From f432287207776f110bd454e9340da4def71cb9b6 Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Wed, 9 Apr 2025 15:02:58 -0400 Subject: [PATCH 1/8] update cross-reference for MCMCmetrop1R link --- DESCRIPTION | 6 +++--- NEWS.md | 4 ++++ R/dic.fit.mcmc.R | 2 +- man/dic.fit.mcmc.Rd | 2 +- 4 files changed, 9 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b4549fe..a6a36ef 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: coarseDataTools -Version: 0.7.1 -Date: 2023-07-03 +Version: 0.7.2 +Date: 2025-04-09 Title: Analysis of Coarsely Observed Data Authors@R: c(person("Nicholas G.", "Reich", email = "nick@umass.edu", role = c("aut", "cre")), person("Justin", "Lessler", email = "jlessler@unc.edu", role = "aut"), @@ -39,4 +39,4 @@ Collate: 'sampleSizeSimulation.R' 'coarseDataTools-package.R' VignetteBuilder: knitr -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 diff --git a/NEWS.md b/NEWS.md index 2785efb..5ca561e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# coarseDataTools 0.7.2 + +* update cross-reference link for CRAN compatibility + # coarseDataTools 0.7.1 * Added pkgdown, moved ChangeLog to NEWS.md diff --git a/R/dic.fit.mcmc.R b/R/dic.fit.mcmc.R index e5e87af..964555e 100644 --- a/R/dic.fit.mcmc.R +++ b/R/dic.fit.mcmc.R @@ -27,7 +27,7 @@ ##' @param n.samples number of samples to draw from the posterior (after the burnin) ##' @param dist distribution to be used (L for log-normal,W for weibull, G for Gamma, and E for erlang, off1G for 1 day right shifted gamma) ##' @param seed seed for the random number generator for MCMC -##' @param ... additional parameters to \link{MCMCmetrop1R} +##' @param ... additional parameters to \link[MCMCpack]{MCMCmetrop1R} ##' @return a cd.fit.mcmc S4 object ##' @importFrom MCMCpack MCMCmetrop1R ##' @export diff --git a/man/dic.fit.mcmc.Rd b/man/dic.fit.mcmc.Rd index 649883a..4f14e04 100644 --- a/man/dic.fit.mcmc.Rd +++ b/man/dic.fit.mcmc.Rd @@ -40,7 +40,7 @@ dic.fit.mcmc( \item{seed}{seed for the random number generator for MCMC} -\item{...}{additional parameters to \link{MCMCmetrop1R}} +\item{...}{additional parameters to \link[MCMCpack]{MCMCmetrop1R}} } \value{ a cd.fit.mcmc S4 object From ba872e97fd098734808465c1266f2afcd233ce6b Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Wed, 9 Apr 2025 15:04:43 -0400 Subject: [PATCH 2/8] update cran-comments. --- cran-comments.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index e32d64a..36aed7e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,3 @@ ## updates in this edition - - updated vignette to Rmd/HTML - - fixed s4 documentation issue as requested from CRAN by removing method with problems - - fixed urls in citations + - fixed cross-reference to external package \ No newline at end of file From e9d41ca6e70c50a69c03cc94e0bb8a8349207ece Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Wed, 9 Apr 2025 15:50:29 -0400 Subject: [PATCH 3/8] fixing citation formats, package URL and depends --- DESCRIPTION | 5 +++-- inst/CITATION | 32 ++++++++++++++++---------------- 2 files changed, 19 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a6a36ef..87fec06 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,9 +9,10 @@ Authors@R: c(person("Nicholas G.", "Reich", email = "nick@umass.edu", role = c(" person("Hugo", "Gruson", email = "hugo.gruson@normalesup.org", role = "ctb")) Maintainer: Nicholas G. Reich License: GPL (>= 2) -URL: https://cran.r-project.org/package=coarseDataTools, - http://nickreich.github.io/coarseDataTools/ +URL: http://nickreich.github.io/coarseDataTools/ Encoding: UTF-8 +Depends: + R (>= 3.5.0) Imports: MCMCpack, graphics, diff --git a/inst/CITATION b/inst/CITATION index b295f8b..f3e0f7d 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -6,34 +6,34 @@ vers <- paste("R package version", meta$Version) citHeader("To cite the R package 'coarseDataTools' in publications use:") -citEntry(entry = "Article", - title = "Estimating incubation periods with coarse data.", - author= c(person(c("Nicholas G"), "Reich"), +bibentry(bibtype = "Article", + title = "Estimating incubation periods with coarse data.", + author = c(person(c("Nicholas G"), "Reich"), person(c("Justin"), "Lessler"), person(c("Derek AT"), "Cummings"), person(c("Ron"), "Brookmeyer")), - journal = "Statistics in Medicine", - year = 2009, + journal = "Statistics in Medicine", + year = 2009, textVersion = "Reich NG, Lessler J, Cummings DAT, Brookmeyer R. (2009). Estimating incubation periods with coarse data. Statistics in Medicine. 