diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index f318be6..179fff5 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: 2025-04-11 20:15:41 UTC +SHA: d8af1df1b780ebf57345882cddc53aaa1eb5bd67 diff --git a/DESCRIPTION b/DESCRIPTION index b4549fe..87fec06 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"), @@ -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, @@ -39,4 +40,4 @@ 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/coarseDataTools-package.R b/R/coarseDataTools-package.R index 9177ce1..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://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. \doi{10.1056/NEJMoa0906089} ##' ##' @examples ##' data(exp.win.lengths) 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/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/cran-comments.md b/cran-comments.md index e32d64a..cb5f42c 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 and other broken links \ No newline at end of file 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 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 diff --git a/man/exp.win.lengths.Rd b/man/exp.win.lengths.Rd index e9bd271..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://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. \doi{10.1056/NEJMoa0906089} } \usage{ data(exp.win.lengths)