diff -Nru r-cran-epitools-0.5-7/debian/changelog r-cran-epitools-0.5-9/debian/changelog --- r-cran-epitools-0.5-7/debian/changelog 2017-09-28 10:33:11.000000000 +0000 +++ r-cran-epitools-0.5-9/debian/changelog 2017-10-12 15:00:14.000000000 +0000 @@ -1,14 +1,17 @@ -r-cran-epitools (1:0.5-7-1build2) artful; urgency=medium +r-cran-epitools (1:0.5-9-1) unstable; urgency=medium - * No-change rebuild to pick up r-api-3.4 + * New upstream version + * Moved packaging from SVN to Git + * Convert packaging from cdbs do dh-r + * debhelper 10 + * Standards-Version: 4.1.1 + * Canonical homepage for CRAN packages + * DEP5 fixes + * Remove useless comment from watch file + * Add Testsuite: autopkgtest-pkg-r + * Add debian/README.source to document binary data files - -- Graham Inggs Thu, 28 Sep 2017 10:33:11 +0000 - -r-cran-epitools (1:0.5-7-1build1) saucy; urgency=low - - * Rebuild against R 3.0.0. - - -- Colin Watson Mon, 20 May 2013 10:05:29 +0100 + -- Andreas Tille Thu, 12 Oct 2017 17:00:17 +0200 r-cran-epitools (1:0.5-7-1) unstable; urgency=low diff -Nru r-cran-epitools-0.5-7/debian/compat r-cran-epitools-0.5-9/debian/compat --- r-cran-epitools-0.5-7/debian/compat 2013-04-21 00:45:52.000000000 +0000 +++ r-cran-epitools-0.5-9/debian/compat 2017-10-12 15:00:14.000000000 +0000 @@ -1 +1 @@ -9 +10 diff -Nru r-cran-epitools-0.5-7/debian/control r-cran-epitools-0.5-9/debian/control --- r-cran-epitools-0.5-7/debian/control 2013-04-21 01:06:53.000000000 +0000 +++ r-cran-epitools-0.5-9/debian/control 2017-10-12 15:00:14.000000000 +0000 @@ -4,21 +4,21 @@ Charles Plessy Section: gnu-r Priority: optional -Build-Depends: debhelper (>= 9), - cdbs, +Testsuite: autopkgtest-pkg-r +Build-Depends: debhelper (>= 10), + dh-r, r-base-dev -Standards-Version: 3.9.4 -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-epitools/trunk/ -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-epitools/trunk/ -Homepage: http://medepi.com/epitools/ +Standards-Version: 4.1.1 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-cran-epitools.git +Vcs-Git: https://anonscm.debian.org/git/debian-med/r-cran-epitools.git +Homepage: https://cran.r-project.org/package=epitools Package: r-cran-epitools Architecture: all -Depends: ${shlibs:Depends}, +Depends: ${misc:Depends}, ${R:Depends} -Suggests: r-cran-surveillance, - r-cran-epi, - r-cran-epibasix +Recommends: ${R:Recommends} +Suggests: ${R:Suggests} Description: GNU R Epidemiology Tools for Data and Graphics GNU R Tools for public health epidemiologists and data analysts. Epitools provides numerical tools and programming solutions that @@ -35,4 +35,3 @@ available for the problem in front of them. The availability of these tools will encourage wider use of appropriate methods and promote evidence-based public health practices. - diff -Nru r-cran-epitools-0.5-7/debian/copyright r-cran-epitools-0.5-9/debian/copyright --- r-cran-epitools-0.5-7/debian/copyright 2013-04-21 01:06:20.000000000 +0000 +++ r-cran-epitools-0.5-9/debian/copyright 2017-10-12 15:00:14.000000000 +0000 @@ -1,8 +1,17 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Source: http://cran.r-project.org/src/contrib/epitools_0.5-7.tar.gz +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Contact: Adam Omidpanah +Upstream-Name: epitools +Source: https://cran.r-project.org/package=epitools Files: * -Copyright: 2003-2009 Tomas Aragon +Copyright: 2003-2017 Tomas Aragon +License: GPL-2+ + +Files: debian/* +Copyright: 2008-2017 Andreas Tille + 2009-2017 Charles Plessy +License: GPL-2+ + License: GPL-2+ 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 @@ -14,14 +23,5 @@ 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, see . -Comment: On Debian systems, the complete text of the GNU Public + On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. - -Files: debian/* -Copyright: 2008 Andreas Tille - 2009 Charles Plessy -License: same - Same as r-cran-epitools itelf - diff -Nru r-cran-epitools-0.5-7/debian/README.source r-cran-epitools-0.5-9/debian/README.source --- r-cran-epitools-0.5-7/debian/README.source 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-epitools-0.5-9/debian/README.source 2017-10-12 15:00:14.000000000 +0000 @@ -0,0 +1,16 @@ +Explanation for binary