr-2.7/pkg/SweaveListingUtils/vignettes pkg/SweaveListingUtils pkg/SweaveListingUtils/man pkg/SweaveListingUtils/vignettes pkg/distr pkg/distr/man pkg/distrDoc pkg/distrDoc/man pkg/distrDoc/vignettes pkg/distrEx pkg/distrEx/man pkg/distrMod/vignettes Message-ID: <20170422102345.706D01886A2@r-forge.r-project.org> Author: ruckdeschel Date: 2017-04-22 12:23:44 +0200 (Sat, 22 Apr 2017) New Revision: 1133 Modified: branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw pkg/SweaveListingUtils/DESCRIPTION pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw pkg/distr/DESCRIPTION pkg/distr/man/0distr-package.Rd pkg/distrDoc/DESCRIPTION pkg/distrDoc/man/0distrDoc-package.Rd pkg/distrDoc/vignettes/distr.Rnw pkg/distrEx/DESCRIPTION pkg/distrEx/man/0distrEx-package.Rd pkg/distrMod/vignettes/distrMod.Rnw Log: prepared minor fixes in distr, distrEx, distrDoc, and SweaveListingUtils for submission on CRAN Modified: branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) +++ branches/distr-2.7/pkg/SweaveListingUtils/DESCRIPTION 2017-04-22 10:23:44 UTC (rev 1133) @@ -5,7 +5,7 @@ recent version (or another URL) thereby avoiding inconsistencies between vignette and documented source code. Encoding: latin1 -Version: 0.7.6 +Version: 0.7.8 Depends: R(>= 2.14.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines Imports: methods Modified: branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw =================================================================== --- branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-21 15:56:01 UTC (rev 1132) +++ branches/distr-2.7/pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-22 10:23:44 UTC (rev 1133) @@ -489,14 +489,14 @@ Leisch, F (2002b) \newblock {Sweave, Part I: Mixing R and \LaTeX.} \newblock \emph{R-News\/}, {\bf 2}(3): 28--31. -\newblock \hreft{http://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf}. +\newblock \hreft{https://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf}. % \bibitem[Leisch (2003)]{Lei:03} Leisch, F (2003) \newblock {Sweave, Part II: Package Vignettes.} \newblock \emph{R-News\/}, {\bf 3}(2): 21--24. -\newblock \hreft{http://cran.r-project.org/doc/Rnews/Rnews_2003-2.pdf}. +\newblock \hreft{https://cran.r-project.org/doc/Rnews/Rnews_2003-2.pdf}. % \bibitem[{Murdoch (2010)}]{Murd:08} @@ -515,7 +515,7 @@ Ruckdeschel P, Kohl M, Stabla T, and Camphausen F (2006) \newblock {S4 Classes for Distributions.} \newblock \emph{R-News\/}, {\bf 6}(2): 10--13. -\newblock \hreft{http://cran.r-project.org/doc/Rnews/Rnews_2006-2.pdf}. +\newblock \hreft{https://cran.r-project.org/doc/Rnews/Rnews_2006-2.pdf}. %\newblock See also {http://www.uni-bayreuth.de/departments/math/org/mathe7/RUCKDESCHEL/pubs/distr.pdf} % Modified: pkg/SweaveListingUtils/DESCRIPTION =================================================================== --- pkg/SweaveListingUtils/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/SweaveListingUtils/DESCRIPTION 2017-04-22 10:23:44 UTC (rev 1133) @@ -1,19 +1,17 @@ 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 (snippets) copied from R-forge in its most - recent version (or another URL) thereby avoiding inconsistencies between vignette - and documented source code. -Version: 0.7.6 +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: 0.7.7 Encoding: latin1 -Date: 2017-04-21 +Date: 2017-04-22 Depends: R(>= 2.14.0), startupmsg Suggests: distr, MASS, survival, distrEx, Matrix, splines Imports: methods ByteCompile: yes -Authors at R: person("Peter", "Ruckdeschel", role=c("cre", "cph"), - email="peter.ruckdeschel at uni-oldenburg.de") +Authors at R: person("Peter", "Ruckdeschel", role=c("cre", "cph", "aut"), email="peter.ruckdeschel at uni-oldenburg.de") License: LGPL-3 LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1133 \ No newline at end of file +SVNRevision: 1132 Modified: pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd =================================================================== --- pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/SweaveListingUtils/man/0SweaveListingUtils-package.Rd 