update cross-reference for MCMCmetrop1R link

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

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 <nick@umass.edu>
 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

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

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)

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
@@ -46,13 +46,13 @@
   check.data.structure(dat)
 
   ## check to make sure distribution is supported
   if (!dist %in% c("G", "W", "L", "E", "off1G", "off1W", "off1L")) stop("Please use one of the following distributions Log-Normal (L) , Weibull (W), Gamma (G), Erlang (E), offset Log-Normal (off1L), offset Weibull (off1W) or offset Gamma (off1G)")
 
   ##        ## don't need MCMCpack for Erlang
   ##        if (dist != "E") require(MCMCpack)
 
   ## check that percentiles are valid
   if (any(ptiles >= 1, ptiles <= 0)) stop("Sorry the percentiles you are requesting are not valid.")
 
   ## default prior parameters if none specified
   if (is.null(prior.par1)) {
@@ -78,7 +78,7 @@
 
   ## random seed based off current time if none specified
   if (is.null(seed)) {
     t <- as.numeric(Sys.time())
     seed <- 1e8 * (t - floor(t))
   }
 
@@ -135,7 +135,7 @@
 
 
 
   if (!fail) {
     ## untransform MCMC parameter draws to natural scale
     untrans.mcmcs <- t(apply(mcmc.run[, 1:2], 1, function(x) dist.optim.untransform(dist = dist, pars = x)))
 
@@ -143,7 +143,7 @@
     ptiles.appended <- sort(union(0.5, ptiles))
     est.pars <- matrix(nrow = length(ptiles.appended) + 2, ncol = 3)
 
     if (dist == "L") {
       par1.name <- "meanlog"
       par2.name <- "sdlog"
       mcmc.quantiles <- apply(untrans.mcmcs, 1, function(x) qlnorm(ptiles.appended, meanlog = x[1], sdlog = x[2]))
@@ -178,8 +178,8 @@
       par2.name <- "scale"
       mcmc.quantiles <- apply(untrans.mcmcs, 1, function(x) qgamma(ptiles.appended, shape = x[1], scale = x[2]))
     } else {
       stop("Sorry, unknown distribution type. Check the 'dist' option.")
       ## not actually needed but just in case
     }
 
     ## make the return matrix
@@ -211,7 +211,7 @@
     return(rc)
   } else {
     if (msg != "") msg <- paste0("Error: ", msg)
     stop(sprintf("\n%s\nTry adjusting the starting parameters (init.pars), or changing the optimization method (opt.method).", msg))
   }
 }
 
@@ -248,8 +248,8 @@
           log = TRUE
         )),
       error = function(e) {
         warning("Loglik failure, returning -Inf")
         return(-Inf)
       }
     )
   } else if (dist == "W" || dist == "off1W") {

README.md

@@ -3,7 +3,6 @@ coarseDataTools
 
 <!-- badges: start -->
 [![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)
 <!-- badges: end -->
 

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

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, "."))