files inside source package according to + http://lists.debian.org/debian-devel/2013/09/msg00332.html + +Files: data/oswego.rda +Documented: man/oswego.Rd + Outbreak of Gastrointestinal Illness in Oswego County, 1940 + +Files: data/wcgs.rda +Documented: man/wcgs.Rd + Western Collaborative Group Study data + +Files: data/wnv.rda +Documented: man/wnv.Rd + West Nile Virus human cases reported in California, USA, as of December 14, 2004 + + -- Andreas Tille Mon, 09 Oct 2017 17:29:44 +0200 diff -Nru r-cran-epitools-0.5-7/debian/rules r-cran-epitools-0.5-9/debian/rules --- r-cran-epitools-0.5-7/debian/rules 2013-04-21 00:46:39.000000000 +0000 +++ r-cran-epitools-0.5-9/debian/rules 2017-10-12 15:00:14.000000000 +0000 @@ -1,3 +1,4 @@ #!/usr/bin/make -f -include /usr/share/R/debian/r-cran.mk +%: + dh $@ --buildsystem R File /tmp/tmp3aqAye/aRPFhevgnv/r-cran-epitools-0.5-7/debian/upstream is a regular file while file /tmp/tmp3aqAye/njntBJxOoS/r-cran-epitools-0.5-9/debian/upstream is a directory diff -Nru r-cran-epitools-0.5-7/debian/watch r-cran-epitools-0.5-9/debian/watch --- r-cran-epitools-0.5-7/debian/watch 2009-11-19 14:32:02.000000000 +0000 +++ r-cran-epitools-0.5-9/debian/watch 2017-10-12 15:00:14.000000000 +0000 @@ -1,6 +1,2 @@ -version=3 -# Stay with the original version numbering even if it contains a dash -# as agreed with other maintainers of R packages and it should be mentioned -# in a Debian R policy -# opts="dversionmangle=s/([\d.]+)\.(\d)/$1-$2/" \ -http://cran.r-project.org/src/contrib/epitools_([-\d.]+)\.tar\.gz +version=4 +http://cran.r-project.org/src/contrib/epitools_([-\d.]*)\.tar\.gz diff -Nru r-cran-epitools-0.5-7/DESCRIPTION r-cran-epitools-0.5-9/DESCRIPTION --- r-cran-epitools-0.5-7/DESCRIPTION 2012-09-30 09:29:17.000000000 +0000 +++ r-cran-epitools-0.5-9/DESCRIPTION 2017-04-14 23:04:36.000000000 +0000 @@ -1,19 +1,21 @@ Package: epitools -Version: 0.5-7 -Date: 2012-09-30 +Version: 0.5-9 +Date: 2017-04-13 Title: Epidemiology Tools -Authors@R: c(person("Tomas J. Aragon", "Developer", role = c("aut", - "cre"), email = "aragon@berkeley.edu"), person("Michael P. - Fay", "User", role = "ctb", email = "mfay@niaid.nih.gov"), - person("Daniel Wollschlaeger", "User", role = "ctb", email = - "dwoll@psychologie.uni-kiel.de")) +Authors@R: c(person("Tomas J.", "Aragon", role = "aut", + email = "aragon@berkeley.edu"), person("Michael P.", + "Fay", role = "ctb", email = "mfay@niaid.nih.gov"), + person("Daniel", "Wollschlaeger", role = "ctb", email = + "dwoll@psychologie.uni-kiel.de"), + person("Adam", "Omidpanah", role = c("cre", "ctb"), email = + "adam.omidpanah@wsu.edu")) Depends: R (>= 2.1.0) -Description: EpiTools: R Package for Epidemiologic Data and Graphics +Description: Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables. License: GPL (>= 2) -URL: http://medepi.com/epitools/ -Packaged: 2012-09-30 09:01:55 UTC; tja -Author: Tomas J. Aragon Developer [aut, cre], Michael P. Fay User - [ctb], Daniel Wollschlaeger User [ctb] -Maintainer: Tomas J. Aragon Developer +Packaged: 2017-04-14 17:48:42 UTC; adam.omidpanah +Author: Tomas J. Aragon [aut], Michael P. Fay + [ctb], Daniel Wollschlaeger [ctb], Adam Omidpanah [cre, ctb] +Maintainer: Adam Omidpanah Repository: CRAN -Date/Publication: 2012-09-30 09:29:17 +Date/Publication: 2017-04-14 23:04:36 UTC +NeedsCompilation: no diff -Nru r-cran-epitools-0.5-7/man/ageadjust.direct.Rd r-cran-epitools-0.5-9/man/ageadjust.direct.Rd --- r-cran-epitools-0.5-7/man/ageadjust.direct.Rd 2012-09-30 08:22:42.000000000 +0000 +++ r-cran-epitools-0.5-9/man/ageadjust.direct.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -62,9 +62,9 @@ } \author{Michael P. Fay, \email{mfay@niaid.nih.gov}; Tomas Aragon, - \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} + \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/man/ageadjust.indirect.Rd r-cran-epitools-0.5-9/man/ageadjust.indirect.Rd --- r-cran-epitools-0.5-7/man/ageadjust.indirect.Rd 2012-09-30 08:22:58.000000000 +0000 +++ r-cran-epitools-0.5-9/man/ageadjust.indirect.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -56,11 +56,11 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}. Thanks to Giles Crane + \url{http://www.phdata.science}. Thanks to Giles Crane (\email{giles.crane@doh.state.nj.us}) for reporting error in 'ageadjust.indirect' function.