diff -Nru r-cran-ellipse-0.3-8/debian/changelog r-cran-ellipse-0.4.1/debian/changelog --- r-cran-ellipse-0.3-8/debian/changelog 2017-09-29 12:36:46.000000000 +0000 +++ r-cran-ellipse-0.4.1/debian/changelog 2018-02-22 08:08:25.000000000 +0000 @@ -1,3 +1,13 @@ +r-cran-ellipse (0.4.1-1) unstable; urgency=medium + + * New upstream version + * Secure URI in watch file + * Standards-Version: 4.1.3 + * debhelper 11 + * Testsuite: autopkgtest-pkg-r + + -- Andreas Tille Thu, 22 Feb 2018 09:08:25 +0100 + r-cran-ellipse (0.3-8-2) unstable; urgency=medium * Moved packaging from SVN to Git diff -Nru r-cran-ellipse-0.3-8/debian/compat r-cran-ellipse-0.4.1/debian/compat --- r-cran-ellipse-0.3-8/debian/compat 2017-09-29 12:36:46.000000000 +0000 +++ r-cran-ellipse-0.4.1/debian/compat 2018-02-22 08:08:25.000000000 +0000 @@ -1 +1 @@ -10 +11 diff -Nru r-cran-ellipse-0.3-8/debian/control r-cran-ellipse-0.4.1/debian/control --- r-cran-ellipse-0.3-8/debian/control 2017-09-29 12:36:46.000000000 +0000 +++ r-cran-ellipse-0.4.1/debian/control 2018-02-22 08:08:25.000000000 +0000 @@ -3,10 +3,11 @@ Uploaders: Andreas Tille Section: gnu-r Priority: optional -Build-Depends: debhelper (>= 10), +Testsuite: autopkgtest-pkg-r +Build-Depends: debhelper (>= 11~), dh-r, r-base-dev -Standards-Version: 4.1.0 +Standards-Version: 4.1.3 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-cran-ellipse.git Vcs-Git: https://anonscm.debian.org/git/debian-med/r-cran-ellipse.git Homepage: https://cran.r-project.org/package=ellipse diff -Nru r-cran-ellipse-0.3-8/debian/watch r-cran-ellipse-0.4.1/debian/watch --- r-cran-ellipse-0.3-8/debian/watch 2017-09-29 12:36:46.000000000 +0000 +++ r-cran-ellipse-0.4.1/debian/watch 2018-02-22 08:08:25.000000000 +0000 @@ -1,2 +1,2 @@ -version=3 -http://cran.r-project.org/src/contrib/ellipse_([-\d.]*)\.tar\.gz +version=4 +https://cran.r-project.org/src/contrib/ellipse_([-\d.]*)\.tar\.gz diff -Nru r-cran-ellipse-0.3-8/DESCRIPTION r-cran-ellipse-0.4.1/DESCRIPTION --- r-cran-ellipse-0.3-8/DESCRIPTION 2013-04-13 16:32:27.000000000 +0000 +++ r-cran-ellipse-0.4.1/DESCRIPTION 2018-01-05 23:52:13.000000000 +0000 @@ -1,23 +1,21 @@ Package: ellipse -Version: 0.3-8 -Date: 2013-04-13 -Title: Functions for drawing ellipses and ellipse-like confidence - regions -Author: Duncan Murdoch and E. D. Chow (porting - to R by Jesus M. Frias Celayeta ) +Version: 0.4.1 +Title: Functions for Drawing Ellipses and Ellipse-Like Confidence + Regions +Author: Duncan Murdoch and E. D. Chow + (porting to R by Jesus M. Frias Celayeta ) Maintainer: Duncan Murdoch -Description: This package contains various routines for drawing - ellipses and ellipse-like confidence regions, implementing the - plots described in Murdoch and Chow (1996), A graphical display - of large correlation matrices, The American Statistician 50, - 178-180. There are also routines implementing the profile plots - described in Bates and Watts (1988), Nonlinear Regression - Analysis and its Applications. +Description: Contains various routines for drawing + ellipses and ellipse-like confidence regions, implementing the plots + described in Murdoch and Chow (1996), A graphical display of large + correlation matrices, The American Statistician 50, 178-180. There are + also routines implementing the profile plots described in Bates and + Watts (1988), Nonlinear Regression Analysis and its Applications. Depends: R (>= 2.0.0),graphics,stats Suggests: MASS LazyLoad: yes License: GPL (>= 2) -Packaged: 2013-04-13 14:23:12 UTC; murdoch NeedsCompilation: no +Packaged: 2018-01-05 17:15:30 