Further smaller changes related to the CRAN submission, additionally: Paper published!

Author: nmueller18

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: baytaAAR
 Type: Package
 Title: Bayesian Transition Analysis with Markov Chain Monte Carlo
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: c(person(given = "Nils", family = "Müller-Scheeßel",
                       email = "nils.mueller-scheessel@ufg.uni-kiel.de",
                       role = c("aut", "cre", "cph"),
@@ -16,8 +16,9 @@ Description: Provides Bayesian age estimation for bioarchaeological skeletal
     The package is designed to handle multiple ordinal traits of adult individuals
     and incorporates a Gompertz prior on age to reflect population-level mortality. 
     It accounts for estimation uncertainties and supports full customization of 
-    model parameters and Markov Chain Monte Carlo settings.
-License: GPL-3 | file LICENSE
+    model parameters and Markov Chain Monte Carlo settings. For more details
+    see Müller-Scheeßel et al. (2026) <doi:10.1002/ajpa.70289>.
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Imports:

LICENSE

@@ -66,10 +66,12 @@
 #'   saved. Default: \code{1} (no thinning).
 #' @param numSavedSteps integer. Number of saved steps. Default: \code{10000}.
 #'  The total number of steps equals \code{thinSteps × numSavedSteps}.
-#' @param silent.jags TRUE/FALSE Silent mode to run JAGS. Default: \code{FALSE}.
+#' @param silent.jags TRUE/FALSE. Silent mode to run JAGS. Default: \code{FALSE}.
 #'   Ignored when \code{framework} is set to \code{NIMBLE}.
 #' @param silent.runjags TRUE/FALSE Silent mode to run runjags. Default:
 #'  \code{FALSE}. Ignored when \code{framework} is set to \code{NIMBLE}.
+#' @param verbose TRUE/FALSE. If TRUE, the current time stamp is displayed in
+#' the console, and after completion the elapsed time. Default: \code{TRUE}.
 #'
 #'
 #' @return A list of MCMC chains of class \code{coda::mcmc.list}.
@@ -121,8 +123,9 @@ bay.ta  <- function(
     burnInSteps = 3000,
     thinSteps = 1,
     numSavedSteps = 10000,
-    silent.jags = F,
-    silent.runjags = F) {
+    silent.jags = FALSE,
+    silent.runjags = FALSE,
+    verbose = TRUE) {
 
   checkmate::assertChoice(framework, c("JAGS", "NIMBLE"))
   checkmate::assertChoice(algorithm, c("norm", "mnorm"))
@@ -154,22 +157,22 @@ bay.ta  <- function(
     stop(message("Framework is set to JAGS. However, JAGS currently does not
                  support multinormal ordinal regression.\n"))
   }
-  if(multicore == TRUE & nChains > available_cores - 1) {
+  if(multicore & nChains > available_cores - 1) {
     stop(message(paste0("
     Your machine has only ", available_cores, " physical cores. To maintain usability,
     it is advisable to reduce the number of concurring chains or to set multicore to FALSE.\n")))
   }
   if(algorithm == "mnorm" & ncol(method) < 2) {
     stop(message("With multinormal ordinal regression, there need to be two traits or more.\n"))
   }
-  if(multicore == TRUE) {
+  if(multicore) {
     runjagsMethod <- "parallel"
   } else {
     runjagsMethod <- "rjags"
   }
 
   start_time <- Sys.time()
-  cat("Starting Time:", format(start_time, "%d %b %Y %X"), "\n")
+  if (verbose) cat("Starting Time:", format(start_time, "%d %b %Y %X"), "\n")
 
   # single core or multi core
   if(framework == "JAGS") { # simple ordinal probit regression with JAGS,
@@ -262,15 +265,17 @@ bay.ta  <- function(
   time_diff <- difftime(Sys.time(), start_time, units = "secs")
   time_secs <- as.numeric(time_diff)
 
-  # Convert to readable format
-  if (time_secs < 60) {
-    cat("Execution Time:", round(time_secs, 2), "seconds\n")
-  } else if (time_secs < 3600) {
-    cat("Execution Time:", round(time_secs / 60, 2), "minutes\n")
-  } else if (time_secs < 86400) {
-    cat("Execution Time:", round(time_secs / 3600, 2), "hours\n")
-  } else {
-    cat("Execution Time:", round(time_secs / 86400, 2), "days\n")
+  if (verbose) {
+    # Convert to readable format
+    if (time_secs < 60) {
+      cat("Execution Time:", round(time_secs, 2), "seconds\n")
+    } else if (time_secs < 3600) {
+      cat("Execution Time:", round(time_secs / 60, 2), "minutes\n")
+    } else if (time_secs < 86400) {
+      cat("Execution Time:", round(time_secs / 3600, 2), "hours\n")
+    } else {
+      cat("Execution Time:", round(time_secs / 86400, 2), "days\n")
+    }
   }
 
   results <- coda::as.mcmc.list(lapply(results, function(chain) {

R/bay_ta.R

@@ -33,8 +33,8 @@ bay.ta.jags <- function(
     nChains = 3,
     thinSteps = 1,
     numSavedSteps = 10000,
-    silent.jags = F,
-    silent.runjags = F,
+    silent.jags = FALSE,
+    silent.runjags = FALSE,
     seed = seed) {
 
   checkmate::assertMatrix(method)

R/bay_ta_jags.R

@@ -2,11 +2,13 @@
 
 0 errors | 0 warnings | 1 note
 
-* This is a resubmission. In this version we have:
+* This is a resubmission. In this version we have as requested:
 
-- reduced the time to generate the vignettes substantially by providing
-pre-computed results and reducing the number of iterations. win-devel now
-reports 6 minutes for checking the package.
+- deleted the LICENCE file and the reference to it in DESCRIPTION
+- added a reference to the method in DESCRIPTION
+- wrote TRUE and FALSE instead of T and F
+- introduced an additional variable "verbose" to give the user the opportunity
+to suppress printing to the console.
 
 
 ## Comments

cran-comments.md

@@ -3,5 +3,9 @@ bibentry(
   title = "A Fully Bayesian Approach to Adult Skeletal Age Estimation: Multivariate Latent Trait Modeling with Markov Chain Monte Carlo sampling",
   author = "Nils Müller-Scheeßel, Katharina Fuchs, Christoph Rinne",
   journal = "American Journal of Biological Anthropology",
+  volume = 190,
+  number = 2,
+  doi = "10.1002/ajpa.70289",
+  pages = "e70289",
   year = 2026
 )

inst/CITATION

@@ -220,9 +220,10 @@ @Article{ref_299013
 author = {Müller-Scheeßel, Nils and Rinne, Christoph and Fuchs, Katharina},
 title = {{A Fully Bayesian Approach to Adult Skeletal Age Estimation: Multivariate Latent Trait Modeling with Markov Chain Monte Carlo Sampling}},
 journal = {{American Journal of Biological Anthropology}},
-volume = {},
-number = {},
-pages = {},
+volume = {190},
+number = {2},
+doi = {10.1002/ajpa.70289},
+pages = {e70289},
 year = {2026},
 abstract = {},
 location = {},