} -\note{Visit \url{http://medepi.com} for the latest} +\note{Visit \url{https://repitools.wordpress.com/} for the latest} %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/man/as.hour.Rd r-cran-epitools-0.5-9/man/as.hour.Rd --- r-cran-epitools-0.5-7/man/as.hour.Rd 2012-09-30 08:23:10.000000000 +0000 +++ r-cran-epitools-0.5-9/man/as.hour.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -86,9 +86,9 @@ \references{none} \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ epitools: \code{\link{as.month}}, \code{\link{epicurve.dates}} diff -Nru r-cran-epitools-0.5-7/man/as.month.Rd r-cran-epitools-0.5-9/man/as.month.Rd --- r-cran-epitools-0.5-7/man/as.month.Rd 2012-09-30 08:23:23.000000000 +0000 +++ r-cran-epitools-0.5-9/man/as.month.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -114,9 +114,9 @@ \references{none} -\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} +\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ epitools: \code{\link{as.week}}, \code{\link{epicurve.dates}} diff -Nru r-cran-epitools-0.5-7/man/as.week.Rd r-cran-epitools-0.5-9/man/as.week.Rd --- r-cran-epitools-0.5-7/man/as.week.Rd 2012-09-30 08:23:35.000000000 +0000 +++ r-cran-epitools-0.5-9/man/as.week.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -123,9 +123,9 @@ \references{none} \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ epitools: \code{\link{as.month}}, \code{\link{epicurve.dates}} diff -Nru r-cran-epitools-0.5-7/man/binom.conf.int.Rd r-cran-epitools-0.5-9/man/binom.conf.int.Rd --- r-cran-epitools-0.5-7/man/binom.conf.int.Rd 2012-09-30 08:23:47.000000000 +0000 +++ r-cran-epitools-0.5-9/man/binom.conf.int.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -51,16 +51,16 @@ \references{ Tomas Aragon, et al. Applied Epidemiology Using R. Available at - \url{http://medepi.com} + \url{http://www.phdata.science} Kenneth Rothman (2002), Epidemiology: An Introduction, Oxford University Press, 1st Edition. } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{pois.exact}}, \code{\link[stats]{binom.test}} diff -Nru r-cran-epitools-0.5-7/man/colorbrewer.Rd r-cran-epitools-0.5-9/man/colorbrewer.Rd --- r-cran-epitools-0.5-7/man/colorbrewer.Rd 2012-09-30 08:24:31.000000000 +0000 +++ r-cran-epitools-0.5-9/man/colorbrewer.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -82,10 +82,10 @@ \author{ Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com} + \url{http://www.phdata.science} } -\note{Visit \url{http://medepi.com} for the latest.} + %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/man/colors.plot.Rd r-cran-epitools-0.5-9/man/colors.plot.Rd --- r-cran-epitools-0.5-7/man/colors.plot.Rd 2012-09-30 08:24:40.000000000 +0000 +++ r-cran-epitools-0.5-9/man/colors.plot.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -55,9 +55,9 @@ none } -\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} +\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/man/epicurve.Rd r-cran-epitools-0.5-9/man/epicurve.Rd --- r-cran-epitools-0.5-7/man/epicurve.Rd 2012-09-30 08:24:49.000000000 +0000 +++ r-cran-epitools-0.5-9/man/epicurve.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -340,9 +340,9 @@ \references{none} \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link[graphics]{barplot}}, \code{\link[base]{strptime}} diff -Nru r-cran-epitools-0.5-7/man/epidate.Rd r-cran-epitools-0.5-9/man/epidate.Rd --- r-cran-epitools-0.5-7/man/epidate.Rd 2012-09-30 08:24:57.000000000 +0000 +++ r-cran-epitools-0.5-9/man/epidate.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -61,9 +61,9 @@ \references{none} -\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} +\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{epitools}: \code{\link{as.week}} diff -Nru r-cran-epitools-0.5-7/man/epitable.Rd r-cran-epitools-0.5-9/man/epitable.Rd --- r-cran-epitools-0.5-7/man/epitable.Rd 2012-09-30 08:25:06.000000000 +0000 +++ r-cran-epitools-0.5-9/man/epitable.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -52,9 +52,9 @@ \references{none} \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{epitable}} diff -Nru r-cran-epitools-0.5-7/man/epitab.Rd r-cran-epitools-0.5-9/man/epitab.Rd --- r-cran-epitools-0.5-7/man/epitab.Rd 2012-09-30 08:25:17.000000000 +0000 +++ r-cran-epitools-0.5-9/man/epitab.