28(22):2769--2784.") -citEntry(entry = "Article", - title = "Estimating absolute and relative case fatality ratios from infectious disease surveillance data.", - author= c(person(c("Nicholas G"), "Reich"), +bibentry(bibtype = "Article", + title = "Estimating absolute and relative case fatality ratios from infectious disease surveillance data.", + author = c(person(c("Nicholas G"), "Reich"), person(c("Justin"), "Lessler"), person(c("Derek AT"), "Cummings"), person(c("Ron"), "Brookmeyer")), - journal = "Biometrics", - year = 2012, + journal = "Biometrics", + year = 2012, textVersion = "Reich NG, Lessler J, Cummings DAT, Brookmeyer R. Estimating absolute and relative case fatality ratios from infectious disease surveillance data. Biometrics. 2012, 68(2): 598--606.") -citEntry(entry = "Manual", - title = "coarseDataTools: A collection of functions to help with analysis of coarsely observed data", - author= c(person(c("Nicholas G"), "Reich"), +bibentry(bibtype = "Manual", + title = "coarseDataTools: A collection of functions to help with analysis of coarsely observed data", + author = c(person(c("Nicholas G"), "Reich"), person(c("Justin"), "Lessler"), person(c("Andrew S"), "Azman")), - year = year, - note = vers, - url = meta$URL, + year = year, + note = vers, + url = meta$URL, textVersion = paste0("Reich NG, Lessler J, Azman AS. (", year, "). coarseDataTools: A collection of functions to help with analysis of coarsely observed data. <", meta$URL, ">. ", vers, ".")) \ No newline at end of file From a41e9762e9d4d0ac5307145819fb8c0d9742169d Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Wed, 9 Apr 2025 16:00:53 -0400 Subject: [PATCH 4/8] adding cran-submission file. --- CRAN-SUBMISSION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index f318be6..235473a 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 0.6-6 -Date: 2021-12-09 15:50:23 UTC -SHA: 9031cb87f2972541498e5b5a2d9b391066091cc8 +Version: 0.7.2 +Date: 2025-04-09 19:59:53 UTC +SHA: e9d41ca6e70c50a69c03cc94e0bb8a8349207ece From b777b9a96bb67cfd8c4a9b54a1e683ca3ed2d432 Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Fri, 11 Apr 2025 13:13:39 -0400 Subject: [PATCH 5/8] updating package links. --- R/coarseDataTools-package.R | 2 +- README.md | 1 - man/exp.win.lengths.Rd | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/R/coarseDataTools-package.R b/R/coarseDataTools-package.R index 9177ce1..1173e9d 100644 --- a/R/coarseDataTools-package.R +++ b/R/coarseDataTools-package.R @@ -13,7 +13,7 @@ ##' @format A numeric vector with 134 positive values. Each value represents an exposure window length from an observation of the incubation period for that individual. The exposure window length is the length of time during which exposure could have occurred. For example, if an individual could have been exposed anytime between 6am on Monday to 6am on Wednesday, her exposure window length would be 2 days. ##' ##' @usage data(exp.win.lengths) -##' @source Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \url{https://www.nejm.org/doi/full/10.1056/nejmoa0906089} +##' @source Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \url{https://doi.org/10.1056/NEJMoa0906089} ##' ##' @examples ##' data(exp.win.lengths) diff --git a/README.md b/README.md index f46b0f3..48ae395 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,6 @@ coarseDataTools [![CRAN](http://cranlogs.r-pkg.org/badges/coarseDataTools)](https://cran.r-project.org/package=coarseDataTools) -[![Travis build