From noreply at r-forge.r-project.org Tue Feb 3 14:26:46 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 3 Feb 2015 14:26:46 +0100 (CET) Subject: [Distr-commits] r991 - branches/distr-2.6/pkg/distrDoc/inst branches/distr-2.6/pkg/distrDoc/vignettes pkg/distrDoc pkg/distrDoc/inst pkg/distrDoc/vignettes Message-ID: <20150203132646.EDFE01805B3@r-forge.r-project.org> Author: ruckdeschel Date: 2015-02-03 14:26:46 +0100 (Tue, 03 Feb 2015) New Revision: 991 Modified: branches/distr-2.6/pkg/distrDoc/inst/NEWS branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw pkg/distrDoc/DESCRIPTION pkg/distrDoc/inst/NEWS pkg/distrDoc/vignettes/distr.Rnw Log: [distrDoc] both devel branch and trunc: fixed \VignetteKeyword issue detected as in mail by K. Hornik 2015-02-03 Modified: branches/distr-2.6/pkg/distrDoc/inst/NEWS =================================================================== --- branches/distr-2.6/pkg/distrDoc/inst/NEWS 2015-01-25 14:20:44 UTC (rev 990) +++ branches/distr-2.6/pkg/distrDoc/inst/NEWS 2015-02-03 13:26:46 UTC (rev 991) @@ -20,6 +20,7 @@ functions according to argument withSubst under the hood ++ fixed \VignetteKeyword issue detected as in mail by K. Hornik 2015-02-03 + added svn-properties to distr.Rnw + enhanced imports in DESCRIPTION by explicating second order imports Modified: branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw 2015-01-25 14:20:44 UTC (rev 990) +++ branches/distr-2.6/pkg/distrDoc/vignettes/distr.Rnw 2015-02-03 13:26:46 UTC (rev 991) @@ -1,6 +1,8 @@ %\VignetteIndexEntry{distr - manual} %\VignetteDepends{distr} -%\VignetteKeyword{probability distribution,simulation,estimation} +%\VignetteKeyword{probability distribution} +%\VignetteKeyword{simulation} +%\VignetteKeyword{estimation} %\VignettePackage{distr} % \documentclass[11pt]{article} Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2015-01-25 14:20:44 UTC (rev 990) +++ pkg/distrDoc/DESCRIPTION 2015-02-03 13:26:46 UTC (rev 991) @@ -1,6 +1,6 @@ Package: distrDoc -Version: 2.5 -Date: 2013-09-12 +Version: 2.5.1 +Date: 2015-02-04 Title: Documentation for packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod, and distrEllipse Description: provides documentation in form of a common vignette to packages distr, distrEx, Modified: pkg/distrDoc/inst/NEWS =================================================================== --- pkg/distrDoc/inst/NEWS 2015-01-25 14:20:44 UTC (rev 990) +++ pkg/distrDoc/inst/NEWS 2015-02-03 13:26:46 UTC (rev 991) @@ -8,6 +8,12 @@ information) ############## +v 2.5.1 +############## + ++ fixed \VignetteKeyword issue detected as in mail by K. Hornik 2015-02-03 + +############## v 2.5 ############## Modified: pkg/distrDoc/vignettes/distr.Rnw =================================================================== --- pkg/distrDoc/vignettes/distr.Rnw 2015-01-25 14:20:44 UTC (rev 990) +++ pkg/distrDoc/vignettes/distr.Rnw 2015-02-03 13:26:46 UTC (rev 991) @@ -1,6 +1,8 @@ %\VignetteIndexEntry{distr - manual} %\VignetteDepends{distr} -%\VignetteKeyword{probability distribution,simulation,estimation} +%\VignetteKeyword{probability distribution} +%\VignetteKeyword{simulation} +%\VignetteKeyword{estimation} %\VignettePackage{distr} % \documentclass[11pt]{article} From noreply at r-forge.r-project.org Tue Feb 3 14:27:42 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 3 Feb 2015 14:27:42 +0100 (CET) Subject: [Distr-commits] r992 - pkg/distrDoc Message-ID: <20150203132742.8138018575C@r-forge.r-project.org> Author: ruckdeschel Date: 2015-02-03 14:27:42 +0100 (Tue, 03 Feb 2015) New Revision: 992 Modified: pkg/distrDoc/DESCRIPTION Log: distrDoc: updated DESCRIPTION file in trunc Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2015-02-03 13:26:46 UTC (rev 991) +++ pkg/distrDoc/DESCRIPTION 2015-02-03 13:27:42 UTC (rev 992) @@ -18,4 +18,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 913 +SVNRevision: 992 From noreply at r-forge.r-project.org Tue Feb 3 14:57:29 