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -153,9 +153,9 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/man/expand.table.Rd r-cran-epitools-0.5-9/man/expand.table.Rd --- r-cran-epitools-0.5-7/man/expand.table.Rd 2012-09-30 08:27:21.000000000 +0000 +++ r-cran-epitools-0.5-9/man/expand.table.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -53,13 +53,11 @@ \references{none} \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}; Daniel Wollschlaeger, + \url{http://www.phdata.science}; Daniel Wollschlaeger, \email{dwoll@psychologie.uni-kiel.de}, \url{http://www.uni-kiel.de/psychologie/dwoll/} } -\note{Visit \url{http://www.epitools.net} for the latest.} - %- ~Make other sections like Warning with \section{Warning }{....} ~ \seealso{ diff -Nru r-cran-epitools-0.5-7/man/expected.Rd r-cran-epitools-0.5-9/man/expected.Rd --- r-cran-epitools-0.5-7/man/expected.Rd 2012-09-30 08:27:35.000000000 +0000 +++ r-cran-epitools-0.5-9/man/expected.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -33,9 +33,9 @@ Oxford University Press } -\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} +\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/man/julian2date.Rd r-cran-epitools-0.5-9/man/julian2date.Rd --- r-cran-epitools-0.5-7/man/julian2date.Rd 2012-09-30 08:27:44.000000000 +0000 +++ r-cran-epitools-0.5-9/man/julian2date.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -33,9 +33,9 @@ \references{none} -\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} +\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link[base]{format.Date}}, \code{\link[base]{weekdays}} diff -Nru r-cran-epitools-0.5-7/man/kapmeier.Rd r-cran-epitools-0.5-9/man/kapmeier.Rd --- r-cran-epitools-0.5-7/man/kapmeier.Rd 2012-09-30 08:27:53.000000000 +0000 +++ r-cran-epitools-0.5-9/man/kapmeier.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -54,9 +54,9 @@ edition (May 1, 2004) } -\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} +\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/man/oddsratio.Rd r-cran-epitools-0.5-9/man/oddsratio.Rd --- r-cran-epitools-0.5-7/man/oddsratio.Rd 2012-09-30 08:28:02.000000000 +0000 +++ r-cran-epitools-0.5-9/man/oddsratio.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -156,9 +156,9 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{tab2by2.test}}, \code{\link{riskratio}}, diff -Nru r-cran-epitools-0.5-7/man/or.midp.Rd r-cran-epitools-0.5-9/man/or.midp.Rd --- r-cran-epitools-0.5-7/man/or.midp.Rd 2012-09-30 08:28:11.000000000 +0000 +++ r-cran-epitools-0.5-9/man/or.midp.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -51,9 +51,9 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{oddsratio}} diff -Nru r-cran-epitools-0.5-7/man/ormidp.test.Rd r-cran-epitools-0.5-9/man/ormidp.test.Rd --- r-cran-epitools-0.5-7/man/ormidp.test.Rd 2012-09-30 08:28:20.000000000 +0000 +++ r-cran-epitools-0.5-9/man/ormidp.test.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -52,9 +52,9 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{tab2by2.test}}, \code{\link{oddsratio}}, diff -Nru r-cran-epitools-0.5-7/man/oswego.Rd r-cran-epitools-0.5-9/man/oswego.Rd --- r-cran-epitools-0.5-7/man/oswego.Rd 2009-04-12 07:57:46.000000000 +0000 +++ r-cran-epitools-0.5-9/man/oswego.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -112,6 +112,6 @@ Supper (updated 2003): S. aureus outbreak among church picnic attendees, 1940; the classic, straightforward outbreak investigation in a defined population. Training modules available at - \url{http://www.cdc.gov/eis/casestudies/casestudyex.htm}. + \url{https://www.cdc.gov/eis/casestudies/xoswego.401-303.student.pdf}. } \keyword{datasets} diff -Nru r-cran-epitools-0.5-7/man/pois.conf.int.Rd r-cran-epitools-0.5-9/man/pois.conf.int.Rd --- r-cran-epitools-0.5-7/man/pois.conf.int.Rd 2012-09-30 08:28:45.000000000 +0000 +++ r-cran-epitools-0.5-9/man/pois.conf.int.