UTC; murdoch Repository: CRAN -Date/Publication: 2013-04-13 18:32:27 +Date/Publication: 2018-01-05 23:52:13 UTC diff -Nru r-cran-ellipse-0.3-8/man/ellipse.profile.nls.Rd r-cran-ellipse-0.4.1/man/ellipse.profile.nls.Rd --- r-cran-ellipse-0.3-8/man/ellipse.profile.nls.Rd 2013-04-13 14:23:11.000000000 +0000 +++ r-cran-ellipse-0.4.1/man/ellipse.profile.nls.Rd 2018-01-04 23:50:46.000000000 +0000 @@ -8,8 +8,9 @@ model. } \usage{ -\method{ellipse}{profile.nls}(x, which = c(1, 2), level = 0.95, t = sqrt(2 * qf(level, 2, attr(x, "summary")$df[2])), - npoints = 100, \dots) +\method{ellipse}{profile.nls}(x, which = c(1, 2), level = 0.95, + t = sqrt(2 * qf(level, 2, attr(x, "summary")$df[2])), + npoints = 100, \dots) } \arguments{ \item{x}{ diff -Nru r-cran-ellipse-0.3-8/man/pairs.profile.Rd r-cran-ellipse-0.4.1/man/pairs.profile.Rd --- r-cran-ellipse-0.3-8/man/pairs.profile.Rd 2013-04-13 14:23:11.000000000 +0000 +++ r-cran-ellipse-0.4.1/man/pairs.profile.Rd 2018-01-05 15:16:36.000000000 +0000 @@ -52,6 +52,30 @@ \details{ This function implements the plots used in Bates and Watts (1988) for nonlinear regression diagnostics. + +Unfortunately, the \pkg{MASS} package also defines a +\code{\link[MASS:plot.profile]{pairs.profile}} method. The \code{ellipse::\link{pairs}} +generic is supplied to allow users to choose to use +the version in this package. + +If \code{x} is a profile object, then \code{ellipse::pairs(x)} +is guaranteed to call the method from this package. If you'd rather use +the \pkg{MASS} method, then two steps are needed: you need to +be sure that \pkg{MASS} is loaded, then call \code{graphics::pairs(x)}. +(If \pkg{MASS} is not loaded, you'll get the default method from the \pkg{graphics} package, which will +trigger an error since it doesn't know about profile +objects.) + +If both \pkg{ellipse} and \pkg{MASS} are loaded, then \code{pairs(x)} +is slightly ambiguous: the method that is called depends +on the ordering of \pkg{ellipse} and \pkg{graphics} (not \pkg{MASS}!) in the search list. In almost all cases +\pkg{ellipse} will precede \pkg{graphics}, so the \pkg{ellipse} method will usually be the default. + + +If \code{x} is any object +other than a profile object, \code{ellipse::pairs(x)} +will pass the call on to \code{graphics::pairs(x)}, +and the standard method will be called. } \references{ Bates and Watts (1988), Nonlinear Regression Analysis \& its @@ -67,7 +91,11 @@ * conc)/(K + conc), data = Puromycin, start = list(Vm = 160, delV = 40, K = 0.05)) Pur.prof <- profile(Purboth) - pairs(Pur.prof, plot.ellipse = TRUE) + ellipse::pairs(Pur.prof, plot.ellipse = TRUE) + + # Show the corresponding plot from MASS: + if (requireNamespace("MASS")) + graphics::pairs(Pur.prof) } \keyword{dplot} \keyword{regression} diff -Nru r-cran-ellipse-0.3-8/man/pairs.Rd r-cran-ellipse-0.4.1/man/pairs.Rd --- r-cran-ellipse-0.3-8/man/pairs.Rd 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-ellipse-0.4.1/man/pairs.Rd 2018-01-05 14:17:38.000000000 +0000 @@ -0,0 +1,44 @@ +\name{pairs} +\alias{pairs} +\alias{pairs.default} +\alias{pairs.formula} +\title{ +Scatterplot Matrix +} +\description{ +A matrix of scatterplots is produced. +} +\usage{ +pairs(x, ...) +\method{pairs}{default}(x, ...) +\method{pairs}{formula}(formula, data = NULL, ..., subset, + na.action = stats::na.pass) +} +\arguments{ + \item{x}{ +An object containing the data to plot. +} + \item{formula, data, subset, na.action}{See \code{\link[graphics]{pairs}}}. + \item{\dots}{ +Other arguments to pass to the methods. +} +} +\details{ +The \pkg{ellipse} package