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 3 Feb 2015 14:57:29 +0100 (CET) Subject: [Distr-commits] r993 - in pkg/distrDoc: . inst Message-ID: <20150203135729.48738184426@r-forge.r-project.org> Author: ruckdeschel Date: 2015-02-03 14:57:28 +0100 (Tue, 03 Feb 2015) New Revision: 993 Modified: pkg/distrDoc/DESCRIPTION pkg/distrDoc/inst/CITATION pkg/distrDoc/inst/NEWS Log: distrDoc: yet som polishing before submitting 2.5.1 to CRAN Modified: pkg/distrDoc/DESCRIPTION =================================================================== --- pkg/distrDoc/DESCRIPTION 2015-02-03 13:27:42 UTC (rev 992) +++ pkg/distrDoc/DESCRIPTION 2015-02-03 13:57:28 UTC (rev 993) @@ -1,12 +1,14 @@ Package: distrDoc Version: 2.5.1 Date: 2015-02-04 -Title: Documentation for packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod, +Title: Documentation for Packages distr, distrEx, distrSim, distrTEst, distrTeach, distrMod, and distrEllipse Description: provides documentation in form of a common vignette to packages distr, distrEx, distrMod, distrSim, distrTEst, distrTeach, and distrEllipse -Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas Stabla -Maintainer: Peter Ruckdeschel +Authors at R: c(person("Florian", "Camphausen", role="ctb", comment="contributed as student to the documented packages in the initial phase --2005"), + person("Matthias", "Kohl", role=c("aut", "cph")), + person("Peter", "Ruckdeschel", role=c("cre", "cph"), email="Peter.Ruckdeschel at itwm.fraunhofer.de"), + person("Thomas", "Stabla", role="ctb", comment="contributed as student to the documented packages in the initial phase --2005")) 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, @@ -18,4 +20,4 @@ URL: http://distr.r-forge.r-project.org/ LastChangedDate: {$LastChangedDate$} LastChangedRevision: {$LastChangedRevision$} -SVNRevision: 992 +SVNRevision: 993 Modified: pkg/distrDoc/inst/CITATION =================================================================== --- pkg/distrDoc/inst/CITATION 2015-02-03 13:27:42 UTC (rev 992) +++ pkg/distrDoc/inst/CITATION 2015-02-03 13:57:28 UTC (rev 993) @@ -14,7 +14,27 @@ number = 2, pages = "2--6", month = "May", - url = "http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/distr.pdf", + url = "http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf", pdf = "http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf", textVersion = paste("Ruckdeschel, P., Kohl, M., Stabla, T., & Camphausen, F. (2006)", "S4 Classes for Distributions")) + +citEntry(entry = "Article", + title = "General Purpose Convolution Algorithm in {S}4 Classes by Means of FFT", + author = personList(as.person("Peter Ruckdeschel"), + as.person("Matthias Kohl")), + journal = "Journal of Statistical Software", + year = "2014", + volume = "59", + number = "4", + pages = "1--25", + url = "http://www.jstatsoft.org/v59/i04/", + textVersion = + paste("Peter Ruckdeschel, Matthias Kohl (2014).", + "General Purpose Convolution Algorithm in S4 Classes by Means of FFT.", + "Journal of Statistical Software, 59(4), 1-25.", + "URL http://www.jstatsoft.org/v59/i04/."), + header = "If you employ convolution, please also cite:" +) + + \ No newline at end of file Modified: pkg/distrDoc/inst/NEWS =================================================================== --- pkg/distrDoc/inst/NEWS 2015-02-03 13:27:42 UTC (rev 992) +++ pkg/distrDoc/inst/NEWS 2015-02-03 13:57:28 UTC (rev 993) @@ -10,6 +10,9 @@ ############## v 2.5.1 ############## +user-visible CHANGES: ++ title changed to title style / capitalization ++ updated CITATION file + fixed \VignetteKeyword issue detected as in mail by K. Hornik 2015-02-03 From noreply at r-forge.r-project.org Wed Feb 18 14:19:24 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 18 Feb 2015 14:19:24 +0100 (CET) Subject: [Distr-commits] r994 - in branches/distr-2.6/pkg/distr: R inst man Message-ID: <20150218131924.B508E1860E5@r-forge.r-project.org> Author: ruckdeschel Date: 2015-02-18 14:19:24 +0100 (Wed, 18 Feb 2015) New Revision: 994 Modified: branches/distr-2.6/pkg/distr/R/internals-qqplot.R branches/distr-2.6/pkg/distr/inst/NEWS branches/distr-2.6/pkg/distr/man/internals-qqplot.Rd Log: [distr] changed helper .isReplicated Modified: branches/distr-2.6/pkg/distr/R/internals-qqplot.R =================================================================== --- branches/distr-2.6/pkg/distr/R/internals-qqplot.R 2015-02-03 13:57:28 UTC (rev 993) +++ branches/distr-2.6/pkg/distr/R/internals-qqplot.R 2015-02-18 13:19:24 UTC (rev 994) @@ -10,10 +10,10 @@ sapply(x, function(y) length(which(fct(y,gapm)))>0) } -.isReplicated <- function(x){ +.isReplicated <- function(x, tol=.Machine$double.eps){ tx <- table(x) rx <- as.numeric(names(tx[tx>1])) - sapply(x, function(y) any(abs(y-rx)<.Machine$double.eps)) + sapply(x, function(y) any(abs(y-rx) now use dots.lowlevel ... - +-helper function .isReplicated gains an optional argument tol + ############## v 2.5.3 ############## Modified: branches/distr-2.6/pkg/distr/man/internals-qqplot.Rd =================================================================== --- branches/distr-2.6/pkg/distr/man/internals-qqplot.Rd 2015-02-03 13:57:28 UTC (rev 993) +++ branches/distr-2.6/pkg/distr/man/internals-qqplot.Rd 2015-02-18 13:19:24 UTC (rev 994) @@ -21,7 +21,7 @@ \usage{ .inGaps(x,gapm) -.isReplicated(x) +.isReplicated(x, tol = .Machine$double.eps) .NotInSupport(x,D) .SingleDiscrete(x,D) .makeLenAndOrder(x,ord) @@ -53,6 +53,7 @@ an \code{"AbscontDistribution"} or \code{"UnivarLebDecDistribution"} object. } +\item{tol}{numeric; tolerance for separating points.} \item{D}{object of class \code{"UnivariateDistribution"}} \item{datax}{logical; (to be used in \pkg{distrMod}) shall data be plotted on x-axis?} \item{ord}{integer; the result of a call to \code{order}} From noreply at r-forge.r-project.org Wed Feb 18 14:22:32 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 18 Feb 2015 14:22:32 +0100 (CET) Subject: [Distr-commits] r995 - branches/distr-2.6/pkg/distrDoc/inst Message-ID: <20150218132232.32C4B1848D6@r-forge.r-project.org> Author: ruckdeschel Date: 2015-02-18 14:22:31 +0100 (Wed, 18 Feb 2015) New Revision: 995 Modified: branches/distr-2.6/pkg/distrDoc/inst/CITATION Log: [distrDoc] updated web reference Modified: branches/distr-2.6/pkg/distrDoc/inst/CITATION =================================================================== --- branches/distr-2.6/pkg/distrDoc/inst/CITATION 2015-02-18 13:19:24 UTC (rev 994) +++ branches/distr-2.6/pkg/distrDoc/inst/CITATION 2015-02-18 13:22:31 UTC (rev 995) @@ -14,7 +14,7 @@ number = 2, pages = "2--6", month = "May", - url = "http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/distr.pdf", + url = "http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf", pdf = "http://CRAN.R-project.org/doc/Rnews/Rnews_2006-2.pdf", textVersion = paste("Ruckdeschel, P., Kohl, M., Stabla, T., & Camphausen, F. (2006)", "S4 Classes for Distributions")) From noreply at r-forge.r-project.org Wed Feb 18 14:34:25 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 18 Feb 2015 14:34:25 +0100 (CET) Subject: [Distr-commits] r996 - in branches/distr-2.6/pkg/distrMod: R inst man Message-ID: <20150218133425.59C741848D6@r-forge.r-project.org> Author: ruckdeschel Date: 2015-02-18 14:34:24 +0100 (Wed, 18 Feb 2015) New Revision: 996 Modified: branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R branches/distr-2.6/pkg/distrMod/R/qqplot.R branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R branches/distr-2.6/pkg/distrMod/inst/NEWS branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd branches/distr-2.6/pkg/distrMod/man/qqplot.Rd branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd Log: [distrMod] helper .isReplicated gains argument tol to be able to identify observations from a continuous distribution "too" close to each other, hence requiring jittering; jittering uses this tolerance now and is available for continuous