2017-04-22 10:23:44 UTC (rev 1133) @@ -15,14 +15,14 @@ \details{ \tabular{ll}{ Package: \tab SweaveListingUtils \cr -Version: \tab 0.7.5 \cr -Date: \tab 2016-04-25 \cr +Version: \tab 0.7.6 \cr +Date: \tab 2017-04-22 \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 1110 \cr +SVNRevision: \tab 1132 \cr } TeX-package \file{listings}, confer \url{http://www.ctan.org/tex-archive/macros/latex/contrib/listings/}, Modified: pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw =================================================================== --- pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw 2017-04-22 10:23:44 UTC (rev 1133) @@ -489,14 +489,14 @@ Leisch, F (2002b) \newblock {Sweave, Part I: Mixing R and \LaTeX.} \newblock \emph{R-News\/}, {\bf 2}(3): 28--31. -\newblock \hreft{http://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf}. +\newblock \hreft{https://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf}. % \bibitem[Leisch (2003)]{Lei:03} Leisch, F (2003) \newblock {Sweave, Part II: Package Vignettes.} \newblock \emph{R-News\/}, {\bf 3}(2): 21--24. -\newblock \hreft{http://cran.r-project.org/doc/Rnews/Rnews_2003-2.pdf}. +\newblock \hreft{https://cran.r-project.org/doc/Rnews/Rnews_2003-2.pdf}. % \bibitem[{Murdoch (2010)}]{Murd:08} @@ -515,7 +515,7 @@ Ruckdeschel P, Kohl M, Stabla T, and Camphausen F (2006) \newblock {S4 Classes for Distributions.} \newblock \emph{R-News\/}, {\bf 6}(2): 10--13. -\newblock \hreft{http://cran.r-project.org/doc/Rnews/Rnews_2006-2.pdf}. +\newblock \hreft{https://cran.r-project.org/doc/Rnews/Rnews_2006-2.pdf}. %\newblock See also {http://www.uni-bayreuth.de/departments/math/org/mathe7/RUCKDESCHEL/pubs/distr.pdf} % Modified: pkg/distr/DESCRIPTION =================================================================== --- pkg/distr/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distr/DESCRIPTION 2017-04-22 10:23:44 UTC (rev 1133) @@ -1,15 +1,13 @@ Package: distr Version: 2.6.2 -Date: 2017-04-21 +Date: 2017-04-22 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 - initial phase --2005"), person("Matthias", "Kohl", role=c("aut", "cph")), - person("Peter", "Ruckdeschel", role=c("cre", "cph"), - email="peter.ruckdeschel at uni-oldenburg.de"), person("Thomas", "Stabla", role="ctb", - comment="contributed as student in the initial phase --2005"), person("R Core Team", - role = c("ctb", "cph"), comment="for source file ks.c/ routines 'pKS2' and - 'pKolmogorov2x'")) +Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student in the initial phase --2005"), + person("Matthias", "Kohl", role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "cph"), + email="peter.ruckdeschel at uni-oldenburg.de"), person("Thomas", "Stabla", role="ctb", comment="contributed as student in the + initial phase --2005"), person("R Core Team", role = c("ctb", "cph"), comment="for source file ks.c/ routines 'pKS2' and + 'pKolmogorov2x'")) Depends: R(>= 2.14.0), methods, graphics, startupmsg, sfsmisc, SweaveListingUtils Suggests: distrEx, svUnit (>= 0.7-11) Imports: stats, grDevices, utils, MASS Modified: pkg/distr/man/0distr-package.Rd =================================================================== --- pkg/distr/man/0distr-package.Rd 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distr/man/0distr-package.Rd 2017-04-22 10:23:44 UTC (rev 1133) @@ -44,7 +44,7 @@ \tabular{ll}{ Package: \tab distr \cr Version: \tab 2.6.2 \cr -Date: \tab 2017-04-21 \cr +Date: \tab 2017-04-22 \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 Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distrDoc/DESCRIPTION 2017-04-22 10:23:44 UTC (rev 1133) @@ -1,19 +1,16 @@ Package: distrDoc Version: 2.6.1 -Date: 2017-04-21 +Date: 2017-04-22 Title: Documentation for 'distr' Family of R Packages -Description: Provides documentation in form of a common vignette to packages 'distr', 'distrEx', - 'distrMod', 'distrSim', 'distrTEst', 'distrTeach', and 'distrEllipse'. -Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the - documented packages in the initial phase --2005"), person("Matthias", "Kohl", - role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "cph"), - email="peter.ruckdeschel at uni-oldenburg.de"), person("Thomas", "Stabla", role="ctb", - comment="contributed as student to the documented packages in the initial phase - --2005")) +Description: Provides documentation in form of a common vignette to packages 'distr', 'distrEx', 'distrMod', 'distrSim', 'distrTEst', + 'distrTeach', and 'distrEllipse'. +Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the documented packages in the initial + phase --2005"), person("Matthias", "Kohl", role=c("aut", "cph")), person("Peter", "Ruckdeschel", role=c("cre", "cph"), + email="peter.ruckdeschel at uni-oldenburg.de"), person("Thomas", "Stabla", role="ctb", comment="contributed as student to the + documented packages in the initial phase --2005")) Depends: R(>= 2.14.0) -Imports: distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0), - distrTeach(>= 2.2.0), RandVar(>= 0.7), distrMod(>= 2.2.0), MASS, methods, - SweaveListingUtils, startupmsg +Imports: distr(>= 2.2.0), distrEx(>= 2.2.0), distrSim(>= 2.2.0), distrTEst(>= 2.2.0), distrTeach(>= 2.2.0), RandVar(>= 0.7), + distrMod(>= 2.2.0), MASS, methods, SweaveListingUtils, startupmsg Suggests: Biobase ByteCompile: yes Encoding: latin1 Modified: pkg/distrDoc/man/0distrDoc-package.Rd =================================================================== --- pkg/distrDoc/man/0distrDoc-package.Rd 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distrDoc/man/0distrDoc-package.Rd 2017-04-22 10:23:44 UTC (rev 1133) @@ -13,8 +13,8 @@ \details{ \tabular{ll}{ Package: \tab distrDoc \cr -Version: \tab 2.6 \cr -Date: \tab 2016-04-23 \cr +Version: \tab 2.6.1 \cr +Date: \tab 2017-04-22 \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 1097 \cr +SVNRevision: \tab 1132 \cr }} Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distrDoc/vignettes/distr.Rnw 2017-04-22 10:23:44 UTC (rev 1133) @@ -179,7 +179,7 @@ \pkg{RobExtremes}. This concerns the Gumbel, Weibull, Pareto distributions. %\noindent The latter two of them require package \pkg{setRNG} by %\href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert} -%to be installed from \href{http://cran.r-project.org/mirrors.html}{\tt CRAN}. +%to be installed from \href{https://cran.r-project.org/mirrors.html}{\tt CRAN}. % \\ %\noindent Additionally, mainly contributed by \cite{MK:05}, in \pkg{distrEx} we @@ -2766,7 +2766,7 @@ In package \pkg{distrSim}, and conseqently also in package \pkg{distrTEst} we use \href{mailto:pgilbert at bank-banque-canada.ca}{Paul Gilbert's} package \pkg{setRNG} -to be installed from \href{http://cran.r-project.org/mirrors.html}{\tt CRAN} +to be installed from \href{https://cran.r-project.org/mirrors.html}{\tt CRAN} for the control of the seed of the random number generator in our simulation classes. More precisely, for our version $\le$ {\tt 1.6} we need his @@ -2775,7 +2775,7 @@ From package version {\tt 1.7}/{\tt 0.4-3} on, we also need package \pkg{startupmsg} by the first of the present authors, which also is available - on \href{http://cran.r-project.org/mirrors.html}{\tt CRAN}. + on \href{https://cran.r-project.org/mirrors.html}{\tt CRAN}. \subsection{License} This software is distributed under the terms of the GNU GENERAL Modified: pkg/distrEx/DESCRIPTION =================================================================== --- pkg/distrEx/DESCRIPTION 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distrEx/DESCRIPTION 2017-04-22 10:23:44 UTC (rev 1133) @@ -1,18 +1,17 @@ Package: distrEx Version: 2.6.1 -Date: 2017-04-21 +Date: 2017-04-22 Title: Extensions of Package 'distr' Description: Extends package 'distr' by functionals, distances, and conditional distributions. Depends: R(>= 2.10.0), methods, distr(>= 2.2) Imports: startupmsg, utils, stats Suggests: tcltk -Authors at R: c(person("Matthias", "Kohl", role=c("cre", "cph"), - email="Matthias.Kohl at stamats.de"), person("Peter", "Ruckdeschel", role=c("aut", - "cph"))) +Authors at R: c(person("Matthias", "Kohl", role=c("cre", "cph"), email="Matthias.Kohl