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -53,7 +53,7 @@ \references{ Tomas Aragon, et al. Applied Epidemiology Using R. Available at - \url{http://medepi.com} + \url{http://www.phdata.science} Leslie Day (1992), "Simple SAS macros for the calculation of exact binomial and Poisson confidence limits." Comput Biol Med, @@ -65,12 +65,12 @@ \author{ Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}; + \url{https://repitools.wordpress.com/}; with contributions by Francis Dimzon, \email{fdimzon@yahoo.com}; with contributions by Scott Nabity, \email{scott.nabity@sfdph.org} } -\note{Visit \url{http://medepi.com} for the latest.} + \seealso{ diff -Nru r-cran-epitools-0.5-7/man/probratio.Rd r-cran-epitools-0.5-9/man/probratio.Rd --- r-cran-epitools-0.5-7/man/probratio.Rd 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-epitools-0.5-9/man/probratio.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -0,0 +1,78 @@ +\name{probratio} +\alias{probratio} + +\title{Obtain unbiased probability ratios from logistic regression models} + +\description{ + Estimates probability (prevalence or risk) ratios from logistic regression models using either + maximum likelihood or marginal standardization. + When using the latter, standard errors are calculated using the delta method or bootstrap. +} + +\usage{ +probratio(object, parm, subset, method=c('ML', 'delta', 'bootstrap'), + scale=c('linear', 'log'), level=0.95, seed, NREPS=100, ...) +} + + +\arguments{ +\item{object}{ a glm object with the family attribute equal to "binomial" } +\item{parm}{ a specification of which parameters are to be sequentially assigned predicted responses, either a vector of numbers or a vector of names. If missing, all parameters are considered except the intercept which should not be used except when the method argument is "model".} +\item{subset}{ a logical vector referring to which observations are included in the numerators and denominators of risk calculation. The default is TRUE, corresponding to a total population prediction ratios. User can supply subsets to calculate exposed population prediction ratios.} +\item{method}{ One of three ways that standard errors of prediction ratios are calculate. Maximum likelihood uses relative risk regression directly. Delta-method uses asymptotically correct normal approximations to prediction ratios. } +\item{scale}{ The scale on which marginal standardization calculates normal approximations to variability. When using ML, the log scale is the efficient parameterization.} +\item{level}{ The confidence level for confidence intervals.} +\item{seed}{ The random number generation seed} +\item{NREPS}{ The number of bootstrap samples to be drawn} +\item{...}{ Further arguments to glm when using maximum likelihood} +} + +\details{ + Estimates prevalence and risk ratios from logistic regression models using either maximum likelihood or marginal standardization. + Maximum likelihood is relative risk regression: a GLM with binomial variance structure and a log link. + Marginal standardization averages predicted probabilities from logistic regression models in the total sample or exposed sample to obtain prevalence or risk ratios. + Standard errors for marginal standardization estimates are calculated with the delta method or the normal bootstrap, which is not bias corrected. + Ratios can be estimated on the linear or log scale, which may lead to different inference due to the invariance of Wald statistics. +} + + +\value{ + An array of ratios or log ratios, their standard errors, a z-score for a hypothesis test for the log ratio being different from 0 or the ratio being different from 1, the corresponding p-value, and the confidence interval for the estimate. +} + +\references{ +Muller, Clemma J., and Richard F. MacLehose. "Estimating predicted probabilities from logistic regression: different methods correspond to different target populations." International journal of epidemiology 43.3 (2014): 962-970. + +Lumley, Thomas, Richard Kronmal, and Shuangge Ma. "Relative risk regression in medical research: models, contrasts, estimators, and algorithms." (2006). +} + +\author{Adam Omidpanah, \email{adam.omidpanah@wsu.edu}} + +\note{Maximum likelihood estimation via Newton Raphson may result in predicted probabilities greater than 1. This dominates estimating functions and leads to either false convergence or failure. Users should