distributions, too. Modified: branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R =================================================================== --- branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R 2015-02-18 13:22:31 UTC (rev 995) +++ branches/distr-2.6/pkg/distrMod/R/0distrModUtils.R 2015-02-18 13:34:24 UTC (rev 996) @@ -610,10 +610,10 @@ sapply(x, function(y) length(which(fct(y,gapm)))>0) } -.isReplicated <- function(x){ +.isReplicated <- function(x, tol=.Machine$double.eps){ tx <- table(x) rx <- as.numeric(names(tx[tx>1])) - sapply(x, function(y) any(abs(y-rx)<.Machine$double.eps)) + sapply(x, function(y) any(abs(y-rx)0) + xj[.isReplicated(x, jit.tol)] <- jitter(x[.isReplicated(x, jit.tol)], factor=jit.fac) ord.x <- order(xj) Modified: branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R =================================================================== --- branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R 2015-02-18 13:22:31 UTC (rev 995) +++ branches/distr-2.6/pkg/distrMod/R/returnlevelplot.R 2015-02-18 13:34:24 UTC (rev 996) @@ -57,6 +57,8 @@ adj.lbl = NULL, ## adj parameter for the plotted observation labels alpha.trsp = NA, ## alpha transparency to be added afterwards jit.fac = 0, ## jittering factor used for discrete distributions + jit.tol = .Machine$double.eps, ## tolerance for jittering: if distance + #is smaller than jit.tol, points are considered replicates check.NotInSupport = TRUE, ## shall we check if all x lie in support(y) col.NotInSupport = "red", ## if preceding check TRUE color of x if not in support(y) with.legend = TRUE, ## shall a legend be plotted @@ -106,8 +108,8 @@ } xj <- sort(x) - if(any(.isReplicated(x))&&jit.fac>0) - xj[.isReplicated(x)] <- jitter(x[.isReplicated(x)], factor=jit.fac) + if(any(.isReplicated(x, jit.tol))&&jit.fac>0) + xj[.isReplicated(x, jit.tol)] <- jitter(x[.isReplicated(x, jit.tol)], factor=jit.fac) xj <- sort(xj) ord.x <- order(xj) Modified: branches/distr-2.6/pkg/distrMod/inst/NEWS =================================================================== --- branches/distr-2.6/pkg/distrMod/inst/NEWS 2015-02-18 13:22:31 UTC (rev 995) +++ branches/distr-2.6/pkg/distrMod/inst/NEWS 2015-02-18 13:34:24 UTC (rev 996) @@ -41,11 +41,15 @@ * now by default has datax = TRUE * fixed issue with labeling * issues with datax fixed + * gains argument jit.tol to allow jittering to take place also for + continuous observations, if observations are "too" close to each other + returnlevelplot * similar as qqplot as to additional methods * returnlevelplot now gains an argument threshold for POT * set datax argument in case it is missing in returnlevelplot ... * issues with datax fixed + * gains argument jit.tol to allow jittering to take place also for + continuous observations, if observations are "too" close to each other + new internal method .checkEstClassForParamFamily-method to be called immediately before returning an Estimate object (in functions Estimator(), MCEstimator(), MDEstimator(), MLEstimator()); this allows to return an @@ -55,6 +59,7 @@ "MCEstimate" and "GEVEstimate", so that a diag-method for "GEVEstimate" becomes available for this class. + enhanced imports in DESCRIPTION by explicating second order imports ++ helper function .isReplicated gains an optional argument tol BUGFIXES: Modified: branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd =================================================================== --- branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd 2015-02-18 13:22:31 UTC (rev 995) +++ branches/distr-2.6/pkg/distrMod/man/internals-qqplot.Rd 2015-02-18 13:34:24 UTC (rev 996) @@ -26,8 +26,9 @@ \details{ \code{.labelprep} prepares the labels for later output: -first we (optionally) select some indices among \code{x} according -to \code{which.lbs}, then orders both \code{x} and \code{y} according to the +first some indices among \code{x} according +to \code{which.lbs} are (optionally) selected, +then orders both \code{x} and \code{y} according to the order of the remaining (optionally transformed by \code{order.traf}) values of \code{x} (decreasing); finally only the order statistics (w.r.t. the preceding ordering) as specified in \code{which.Order} are returned; Modified: branches/distr-2.6/pkg/distrMod/man/qqplot.Rd =================================================================== --- branches/distr-2.6/pkg/distrMod/man/qqplot.Rd 2015-02-18 13:22:31 UTC (rev 995) +++ branches/distr-2.6/pkg/distrMod/man/qqplot.Rd 2015-02-18 13:34:24 UTC (rev 996) @@ -10,7 +10,7 @@ ylab = deparse(substitute(y)), ..., width = 10, height = 5.5, withSweave = getdistrOption("withSweave"), mfColRow = TRUE, n.CI = n, withLab = FALSE, lab.pts = NULL, which.lbs = NULL, - which.Order = NULL, order.traf = NULL, + which.Order = NULL, order.traf = NULL, col.IdL = "red", lty.IdL = 2, lwd.IdL = 2, alpha.CI = .95, exact.pCI = (n<100), exact.sCI = (n<100), nosym.pCI = FALSE, col.pCI = "orange", lty.pCI = 3, lwd.pCI = 2, pch.pCI = par("pch"), @@ -19,7 +19,7 @@ cex.sCI = par("cex"), added.points.CI = TRUE, cex.pch = par("cex"), col.pch = par("col"), cex.lbl = par("cex"), col.lbl = par("col"), adj.lbl = NULL, - alpha.trsp = NA, jit.fac = 0, + alpha.trsp = NA, jit.fac = 0, jit.tol = .Machine$double.eps, check.NotInSupport = TRUE, col.NotInSupport = "red", with.legend = TRUE, legend.bg = "white", legend.pos = "topleft", legend.cex = 0.8, @@ -107,7 +107,9 @@ while for the remaining ones, the alpha channel in rgb space is set to the respective coordinate value of \code{alpha.trsp}. The non-NA entries must be integers in [0,255] (0 invisible, 255 opaque).} -\item{jit.fac}{jittering factor used for discrete distributions} +\item{jit.fac}{jittering factor used for discrete distributions.} +\item{jit.tol}{threshold for jittering: if distance between points is smaller + than \code{jit.tol}, points are considered replicates.} \item{check.NotInSupport}{logical; shall we check if all \code{x}-quantiles lie in \code{support(y)}?} \item{col.NotInSupport}{logical; if preceding check \code{TRUE} color of Modified: branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd =================================================================== --- branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd 2015-02-18 13:22:31 UTC (rev 995) +++ branches/distr-2.6/pkg/distrMod/man/returnlevelplot.Rd 2015-02-18 13:34:24 UTC (rev 996) @@ -13,7 +13,7 @@ main = "", ..., width = 10, height = 5.5, withSweave = getdistrOption("withSweave"), mfColRow = TRUE, n.CI = n, withLab = FALSE, lab.pts = NULL, which.lbs = NULL, - which.Order = NULL, order.traf = NULL, + which.Order = NULL, order.traf = NULL, col.IdL = "red", lty.IdL = 2, lwd.IdL = 2, alpha.CI = .95, exact.pCI = (n<100), exact.sCI = (n<100), nosym.pCI = FALSE, col.pCI = "orange", lty.pCI = 3, lwd.pCI = 2, pch.pCI = par("pch"), @@ -22,7 +22,7 @@ cex.sCI = par("cex"), added.points.CI = TRUE, cex.pch = par("cex"), col.pch = par("col"), cex.lbl = par("cex"), col.lbl = par("col"), adj.lbl = NULL, - alpha.trsp = NA, jit.fac = 0, + alpha.trsp = NA, jit.fac = 0, jit.tol = .Machine$double.eps, check.NotInSupport = TRUE, col.NotInSupport = "red", with.legend = TRUE, legend.bg = "white", legend.pos = "topleft", legend.cex = 0.8, @@ -120,7 +120,9 @@ while for the remaining ones, the alpha channel in rgb space is set to the respective coordinate value of \code{alpha.trsp}. The non-NA entries must be integers in [0,255] (0 invisible, 255 opaque).} -\item{jit.fac}{jittering factor used for discrete distributions} +\item{jit.fac}{jittering factor used for discrete distributions.} +\item{jit.tol}{threshold for jittering: if distance between points is smaller + than \code{jit.tol}, points are considered replicates.} \item{check.NotInSupport}{logical; shall we check if all \code{x}-quantiles lie in \code{support(y)}?} \item{col.NotInSupport}{logical; if preceding check \code{TRUE} color of