at stamats.de"), person("Peter", "Ruckdeschel", + role=c("aut", "cph"))) ByteCompile: yes License: LGPL-3 Encoding: latin1 URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 1133 +SVNRevision: 1132 Modified: pkg/distrEx/man/0distrEx-package.Rd =================================================================== --- pkg/distrEx/man/0distrEx-package.Rd 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distrEx/man/0distrEx-package.Rd 2017-04-22 10:23:44 UTC (rev 1133) @@ -28,7 +28,7 @@ \tabular{ll}{ Package: \tab distrEx \cr Version: \tab 2.6.1 \cr -Date: \tab 2017-04-21 \cr +Date: \tab 2017-04-22 \cr Depends: \tab R(>= 2.10.0), methods, distr(>= 2.2) \cr Imports: \tab startupmsg, utils, stats \cr Suggests: \tab tcltk \cr Modified: pkg/distrMod/vignettes/distrMod.Rnw =================================================================== --- pkg/distrMod/vignettes/distrMod.Rnw 2017-04-21 15:56:01 UTC (rev 1132) +++ pkg/distrMod/vignettes/distrMod.Rnw 2017-04-22 10:23:44 UTC (rev 1133) @@ -350,7 +350,7 @@ \textbf{Packages \pkg{distr} and \pkg{distrEx} } Much of our infrastructure relies on our \proglang{R} packages \pkg{distr} and \pkg{distrEx} available on -\href{http://cran.r-project.org/}{\tt CRAN}. +\href{https://cran.r-project.org/}{\tt CRAN}. Package \pkg{distr}, see~\citet{distr,distrTeach}, aims to provide a conceptual treatment of distributions by means of \proglang{S}4 classes. A mother class \code{Distribution} is introduced with slots for a parameter and for functions From noreply at r-forge.r-project.org Sat Apr 22 15:11:47 2017 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 22 Apr 2017 15:11:47 +0200 (CEST) Subject: [Distr-commits] r1134 - in pkg/SweaveListingUtils: . tests/Examples Message-ID: <20170422131147.2FC361874F7@r-forge.r-project.org> Author: ruckdeschel Date: 2017-04-22 15:11:46 +0200 (Sat, 22 Apr 2017) New Revision: 1134 Added: pkg/SweaveListingUtils/SweaveListingUtils-Ex.R Modified: pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save Log: used the wrong reference output Added: pkg/SweaveListingUtils/SweaveListingUtils-Ex.R =================================================================== --- pkg/SweaveListingUtils/SweaveListingUtils-Ex.R (rev 0) +++ pkg/SweaveListingUtils/SweaveListingUtils-Ex.R 2017-04-22 13:11:46 UTC (rev 1134) @@ -0,0 +1,311 @@ +pkgname <- "SweaveListingUtils" +source(file.path(R.home("share"), "R", "examples-header.R")) +options(warn = 1) +options(pager = "console") +library('SweaveListingUtils') + +assign(".oldSearch", 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() + + + +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() +SweaveListingOptions("Rout") +SweaveListingOptions("Rout" = c(0,0,0)) +# or +SweaveListingOptions(Rout = c(0,1,0)) +getSweaveListingOption("Rout") + + + +cleanEx() +nameEx("SweaveListingPreparations") +### * SweaveListingPreparations + +flush(stderr()); flush(stdout()) + +### Name: SweaveListingPreparations +### Title: SweaveListingPreparations +### Aliases: SweaveListingPreparations +### Keywords: utilities + +### ** Examples + +SweaveListingPreparations() +SweaveListingPreparations(pkv="2.1") + + + +cleanEx() +nameEx("changeKeywordstyles") +### * changeKeywordstyles + +flush(stderr()); flush(stdout()) + +### Name: changeKeywordstyles +### Title: changeKeywordstyles +### Aliases: changeKeywordstyles +### Keywords: utilities + +### ** Examples + +require(MASS) +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 = "")) + + + +cleanEx() +nameEx("copySourceFromRForge") +### * copySourceFromRForge + +flush(stderr()); flush(stdout()) + +### Name: copySourceFromRForge +### Title: copySourceFromRForge +### Aliases: copySourceFromRForge +### Keywords: utilities + +### ** Examples + +copySourceFromRForge("distr","R","AllClasses.R","distr", from =2, to =3, + offset.after=2) +copySourceFromRForge("distr","R","AllClasses.R","distr", from ="setClass", + to ="\\}") + + + +cleanEx() +nameEx("isBaseOrRecommended") +### * isBaseOrRecommended + +flush(stderr()); flush(stdout()) + +### Name: isBaseOrRecommended +### Title: isBaseOrRecommended +### Aliases: isBaseOrRecommended +### Keywords: utilities internal + +### ** Examples + +isBaseOrRecommended(pkgs = c("SweaveListingUtils","Matrix","splines")) + + +cleanEx() +nameEx("library") +### * library + +flush(stderr()); flush(stdout()) + +### Name: library +### Title: Loading Packages with registering symbols for TeX package +### 'listing' +### Aliases: library require +### Keywords: utilities + +### ** Examples + +require(survival) + + + +cleanEx() +nameEx("lstinputSourceFromRForge") +### * lstinputSourceFromRForge + +flush(stderr()); flush(stdout()) + +### Name: lstinputSourceFromRForge +### Title: lstinputSourceFromRForge +### Aliases: lstinputSourceFromRForge +### Keywords: utilities + +### ** Examples + +lstinputSourceFromRForge("distr","R","AllClasses.R","distr", + "## Class: BinomParameter", "#-") + +lstinputSourceFromRForge("distr","R","AllClasses.R","distr", + from = "## Class: binomial distribution", + to = "contains = \"LatticeDistribution\"", offset.after = 1) +lstinputSourceFromRForge("distr","man","Binom-class.Rd","distr") + +lstinputSourceFromRForge("distr","R","BinomialDistribution.R","distr", + from = c("## Access Methods", "## wrapped access methods"), + to = c("setReplaceMethod\\(\"prob\", \"BinomParameter\"", + "size = value\\)\\)") , + offset.after = c(1,1)) +lstinputSourceFromRForge("distr","R","BinomialDistribution.R","distr", + from = c(8,43,45), to = c(16,53,45)) +lstinputSourceFromRForge("distr","R","BinomialDistribution.R","distr", + from = c("## Access Methods", "## wrapped access methods"), + to = c("setReplaceMethod\\(\"prob\", \"BinomParameter\"", + "size = value\\)\\)") , + offset.after = c(1,1)) + + + +cleanEx() +nameEx("lstset") +### * lstset + +flush(stderr()); flush(stdout()) + +### Name: lstset +### Title: lstset and friends +### Aliases: lstset lstsetRd lstsetR lstsetRin lstsetRout lstsetRcode +### lstdefRstyle lstsetRall +### Keywords: utilities + +### ** Examples + +lstset(taglist(A="H", b=2, 3),30) +lstset(taglist(A="H", b=2, 3),30, startS = "\\lstdefinestyle{Rstyle}{") +lstsetR() +lstsetRd() + + + +cleanEx() +nameEx("lstsetLanguage") +### * lstsetLanguage + +flush(stderr()); flush(stdout()) + +### Name: lstsetLanguage +### Title: lstsetLanguage +### Aliases: lstsetLanguage +### Keywords: utilities + +### ** Examples + +require(MASS) +lstsetLanguage(pkgs = c("MASS","stats"), + keywordstyles = paste("\\bfseries\\color{",c("blue","red"),"}", + sep="", collapse="")) +### not to be used: +print(SweaveListingUtils:::.alreadyDefinedPkgs) +print(SweaveListingUtils:::.keywordsR) + + + +cleanEx() +nameEx("readPackageVersion") +### * readPackageVersion + +flush(stderr()); flush(stdout()) + +### Name: readPkgVersion +### Title: readPkgVersion +### Aliases: readPkgVersion +### Keywords: utilities + +### ** Examples + +readPkgVersion(package = "distr") + + + +cleanEx() +nameEx("readSourceFromRForge") +### * readSourceFromRForge + +flush(stderr()); flush(stdout()) + +### Name: readSourceFromRForge +### Title: readSourceFromRForge +### Aliases: readSourceFromRForge +### Keywords: utilities + +### ** Examples + +readSourceFromRForge("distr","R","AllClasses.R","distr") + + + +cleanEx() +nameEx("setToBeDefinedPkgs") +### * setToBeDefinedPkgs + +flush(stderr()); flush(stdout()) + +### Name: setToBeDefinedPkgs +### Title: setToBeDefinedPkgs +### Aliases: setToBeDefinedPkgs +### Keywords: utilities + +### ** Examples + +setToBeDefinedPkgs(pkgs = c("distr","distrEx"), + keywordstyles = paste("\\bfseries\\color{",c("blue","red"),"}", + sep="", collapse="")) +### not to be used: +print(SweaveListingUtils:::.tobeDefinedPkgs) + + + +cleanEx() +nameEx("taglist") +### * taglist + +flush(stderr()); flush(stdout()) + +### Name: taglist +### Title: S3 class taglist +### Aliases: print.taglist taglist +### Keywords: utilities + +### ** Examples + + TL <- taglist("HA"=8,"JUI"=7,"butzi", list=list("HU"="AHAL","HA"="BETA","BUZ")) + print(TL) + print(TL, LineLength=10, first.print="myList=", offset.start=4, + withFinalLineBreak = FALSE) + + + +### *