attempt to refit such models themselves using glms with the family argument binomial(link=log). By modifying inputs to glm.control, domination may be averted. An ideal first step is supplying starting coefficients. Input start=c(-log(p), 0,0,...,0) where p is the prevalence of the outcome. +The current implementation of bootstrap standard errors, inference, and confidence intervals are not bias corrected. This will be updated in a later version. +} + +\seealso{ + \code{\link{glm}}, \code{\link{deriv}},w + \code{\link{predict.glm}}, \code{\link{family}} +} + +\examples{ + set.seed(123) + x <- rnorm(500) + y <- rbinom(500, 1, exp(-1 + .3*x)) + logreg <- glm(y ~ x, family=binomial) + confint.default(logreg) ## 95\% CI over-estimates the 0.3 log-RR + pr1 <- probratio(logreg, method='ML', scale='log', start=c(log(mean(y)), 0)) + + ## generally more efficient to calculate log-RR then exponentiate for non-symmetric 95\% CI + pr1 <- probratio(logreg, scale='log', method='delta') + pr2 <- probratio(logreg, scale='linear', method='delta') + exp(pr1[, 5:6]) + pr2[, 5:6] +} + +\keyword{models} +\keyword{risk} + +%- \keyword{ ~kwd2 }% __ONLY ONE__ keyword per line diff -Nru r-cran-epitools-0.5-7/man/rate2by2.test.Rd r-cran-epitools-0.5-9/man/rate2by2.test.Rd --- r-cran-epitools-0.5-7/man/rate2by2.test.Rd 2012-09-30 08:29:06.000000000 +0000 +++ r-cran-epitools-0.5-9/man/rate2by2.test.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -79,9 +79,9 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{rateratio}}, diff -Nru r-cran-epitools-0.5-7/man/rateratio.Rd r-cran-epitools-0.5-9/man/rateratio.Rd --- r-cran-epitools-0.5-7/man/rateratio.Rd 2012-09-30 08:29:23.000000000 +0000 +++ r-cran-epitools-0.5-9/man/rateratio.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -103,9 +103,9 @@ \author{Rita Shiau (original author), \email{rita.shiau@sfdph.org}; Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{rate2by2.test}}, \code{\link{oddsratio}}, diff -Nru r-cran-epitools-0.5-7/man/ratetable.Rd r-cran-epitools-0.5-9/man/ratetable.Rd --- r-cran-epitools-0.5-7/man/ratetable.Rd 2012-09-30 08:29:34.000000000 +0000 +++ r-cran-epitools-0.5-9/man/ratetable.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -56,9 +56,9 @@ \references{none} \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{epitable}} diff -Nru r-cran-epitools-0.5-7/man/riskratio.Rd r-cran-epitools-0.5-9/man/riskratio.Rd --- r-cran-epitools-0.5-7/man/riskratio.Rd 2012-09-30 08:29:46.000000000 +0000 +++ r-cran-epitools-0.5-9/man/riskratio.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -136,9 +136,9 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{tab2by2.test}}, \code{\link{oddsratio}}, diff -Nru r-cran-epitools-0.5-7/man/tab2by2.test.Rd r-cran-epitools-0.5-9/man/tab2by2.test.Rd --- r-cran-epitools-0.5-7/man/tab2by2.test.Rd 2012-09-30 08:29:54.000000000 +0000 +++ r-cran-epitools-0.5-9/man/tab2by2.test.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -85,9 +85,9 @@ } \author{Tomas Aragon, \email{aragon@berkeley.edu}, - \url{http://www.medepi.com}} + \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} \seealso{ \code{\link{oddsratio}}, \code{\link{riskratio}} diff -Nru r-cran-epitools-0.5-7/man/table.margins.Rd r-cran-epitools-0.5-9/man/table.margins.Rd --- r-cran-epitools-0.5-7/man/table.margins.Rd 2012-09-30 08:30:03.000000000 +0000 +++ r-cran-epitools-0.5-9/man/table.margins.Rd 2017-04-14 17:48:41.000000000 +0000 @@ -31,9 +31,9 @@ \references{none} -\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.medepi.com}} +\author{Tomas Aragon, \email{aragon@berkeley.edu}, \url{http://www.phdata.science}} + -\note{Visit \url{http://medepi.com} for the latest.} %- ~Make other sections like Warning with \section{Warning }{....