defines a \code{\link{pairs.profile}} +method for profile objects. Unfortunately, +so does the \pkg{MASS} package. The \code{ellipse::pairs} +generic is supplied to allow users to choose to use +the version in this package. See the \code{\link{pairs.profile}} +help page for more details. +} +\value{ +Typically no useful value is produced; this generic +function is called for the side effect of producing the +display. +} +\seealso{ +\code{\link{pairs.profile}} for the method from this package. +} +\examples{ +example(pairs, "graphics") +} diff -Nru r-cran-ellipse-0.3-8/man/plotcorr.Rd r-cran-ellipse-0.4.1/man/plotcorr.Rd --- r-cran-ellipse-0.3-8/man/plotcorr.Rd 2013-04-13 14:23:11.000000000 +0000 +++ r-cran-ellipse-0.4.1/man/plotcorr.Rd 2018-01-04 23:52:57.000000000 +0000 @@ -1,81 +1,84 @@ -\name{plotcorr} -\alias{plotcorr} -\title{ -Plot correlation matrix ellipses -} -\description{ -This function plots a correlation matrix using ellipse-shaped glyphs for -each entry. The ellipse represents a level curve of the density of a -bivariate normal with the matching correlation. -} -\usage{ -plotcorr(corr, outline = TRUE, col = 'grey', numbers = FALSE, type = c("full","lower","upper"), - diag = (type == "full"), bty = "n", axes = FALSE, xlab = "", ylab = "", asp = 1, - cex.lab = par("cex.lab"), cex = 0.75*par("cex"), mar = 0.1 + c(2,2,4,2), ...) -} -\arguments{ -\item{corr}{ -A matrix containing entries between \code{-1} and \code{1} to be plotted as -correlations. -} -\item{outline}{ -Whether the ellipses should be outlined in the default colour. -} -\item{col}{ -Which colour(s) to use to fill the ellipses. -} -\item{numbers}{ -Whether to plot numerical correlations in place of ellipses. If -numbers is \code{TRUE}, then the correlations will be rounded to a single decimal -place and placed on the plot. -} -\item{type}{Character. Plot \code{"full"} matrix or just \code{"upper"} or - \code{"lower"} triangular part of it.} -\item{diag}{Logical. Plot diagonal elements or not. } -\item{bty, axes, xlab, ylab, asp, mar, cex.lab, ...}{Graphical parameters -which will be passed to \code{\link{plot}} when plotting.} -\item{cex}{Graphical parameter -which will be passed to \code{\link{text}} when plotting.} -} -\details{ -The ellipses being plotted will be tangent to a unit character square, -with the shape chosen to match the required correlation. If \code{numbers = FALSE}, -the \code{col} vector will be recycled to colour each of the ellipses; if -\code{TRUE}, it will be ignored. -} -\references{ -Murdoch, D.J. and Chow, E.D. (1996). A graphical display of large -correlation matrices. The American Statistician 50, 178-180. -} -\seealso{ -\code{\link{ellipse}} -} -\author{Duncan Murdoch; Gregor Gorjanc suggested the \code{type} and \code{diag} -options.} -\examples{ -save.par <- par(ask = interactive()) - -# Plot the correlation matrix for the mtcars data full model fit -data(mtcars) -fit <- lm(mpg ~ ., mtcars) -plotcorr(summary(fit, correlation = TRUE)$correlation) - -# Plot a second figure with numbers in place of the -# ellipses -plotcorr(summary(fit, correlation = TRUE)$correlation, numbers = TRUE) - -# Colour the ellipses to emphasize the differences. The color range -# is based on RColorBrewer's Reds and Blues (suggested by Gregor Gorjanc) - -corr.mtcars <- cor(mtcars) -ord <- order(corr.mtcars[1,]) -xc <- corr.mtcars[ord, ord] -colors <- c("#A50F15","#DE2D26","#FB6A4A","#FCAE91","#FEE5D9","white", - "#EFF3FF","#BDD7E7","#6BAED6","#3182BD","#08519C") -plotcorr(xc, col=colors[5*xc + 6]) - -plotcorr(xc, col=colors[5*xc + 6], type = "upper") -plotcorr(xc, col=colors[5*xc + 6], type = "lower", diag = TRUE) -par(save.par) -} -\keyword{hplot} +\name{plotcorr} +\alias{plotcorr} +\title{ +Plot correlation matrix ellipses +} +\description{ +This function plots a correlation matrix using ellipse-shaped glyphs for +each entry. The ellipse represents a level curve of the density of a +bivariate normal with the matching correlation. +} +\usage{ +plotcorr(corr, outline = TRUE, col = 'grey', numbers = FALSE, + type = c("full","lower","upper"), + diag = (type == "full"), bty = "n", axes = FALSE, + xlab = "", ylab = "", asp = 1, + cex.lab = par("cex.lab"), cex = 0.75*par("cex"), + mar = 0.1 + c(2,2,4,2), ...) +} +\arguments{ +\item{corr}{ +A matrix containing entries between \code{-1} and \code{1} to be plotted as +correlations. +} +\item{outline}{ +Whether the ellipses should be outlined in the default colour. +} +\item{col}{ +Which colour(s) to use to fill the ellipses. +} +\item{numbers}{ +Whether to plot numerical correlations in place of ellipses. If +numbers is \code{TRUE}, then the correlations will be rounded to a single decimal +place and placed on the plot. +} +\item{type}{Character. Plot \code{"full"} matrix or just \code{"upper"} or + \code{"lower"} triangular part of it.} +\item{diag}{Logical. Plot diagonal elements or not. } +\item{bty, axes, xlab, ylab, asp, mar, cex.lab, ...}{Graphical parameters +which will be passed to \code{\link{plot}} when plotting.} +\item{cex}{Graphical parameter +which will be passed to \code{\link{text}} when plotting.} +} +\details{ +The ellipses being plotted will be tangent to a unit character square, +with the shape chosen to match the required correlation. If \code{numbers = FALSE}, +the \code{col} vector will be recycled to colour each of the ellipses; if +\code{TRUE}, it will be ignored. +} +\references{ +Murdoch, D.J. and Chow, E.D. (1996). A graphical display of large +correlation matrices. The American Statistician 50, 178-180. +} +\seealso{ +\code{\link{ellipse}} +} +\author{Duncan Murdoch; Gregor Gorjanc suggested the \code{type} and \code{diag} +options.} +\examples{ +save.par <- par(ask = interactive()) + +# Plot the correlation matrix for the mtcars data full model fit +data(mtcars) +fit <- lm(mpg ~ ., mtcars) +plotcorr(summary(fit, correlation = TRUE)$correlation) + +# Plot a second figure with numbers in place of the +# ellipses +plotcorr(summary(fit, correlation = TRUE)$correlation, numbers = TRUE) + +# Colour the ellipses to emphasize the differences. The color range +# is based on RColorBrewer's Reds and Blues (suggested by Gregor Gorjanc) + +corr.mtcars <- cor(mtcars) +ord <- order(corr.mtcars[1,]) +xc <- corr.mtcars[ord, ord] +colors <- c("#A50F15","#DE2D26","#FB6A4A","#FCAE91","#FEE5D9","white", + "#EFF3FF","#BDD7E7","#6BAED6","#3182BD","#08519C") +plotcorr(xc, col=colors[5*xc + 6]) + +plotcorr(xc, col=colors[5*xc + 6], type = "upper") +plotcorr(xc, col=colors[5*xc + 6], type = "lower", diag = TRUE) +par(save.par) +} +\keyword{hplot} diff -Nru r-cran-ellipse-0.3-8/MD5 r-cran-ellipse-0.4.1/MD5 --- r-cran-ellipse-0.3-8/MD5 2013-04-13 16:32:27.000000000 +0000 +++ r-cran-ellipse-0.4.1/MD5 2018-01-05 23:52:13.000000000 +0000 @@ -1,5 +1,5 @@ -5cb6594dd0fec32696b1c795ff04253a *DESCRIPTION -c0f8e06aa745d323551c9c17bc5080c4 *NAMESPACE +ab362731acc035daf0a26a4174c260d6 *DESCRIPTION +f1c594cb593f80cd82e09f1e562de22b *NAMESPACE 73fea51373da9bbc4ff85c413745b526 *R/ellipse.R 4be8275a614fcb4065c37b8762941247 *R/ellipse.arima0.R caee0c1cfc23e089ee9ba8f4b4798039 *R/ellipse.default.R @@ -9,9 +9,9 @@ 1f6cc6a9602728096e1a5c17db75a3d1 *R/ellipse.profile.R 179ff82c9db9ac24d7c28250d7dbd4ac *R/ellipse.profile.glm.R e9db7c17f6821149220b411bfd6441a6 *R/ellipse.profile.nls.R -84c9bed516bd61a0b4d5a0a6aadda792 *R/pairs.profile.R +51a4f27c99ed5d47d0ce1445435b49b9 *R/pairs.profile.R f410502cb27f5f2cfaee61bcf133abe3 *R/plotcorr.R -99f607a6fdc968d3ac4feeda1f11bbd7 *README +b58cd88bf88e9e6f2f4570d0db93c8bb *README c72cbb10c7117b72c4661f1e985e20e4 *man/ellipse-package.Rd a20be12fc0bc7bd5f179a90dcacfa291 *man/ellipse.Rd 2a7bc110f3041d43ddd9ae601bf81912 *man/ellipse.arima0.Rd @@ -20,6 +20,7 @@ a44b6aebadb5c6335f6e711b23152475 *man/ellipse.nls.Rd 0f2ec2da5cb8932fd631826ca008e366 *man/ellipse.profile.Rd 7c26b34627f1934d7b601edc1fa43b79 *man/ellipse.profile.glm.Rd -a23b5bebb2dc3e1e01018fa9721db2f8 *man/ellipse.profile.nls.Rd -966139fb90ef34fc4cf99889dde5005d *man/pairs.profile.Rd -a5e1d2e0c9bdebccc53aa17b95d7f4a4 *man/plotcorr.Rd +d61933ab53fb8e18ae250244537e6413 *man/ellipse.profile.nls.Rd +41184b50c2f136f5ba50f6884775a19b *man/pairs.Rd +36e788f8569c1c414c7887c07715c4ed *man/pairs.profile.Rd +fc500238b94fb8b704aba56a7abacd44 *man/plotcorr.Rd diff -Nru r-cran-ellipse-0.3-8/NAMESPACE r-cran-ellipse-0.4.1/NAMESPACE --- r-cran-ellipse-0.3-8/NAMESPACE 2013-04-13 14:23:11.000000000 +0000 +++ r-cran-ellipse-0.4.1/NAMESPACE 2018-01-05 15:16:36.000000000 +0000 @@ -1,4 +1,9 @@ -export(ellipse,plotcorr) +export(ellipse,plotcorr,pairs) + +importFrom("graphics", "axis", "box", "lines", "mtext", "par", "plot", + "plot.new", "polygon", "strwidth", "text") +importFrom("stats", "approx", "qchisq", "qf", "spline") + S3method(ellipse,arima0) S3method(ellipse,default) S3method(ellipse,glm) @@ -8,3 +13,5 @@ S3method(ellipse,profile.glm) S3method(ellipse,profile.nls) S3method(pairs,profile) +S3method(pairs,default,.pairs_default) +S3method(pairs,formula,.pairs_formula) diff -Nru r-cran-ellipse-0.3-8/R/pairs.profile.R r-cran-ellipse-0.4.1/R/pairs.profile.R --- r-cran-ellipse-0.3-8/R/pairs.profile.R 2013-04-13 14:23:11.000000000 +0000 +++ r-cran-ellipse-0.4.1/R/pairs.profile.R 2018-01-05 14:12:38.000000000 +0000 @@ -1,3 +1,24 @@ +pairs <- function(x, ...) + UseMethod("pairs") + +.pairs_default <- function(x, ...) + graphics::pairs(x, ...) + +.pairs_formula <- function(formula, data = NULL, ..., subset, na.action = stats::na.pass) { + # This code is copied from graphics:::pairs.formula + # because the non-standard evaluation wouldn't survive + # the indirect call. + + m <- match.call(expand.dots = FALSE) + if (is.matrix(eval(m$data, parent.frame()))) + m$data <- as.data.frame(data) + m$... <- NULL + m$na.action <- na.action + m[[1L]] <- quote(stats::model.frame) + mf <- eval(m, parent.frame()) + graphics::pairs(mf, ...) +} + "pairs.profile" <- function (x, labels = c(names(x), "Profile tau"), panel = lines, invert = TRUE, plot.tau = TRUE, plot.trace = TRUE, plot.sketch = TRUE, diff -Nru r-cran-ellipse-0.3-8/README r-cran-ellipse-0.4.1/README --- r-cran-ellipse-0.3-8/README 2013-04-13 14:23:11.000000000 +0000 +++ r-cran-ellipse-0.4.1/README 2018-01-05 16:40:04.000000000 +0000 @@ -26,4 +26,11 @@ 0.3.5 (Sep 2007) - License clarification 0.3.6 (Apr 2009) - Bug fix: ... was not being passed from methods to - ellipse.default(). \ No newline at end of file + ellipse.default(). + +0.3.7 (Mar 2012) - Minor fix (clean up DESCRIPTION file) + +0.3.8 (Apr 2013) - Minor fix (no more \synopsis tag in help) + +0.4.1 (Jan 2018) - At request of CRAN, added pairs() generic function to avoid + clash with MASS::pairs.profile, and other minor cleanups.