status](https://travis-ci.org/nickreich/coarseDataTools.svg?branch=master)](https://travis-ci.org/nickreich/coarseDataTools) [![R-CMD-check](https://github.com/nickreich/coarseDataTools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nickreich/coarseDataTools/actions/workflows/R-CMD-check.yaml) diff --git a/man/exp.win.lengths.Rd b/man/exp.win.lengths.Rd index e9bd271..17229fa 100644 --- a/man/exp.win.lengths.Rd +++ b/man/exp.win.lengths.Rd @@ -8,7 +8,7 @@ A numeric vector with 134 positive values. Each value represents an exposure window length from an observation of the incubation period for that individual. The exposure window length is the length of time during which exposure could have occurred. For example, if an individual could have been exposed anytime between 6am on Monday to 6am on Wednesday, her exposure window length would be 2 days. } \source{ -Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \url{https://www.nejm.org/doi/full/10.1056/nejmoa0906089} +Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \url{https://doi.org/10.1056/NEJMoa0906089} } \usage{ data(exp.win.lengths) From 3a2786fe862d555a7d976d27fa549353ee148706 Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Fri, 11 Apr 2025 13:30:41 -0400 Subject: [PATCH 6/8] change DOI link to explicit /doi tag. --- R/coarseDataTools-package.R | 2 +- man/exp.win.lengths.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/coarseDataTools-package.R b/R/coarseDataTools-package.R index 1173e9d..6a01adb 100644 --- a/R/coarseDataTools-package.R +++ b/R/coarseDataTools-package.R @@ -13,7 +13,7 @@ ##' @format A numeric vector with 134 positive values. Each value represents an exposure window length from an observation of the incubation period for that individual. The exposure window length is the length of time during which exposure could have occurred. For example, if an individual could have been exposed anytime between 6am on Monday to 6am on Wednesday, her exposure window length would be 2 days. ##' ##' @usage data(exp.win.lengths) -##' @source Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \url{https://doi.org/10.1056/NEJMoa0906089} +##' @source Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \doi{10.1056/NEJMoa0906089} ##' ##' @examples ##' data(exp.win.lengths) diff --git a/man/exp.win.lengths.Rd b/man/exp.win.lengths.Rd index 17229fa..0361e0e 100644 --- a/man/exp.win.lengths.Rd +++ b/man/exp.win.lengths.Rd @@ -8,7 +8,7 @@ A numeric vector with 134 positive values. Each value represents an exposure window length from an observation of the incubation period for that individual. The exposure window length is the length of time during which exposure could have occurred. For example, if an individual could have been exposed anytime between 6am on Monday to 6am on Wednesday, her exposure window length would be 2 days. } \source{ -Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \url{https://doi.org/10.1056/NEJMoa0906089} +Lessler J et al. New England Journal of Medicine. Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School. 2009. 361(27):2628-2636. \doi{10.1056/NEJMoa0906089} } \usage{ data(exp.win.lengths) From d8af1df1b780ebf57345882cddc53aaa1eb5bd67 Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Fri, 11 Apr 2025 16:15:07 -0400 Subject: [PATCH 7/8] update cran-comments. --- cran-comments.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 36aed7e..cb5f42c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,3 @@ ## updates in this edition - - fixed cross-reference to external package \ No newline at end of file + - fixed cross-reference to external package and other broken links \ No newline at end of file From 32c9b49d2058c612f0e99b5af9b0bcb4544016dc Mon Sep 17 00:00:00 2001 From: Nicholas Reich Date: Fri, 11 Apr 2025 16:16:09 -0400 Subject: [PATCH 8/8] CRAN submission hash with url link fixes. --- CRAN-SUBMISSION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 235473a..179fff5 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 0.7.2 -Date: 2025-04-09 19:59:53 UTC -SHA: e9d41ca6e70c50a69c03cc94e0bb8a8349207ece +Date: 2025-04-11 20:15:41 UTC +SHA: d8af1df1b780ebf57345882cddc53aaa1eb5bd67