} ~ diff -Nru r-cran-epitools-0.5-7/MD5 r-cran-epitools-0.5-9/MD5 --- r-cran-epitools-0.5-7/MD5 2012-09-30 09:29:17.000000000 +0000 +++ r-cran-epitools-0.5-9/MD5 2017-04-14 23:04:36.000000000 +0000 @@ -1,5 +1,5 @@ -3587d09cf96a02eb676b8e4e35c9a634 *DESCRIPTION -787a3926ee8dc9d4a58474fda920e746 *NAMESPACE +abef416cd1c730e7137263f9b1791b4a *DESCRIPTION +f259c9f26e82e13a8eb777c4f2fbecc7 *NAMESPACE 2745fc0b8c7dd39e9272b0a8d8d573ae *R/ageadjust.direct.R f57b81c6d42888d11c7673aa911aaaa4 *R/ageadjust.indirect.R 9999f1f5ee9c394bf1a34add54477f64 *R/as.hour.R @@ -36,13 +36,14 @@ b4af057b9684dd25a204d0fdd07bc490 *R/pois.byar.R 92a9a8539406cf2b7891d3c620948f02 *R/pois.daly.R 6f7f8d32c5b17250ab5114fa0eb90ef4 *R/pois.exact.R +f55b48d7e8d39764eacac14d02617368 *R/probratio.r d963dd2d0fd72e1b1852100d3f3a731c *R/rate2by2.test.R 23a6d06d89f020f2632c8167a1c5bfb6 *R/rateratio.R a3353788495494cfe1701acf61e1296b *R/rateratio.midp.R b5a48d34e42c464993cdc31d6f2450af *R/rateratio.wald.R da5914dac422077e09bf4ec11bd0bdcb *R/ratetable.R 7d63605703662d7f708b79875995fafb *R/riskratio.R -125a035ac52a4b51c83231c6621668a3 *R/riskratio.boot.R +5482920348d27e7b2b0e2f44fe908b02 *R/riskratio.boot.R c6786e9f1bec78093f3c8bf3127b990f *R/riskratio.small.R 372dc792ac711f77388e2351cd8529f6 *R/riskratio.wald.R 05e1e91775de4db5b6c40e5064d471a1 *R/tab2by2.test.R @@ -50,32 +51,33 @@ 599db95edbab735f585432c50c915e8f *data/oswego.rda 4bc99d86c08e5e31f6e87132281c6354 *data/wcgs.rda f7ca7daa6bea1cfa48fe3278634836e9 *data/wnv.rda -ef10a1d1ba0896c3adb4a3c7be4a0547 *man/ageadjust.direct.Rd -7339dab6557573a737f5fed7de57b60e *man/ageadjust.indirect.Rd -579531d0b703c5558ea1cffae831f700 *man/as.hour.Rd -e9ad660cdf6d1c31717827d68d4b7caa *man/as.month.Rd -62d84b4b0189396262db2d2c800166e5 *man/as.week.Rd -1b84a495804481aef6bee15877399225 *man/binom.conf.int.Rd -5be14416afb7bf79277c72481ae8426b *man/colorbrewer.Rd -940fa9513363101bc89c2e83abcf5185 *man/colors.plot.Rd -e37acacabd3503a59bc283e7be9196d2 *man/epicurve.Rd -b9514b5241c24fefbd3cf48a98342b35 *man/epidate.Rd 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*man/ageadjust.indirect.Rd +4651e245cf53e65b2d7a3409b80fdc28 *man/as.hour.Rd +828563827b1cc26d6ba1e9ddb85ca321 *man/as.month.Rd +bbc8be41dc8edffcac753bf5e9550c8e *man/as.week.Rd +e4c54b3e4ad98db993e292c289e0c5e2 *man/binom.conf.int.Rd +03dc3e297ee6a20a59bd82584ad7981e *man/colorbrewer.Rd +2ba04a295ec5be831bc257728f4c1b40 *man/colors.plot.Rd +8b2ba43ece30ab1813482df74d2fd524 *man/epicurve.Rd +ccefe1c4ad859cdc5f424432205646aa *man/epidate.Rd +60fdf552393e0d5826ef8a0c6c5d975c *man/epitab.Rd +f1578bc60e2b81620e66d05a1b4ab050 *man/epitable.Rd +5c6fcb8ae2da13dbc3262550652b42e9 *man/expand.table.Rd +505f1a901450169ac054b6ee3c690239 *man/expected.Rd +15f06c30128f8556685bf4b65c083ae1 *man/julian2date.Rd +518a7ea26bd0cd1469797dfa88885440 *man/kapmeier.Rd +50808280b2ab493fbf40ac08c8063597 *man/oddsratio.Rd +f6aea5940cd50004b1cb1891932c26e0 *man/or.midp.Rd +cc44f5cbf9bf742da3fc2812fbb0116d *man/ormidp.test.Rd +60c145e9a59b01973ad1ef5d354e9eda *man/oswego.Rd +7e4aadfb1419d6707259d2dfbced4ba2 *man/pois.conf.int.Rd +87bb14cc9f0590b20b9885172e7e8e1a *man/probratio.Rd +7a6a6a89eda18545c4194f62827dc7b9 *man/rate2by2.test.Rd +065d02278f69456c17b29793d3273956 *man/rateratio.Rd +76d5efb56197e4496efe1e8d14b803bf *man/ratetable.Rd +2ee62232595ea0e0ca866ef586e8a09d *man/riskratio.Rd +5bda8bae7c61e9fbb874d64d247bcff6 *man/tab2by2.test.Rd +649f7061356cd0ae69410c6dc7022e48 *man/table.margins.Rd 6eee4357e4f5efd6ac15912e8c6cbea8 *man/wcgs.Rd b9f7bf52cb42a1a9edb8a505f21f2bc5 *man/wnv.Rd diff -Nru r-cran-epitools-0.5-7/NAMESPACE r-cran-epitools-0.5-9/NAMESPACE --- r-cran-epitools-0.5-7/NAMESPACE 2009-04-12 08:02:48.000000000 +0000 +++ r-cran-epitools-0.5-9/NAMESPACE 2017-04-14 17:48:41.000000000 +0000 @@ -1 +1,9 @@ exportPattern("^[^\\.]") +importFrom("grDevices", "colors", "rgb") +importFrom("graphics", "abline", "axis", "barplot", "matplot", + "points", "rect", "text", "title") +importFrom("stats", "binom.test", "chisq.test", "dbinom", "dpois", + "fisher.test", "ftable", "pbinom", "pchisq", "pnorm", + "ppois", "qgamma", "qnorm", "quantile", "rbinom", "uniroot", + 'confint.default', "binomial", "coef", "deriv", "family", "glm", + "glm.fit", "model.matrix", "sd", "vcov") \ No newline at end of file diff -Nru r-cran-epitools-0.5-7/R/probratio.r r-cran-epitools-0.5-9/R/probratio.r --- r-cran-epitools-0.5-7/R/probratio.r 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-epitools-0.5-9/R/probratio.r 2017-04-14 17:48:42.000000000 +0000 @@ -0,0 +1,113 @@ +probratio <- function(object, parm, subset, method=c('ML', 'delta', 'bootstrap'), scale=c('linear', 'log'), level=0.95, + seed, NREPS=100, ...) { + if (length(match('glm', class(object))) < 0) + stop('Non GLM input to "object"') + if (family(object)$family != 'binomial') + stop('object not a logistic regression model') + nc <- length(cf <- coef(object)) + if (missing(subset)) + subset <- T + if (missing(parm)) + parm <- seq(2, nc) + cf <- cf[parm] + + method <- match.arg(method, c('ML', 'delta', 'bootstrap')) + + scale <- match.arg(scale, c('linear', 'log')) + if (is.na(scale)) + stop('scale cannot take values outside of linear or log') + if (scale == 'linear') { + f <- function(x) x[2]/x[1] + name <- c('Relative risk') + null <- 1 + } else { + name <- c('Log relative risk') + null <- 0 + f <- function(x)log(x[2]) - log(x[1]) + } + cilevel <- c({1-level}/2, 1-{1-level}/2) + ciname <- paste0(c('Lower', 'Upper'), ' ', formatC(100*cilevel, format='f', digits=1), '% CI') + + if (method == 'ML') { + newfit <- glm(object, family=binomial(link=log), subset=subset, ...) + out <- coef(summary(newfit))[parm, , drop=F] + + if (scale == 'log') { + out <- cbind(out[, 1], out[, 2], out[, 3], out[, 4], out[, 1] + qnorm((1-level)/2)*out[, 2], out[, 1] + qnorm(1-(1-level)/2)*out[, 2]) + } else { + val <- exp(out[, 1]) + se <- val * out[, 2] + out <- cbind(val, se, z <- abs(val-1)/se, pnorm(z, lower.tail = F)*2, + val + qnorm((1-level)/2)*se, val + qnorm(1-(1-level)/2)*se) + } + colnames(out) <- c(name, 'Std. Error', 'Z-value', 'p-value', ciname) + return(out) + } + + Mod1 <- Mod0 <- model.matrix(object)[subset, ] + n <- nrow(Mod0) + Nvec <- matrix(rep(c(1/n,0,0,1/n),each=n), n*2, 2) + + if (method == 'delta') { + if (scale == 'linear') { + df <- deriv( ~y/x, c('x', 'y')) + } else { + df <- deriv(~log(y) - log(x), c('x', 'y')) + } + + out <- sapply(parm, function(p) { + Mod0[, p] <- 0 + Mod1[, p] <- 1 + Mod <- rbind(Mod0, Mod1) + allpreds <- family(object)$linkinv(Mod %*% coef(object)) + avgpreds <- t(Nvec)%*% allpreds + val <- f(avgpreds) + V <- sweep(chol(vcov(object)) %*% t(Mod), allpreds*(1-allpreds), '*', MARGIN = 2) %*% Nvec + V <- t(V)%*%V + dxdy <- matrix(attr(eval(df, list('x'=avgpreds[1], 'y'=avgpreds[2])), 'gradient')) + se <- sqrt(t(dxdy)%*%V%*%dxdy) + out <- c(val, se, z <- abs({val-null}/se), pnorm(z, lower.tail=F)*2, val + qnorm(cilevel[1])*se, val + qnorm(cilevel[2])*se) + names(out) <- c(name, 'Std. Error', 'Z-value', 'p-value', ciname) + out + }) + out <- t(out) + rownames(out) <- names(cf) + return(out) + } ## endif delta + + if (method == 'bootstrap') { + if (missing(seed)) + stop('seed must be supplied by the user when obtaining results from random number generation') + set.seed(seed) + out <- replicate(NREPS, { + + index <- sample(1:n, n, replace=T) + Mod <- model.matrix(object)[subset, ][index, ] + newbeta <- glm.fit(Mod, object$y[index], family=binomial())$coef + out <- sapply(parm, function(p) { + Mod1 <- Mod0 <- Mod + Mod1[, p] <- 1 + Mod0[, p] <- 0 + Mod <- rbind(Mod0, Mod1) + newpreds <- family(object)$linkinv(Mod %*% newbeta) + f(t(Nvec) %*% newpreds) + }) + out + }) + + + if (length(parm) == 1) { + out <- c(val <- mean(out), se <- sd(out), z <- abs({val - null}/se), pnorm(z, lower.tail = F)*2, + val + qnorm((1-level)/2)*se, val + qnorm(1-(1-level)/2)*se) + names(out) <- c(name, 'Std. Error', 'Z-value', 'p-value', ciname) + } else { + out <- cbind(val <- rowMeans(out), se <- apply(out, 1, sd), z <- abs({val - null}/se), pnorm(z, lower.tail = F)*2, + val + qnorm(cilevel[1])*se, val + qnorm(cilevel[2])*se) + colnames(out) <- c(name, 'Std. Error', 'Z-value', 'p-value', ciname) + rownames(out) <- names(cf) + } + + return(out) + } +} + diff -Nru r-cran-epitools-0.5-7/R/riskratio.boot.R r-cran-epitools-0.5-9/R/riskratio.boot.R --- r-cran-epitools-0.5-7/R/riskratio.boot.R 2005-02-11 07:01:54.000000000 +0000 +++ r-cran-epitools-0.5-9/R/riskratio.boot.R 2017-04-14 17:48:42.000000000 +0000 @@ -27,8 +27,8 @@ r1 <- rbinom(replicates, n1, p1)/n1 r0 <- rbinom(replicates, n0, p0)/n0 rrboot <- r1/r0 - rrbar <- mean(rrboot) - ci <- quantile(rrboot, c(alpha/2, 1-alpha/2)) + rrbar <- mean(rrboot, na.rm=T) + ci <- quantile(rrboot, c(alpha/2, 1-alpha/2), na.rm = T) list(p0 = p0, p1 = p1, rr = p1/p0, rr.mean = rrbar, conf.level = conf.level, conf.int = unname(ci), replicates = replicates)