diff -Nru multcomp-1.4-3/debian/changelog multcomp-1.4-4/debian/changelog --- multcomp-1.4-3/debian/changelog 2016-02-18 23:14:28.000000000 +0000 +++ multcomp-1.4-4/debian/changelog 2016-02-18 23:14:28.000000000 +0000 @@ -1,3 +1,9 @@ +multcomp (1.4-4-1) unstable; urgency=medium + + * New upstream release + + -- Dirk Eddelbuettel Thu, 18 Feb 2016 07:07:18 -0600 + multcomp (1.4-3-2) unstable; urgency=low * debian/control: Add (Build-)Depends: on TH.data (>= 1.0-7-2) which has diff -Nru multcomp-1.4-3/DESCRIPTION multcomp-1.4-4/DESCRIPTION --- multcomp-1.4-3/DESCRIPTION 2016-02-03 11:26:25.000000000 +0000 +++ multcomp-1.4-4/DESCRIPTION 2016-02-17 15:15:33.000000000 +0000 @@ -1,7 +1,7 @@ Package: multcomp Title: Simultaneous Inference in General Parametric Models -Version: 1.4-3 -Date: 2016-02-01 +Version: 1.4-4 +Date: 2016-02-17 Authors@R: c(person("Torsten", "Hothorn", role = c("aut", "cre"), email = "Torsten.Hothorn@R-project.org"), person("Frank", "Bretz", role = "aut"), @@ -25,7 +25,7 @@ LazyData: yes License: GPL-2 NeedsCompilation: no -Packaged: 2016-02-02 13:45:28 UTC; hothorn +Packaged: 2016-02-17 14:22:07 UTC; hothorn Author: Torsten Hothorn [aut, cre], Frank Bretz [aut], Peter Westfall [aut], @@ -34,4 +34,4 @@ Susan Scheibe [ctb] Maintainer: Torsten Hothorn Repository: CRAN -Date/Publication: 2016-02-03 12:26:25 +Date/Publication: 2016-02-17 16:15:33 Binary files /tmp/tmpx41wSj/cMnKVm09yr/multcomp-1.4-3/inst/doc/chfls1.pdf and /tmp/tmpx41wSj/bH5o2gqHR3/multcomp-1.4-4/inst/doc/chfls1.pdf differ Binary files /tmp/tmpx41wSj/cMnKVm09yr/multcomp-1.4-3/inst/doc/generalsiminf.pdf and /tmp/tmpx41wSj/bH5o2gqHR3/multcomp-1.4-4/inst/doc/generalsiminf.pdf differ Binary files /tmp/tmpx41wSj/cMnKVm09yr/multcomp-1.4-3/inst/doc/multcomp-examples.pdf and /tmp/tmpx41wSj/bH5o2gqHR3/multcomp-1.4-4/inst/doc/multcomp-examples.pdf differ diff -Nru multcomp-1.4-3/inst/NEWS multcomp-1.4-4/inst/NEWS --- multcomp-1.4-3/inst/NEWS 2016-02-02 13:43:14.000000000 +0000 +++ multcomp-1.4-4/inst/NEWS 2016-02-17 14:16:41.000000000 +0000 @@ -1,4 +1,8 @@ +Changes in 1.4-4 (2016-01-17) + + o make cftest() a little more flexible with parm and test arguments + Changes in 1.4-3 (2016-01-02) o update Rout.save to mvtnorm 1.0-5 diff -Nru multcomp-1.4-3/man/cftest.Rd multcomp-1.4-4/man/cftest.Rd --- multcomp-1.4-3/man/cftest.Rd 2015-07-21 14:49:44.000000000 +0000 +++ multcomp-1.4-4/man/cftest.Rd 2016-02-03 10:45:11.000000000 +0000 @@ -6,10 +6,13 @@ estimated model coefficients } \usage{ -cftest(model, ...) +cftest(model, parm, test = univariate(), ...) } \arguments{ \item{model}{a fitted model.} + \item{parm}{a vector of parameters to be tested, either a character vector + of names or an integer.} + \item{test}{ a function for computing p values, see \code{\link{summary.glht}}.} \item{\dots}{additional arguments passed to \code{\link{summary.glht}}.} } \details{ @@ -24,10 +27,6 @@ } \examples{ - ## The function is currently defined as - function(model, ...) - summary(glht(model), test = univariate(), ...) - lmod <- lm(dist ~ speed, data = cars) summary(lmod) cftest(lmod) diff -Nru multcomp-1.4-3/MD5 multcomp-1.4-4/MD5 --- multcomp-1.4-3/MD5 2016-02-03 11:26:26.000000000 +0000 +++ multcomp-1.4-4/MD5 2016-02-17 15:15:33.000000000 +0000 @@ -1,4 +1,4 @@ -458ab45041a8e9fb0b8f5ff1b8be61c5 *DESCRIPTION +8aa72fc95770f804e6ac82ffcc554999 *DESCRIPTION 6f1c37daef616f400da863d7c86124f6 *NAMESPACE 04d2a926addbc79ec5839ed9b86b63a0 *R/cld.R fb371dc9bf3a59db5b2045f190fbd296 *R/contrMat.R @@ -7,7 +7,7 @@ db675272bddabc11f1d37698a34537a5 *R/helpers.R 9dba312a1100ead0426531dc7ef25732 *R/maxsets.R 6306519f879a15332f0cf3dac083d030 *R/mcp.R -57bb109cca04b10b6fff06b164b108a9 *R/methods.R +2a908b5885569f86726f01ed479e104d *R/methods.R 4756b6e2ed189086490109391d2815d5 *R/mmm.R 152aafc38dfa2e01def20851d5ae81da *R/parm.R 89a738f023fdbe16cff5ed42b8c313e3 *R/plot.R @@ -38,24 +38,24 @@ 5ccc54941334fbd572cd4891c2009ccc *inst/MCMT/MCMT.Rout.save 26ccee8d5d8bc87c503e43bde27e282f *inst/MCMT/MCMT.rda abd0ee3bb82571b7fb64e8a2e1cf03a2 *inst/MCMT/multcomp.sas -8b62f7c1704da0603df98b6018f3904c *inst/NEWS +cc2fa7a9df3474ee4257d83144a88ee6 *inst/NEWS 09ce7512593c1be00ee89ee431ca6112 *inst/deprecated/deprecated.R fe4cbe4e17edf996147191527f7e9efa *inst/deprecated/multcomp-deprecated.Rd 4fcad824fe2a0c192b10a18cd7da2146 *inst/deprecated/multcomp-oldtests.R 6f2f2667a0374a4f82e3a01067e18b11 *inst/deprecated/multcomp-oldtests.Rout.save 3218dcf4f93b9f33cb0bf21e2d768131 *inst/doc/chfls1.R 624888bf9e4e1fcb49a0de92f401239d *inst/doc/chfls1.Rnw -0da4794a9bf6453689218bad985559ad *inst/doc/chfls1.pdf +c6e488248b29f535d16152d97c67cd1b *inst/doc/chfls1.pdf 38df3029ad9a35883c803f71fe8728d0 *inst/doc/generalsiminf.R 01edc2335733d9ff0091c32567ebb9eb *inst/doc/generalsiminf.Rnw -404d5b72d41059e64da1c5bde16236ce *inst/doc/generalsiminf.pdf +2139385e74f01e69cdfe32d18ae8f888 *inst/doc/generalsiminf.pdf ebfe06d5557e1d187ff34d3cb5abe225 *inst/doc/multcomp-examples.R 3a8b15057cde66a53b6919441ca87c9b *inst/doc/multcomp-examples.Rnw -31a57bade248fa802caf61e9a94d6bcc *inst/doc/multcomp-examples.pdf +e46f6d22b8af406fb0bc9d60bfa8908e *inst/doc/multcomp-examples.pdf b8db88a39fe73ccefbd7deaaffdec3cd *inst/multcomp_VA.R 625d3532deb47821fb6964cc748cd343 *inst/multcomp_coxme.R 02a0956bb972a95339c890c34435a986 *man/adevent.Rd -7417d8b29766136541d71afaf1a8460b *man/cftest.Rd +5b84b06bb90c685c6752693dbcfcd8bd *man/cftest.Rd 173f1a6dfa71baef3274ee8df22805d7 *man/cholesterol.Rd da4c9f2280f9bd61d6cc596da9b199f2 *man/cld.Rd 78fec2a89429210566b4c18b2adbe784 *man/cml.Rd @@ -74,7 +74,7 @@ 760f47a9610cfb8556b849bd4b55925c *man/sbp.Rd fd77916439e541d1243818afc0a2f88a *man/trees513.Rd e39aa3a890fbaa03f75ef666c4a5c3d7 *man/waste.Rd -4de6dcd6d5caebb0689231d195f99b1b *tests/Examples/multcomp-Ex.Rout.save +dca577d5fc713f9e2866f8b176813fa7 *tests/Examples/multcomp-Ex.Rout.save 65ae23422858c188a5b0d9d99e4be34d *tests/angina.rda 1462e90578c119b70bd1a1c6b4f7f8e0 *tests/bugfix.R 67110f9c809cbea3dab0c8a0bf3d0827 *tests/bugfix.Rout.save diff -Nru multcomp-1.4-3/R/methods.R multcomp-1.4-4/R/methods.R --- multcomp-1.4-3/R/methods.R 2013-10-04 10:20:47.000000000 +0000 +++ multcomp-1.4-4/R/methods.R 2016-02-03 10:58:04.000000000 +0000 @@ -1,5 +1,5 @@ -# $Id: methods.R 288 2010-02-22 16:52:09Z thothorn $ +# $Id: methods.R 431 2016-02-03 10:58:04Z thothorn $ ### methods for `glht' objects coef.glht <- function(object, rhs = FALSE, ...) @@ -63,5 +63,19 @@ return(object) } -cftest <- function(model, ...) - summary(glht(model), test = univariate(), ...) +cftest <- function(model, parm, test = univariate(), ...) { + if (missing(parm)) + return(summary(glht(model), test = test, ...)) + cf <- coef(model) + if (is.character(parm)) { + iparm <- match(parm, names(cf)) + } else { + iparm <- match(parm, 1:length(cf)) + } + if (any(is.na(iparm))) + stop("cannot find variable(s): ", paste(parm[is.na(iparm)], + collapse = ",")) + K <- diag(length(cf))[iparm, , drop = FALSE] + rownames(K) <- names(cf)[iparm] + summary(glht(model, linfct = K), test = test, ...) +} diff -Nru multcomp-1.4-3/tests/Examples/multcomp-Ex.Rout.save multcomp-1.4-4/tests/Examples/multcomp-Ex.Rout.save --- multcomp-1.4-3/tests/Examples/multcomp-Ex.Rout.save 2016-02-02 13:40:34.000000000 +0000 +++ multcomp-1.4-4/tests/Examples/multcomp-Ex.Rout.save 2016-02-17 14:21:37.000000000 +0000 @@ -1,6 +1,6 @@ -R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" -Copyright (C) 2015 The R Foundation for Statistical Computing +R Under development (unstable) (2016-02-15 r70179) -- "Unsuffered Consequences" +Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. @@ -20,6 +20,18 @@ > pkgname <- "multcomp" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) +> base::assign(".ExTimings", "multcomp-Ex.timings", pos = 'CheckExEnv') +> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv')) +> base::assign(".format_ptime", ++ function(x) { ++ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L] ++ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L] ++ options(OutDec = '.') ++ format(x[1L:3L], digits = 7L) ++ }, ++ pos = 'CheckExEnv') +> +> ### * > library('multcomp') Loading required package: mvtnorm Loading required package: survival @@ -40,6 +52,7 @@ > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cftest > ### Title: Testing Estimated Coefficients > ### Aliases: cftest @@ -48,12 +61,6 @@ > ### ** Examples > > -> ## The function is currently defined as -> function(model, ...) -+ summary(glht(model), test = univariate(), ...) -function (model, ...) -summary(glht(model), test = univariate(), ...) -> > lmod <- lm(dist ~ speed, data = cars) > summary(lmod) @@ -93,12 +100,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("cftest", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("cholesterol") > ### * cholesterol > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cholesterol > ### Title: Cholesterol Reduction Data Set > ### Aliases: cholesterol @@ -224,12 +234,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("cholesterol", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("cld") > ### * cld > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cld > ### Title: Set up a compact letter display of all pair-wise comparisons > ### Aliases: cld cld.glht cld.summary.glht cld.confint.glht @@ -278,6 +291,8 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("cld", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > graphics::par(get("par.postscript", pos = 'CheckExEnv')) > cleanEx() > nameEx("cml") @@ -285,6 +300,7 @@ > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cml > ### Title: Chronic Myelogenous Leukemia survival data. > ### Aliases: cml @@ -323,6 +339,8 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("cml", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() detaching ‘package:coxme’, ‘package:bdsmatrix’ @@ -332,6 +350,7 @@ > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: contrMat > ### Title: Contrast Matrices > ### Aliases: contrMat @@ -448,12 +467,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("contrMat", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("detergent") > ### * detergent > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: detergent > ### Title: Detergent Durability Data Set > ### Aliases: detergent @@ -576,12 +598,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("detergent", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("fattyacid") > ### * fattyacid > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fattyacid > ### Title: Fatty Acid Content of Bacillus simplex. > ### Aliases: fattyacid @@ -638,6 +663,8 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("fattyacid", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() detaching ‘package:sandwich’ @@ -647,6 +674,7 @@ > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: glht > ### Title: General Linear Hypotheses > ### Aliases: glht glht.matrix glht.character glht.expression glht.mcp @@ -825,12 +853,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("glht", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("litter") > ### * litter > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: litter > ### Title: Litter Weights Data Set > ### Aliases: litter @@ -985,12 +1016,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("litter", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("methods") > ### * methods > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: glht-methods > ### Title: Methods for General Linear Hypotheses > ### Aliases: summary.glht confint.glht coef.glht vcov.glht plot.glht @@ -1129,12 +1163,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("methods", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("mmm") > ### * mmm > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: mmm > ### Title: Simultaneous Inference for Multiple Marginal Models > ### Aliases: mmm mlf @@ -1488,6 +1525,8 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("mmm", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() detaching ‘package:sandwich’, ‘package:SimComp’ @@ -1497,6 +1536,7 @@ > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: parm > ### Title: Model Parameters > ### Aliases: parm @@ -1535,12 +1575,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("parm", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("plot.cld") > ### * plot.cld > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot.cld > ### Title: Plot a cld object > ### Aliases: plot.cld @@ -1641,6 +1684,8 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("plot.cld", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > graphics::par(get("par.postscript", pos = 'CheckExEnv')) > cleanEx() @@ -1651,6 +1696,7 @@ > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: recovery > ### Title: Recovery Time Data Set > ### Aliases: recovery @@ -1714,12 +1760,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("recovery", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("trees513") > ### * trees513 > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: trees513 > ### Title: Frankonian Tree Damage Data > ### Aliases: trees513 @@ -1741,12 +1790,15 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("trees513", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("waste") > ### * waste > > flush(stderr()); flush(stdout()) > +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: waste > ### Title: Industrial Waste Data Set > ### Aliases: waste @@ -1895,11 +1947,13 @@ > > > +> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") +> base::cat("waste", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > ### *