fix urls

R/deploy_shinystan.R

@@ -14,7 +14,7 @@
 #' Deploy a 'ShinyStan' app on the web using 'shinyapps.io' by 'RStudio'
 #'
 #' Requires a (free or paid) 'ShinyApps' account. Visit
-#' \url{http://www.shinyapps.io/} to sign up.
+#' \url{https://www.shinyapps.io/} to sign up.
 #'
 #' @export
 #' @template args-sso
@@ -46,7 +46,7 @@
 #' @seealso The example in the \emph{Deploying to shinyapps.io} vignette that
 #'   comes with this package.
 #'
-#'   \url{http://www.shinyapps.io/} to sign up for a free or paid 'ShinyApps'
+#'   \url{https://www.shinyapps.io/} to sign up for a free or paid 'ShinyApps'
 #'   account and for details on how to configure your account on your local
 #'   system using the \pkg{rsconnect} package from 'RStudio'.
 #'

R/launch_shinystan.R

@@ -122,7 +122,7 @@ launch_shinystan.shinystan <-
 #'   \describe{
 #'   \item{\code{eight_schools}}{Hierarchical meta-analysis model. See 
 #'    \emph{Meta Analysis} chapter of the 'Stan' manual 
-#'    \url{http://mc-stan.org/users/documentation/}.}
+#'    \url{https://mc-stan.org/users/documentation/}.}
 #'   }
 #' @return An S4 shinystan object.
 #'   

R/shinystan-package.R

@@ -33,13 +33,13 @@
 #' posterior sample, with particular attention to identifying potential problems
 #' with the performance of the MCMC algorithm or the specification of the model.
 #' ShinyStan is powered by the Shiny web application framework by RStudio
-#' (\url{http://shiny.rstudio.com/}) and works with the output of MCMC programs
+#' (\url{https://shiny.rstudio.com/}) and works with the output of MCMC programs
 #' written in any programming language (and has extended functionality for
 #' models fit using the \pkg{rstan} package and the No-U-Turn sampler).
 #'
 #' @section ShinyStan has extended functionality for Stan models:
 #'
-#' Stan (\url{http://mc-stan.org}) models can be run in \R using the
+#' Stan (\url{https://mc-stan.org/}) models can be run in \R using the
 #' \pkg{\link[rstan]{rstan}} package. Other packages like
 #' \pkg{\link[rstanarm]{rstanarm}} and \pkg{\link[brms]{brms}} provide
 #' higher-level interfaces to Stan that use \pkg{rstan} internally.
@@ -71,8 +71,8 @@
 #' @section Resources:
 #' \itemize{
 #'  \item Web page with online documentation
-#'    (\url{http://mc-stan.org/shinystan})
-#'  \item Stan Forums on Discourse (\url{http://discourse.mc-stan.org})
+#'    (\url{https://mc-stan.org/shinystan})
+#'  \item Stan Forums on Discourse (\url{https://discourse.mc-stan.org})
 #'  \item GitHub issue tracker (\url{https://github.com/stan-dev/shinystan/issues})
 #' }
 #'

man-roxygen/reference-bayesvis.R

@@ -1,4 +1,6 @@
-#' @references Gabry, J., Simpson, D., Vehtari, A., Betancourt, M., and Gelman,
-#'   A. (2018). Visualization in Bayesian workflow. \emph{Journal of the Royal
-#'   Statistical Society Series A}, accepted for publication. arXiv preprint:
-#'   \url{http://arxiv.org/abs/1709.01449}.
+#' @references Gabry, J. , Simpson, D. , Vehtari, A. , Betancourt, M. and
+#'   Gelman, A. (2019), Visualization in Bayesian workflow.
+#'   *J. R. Stat. Soc. A*, 182: 389-402. doi:10.1111/rssa.12378
+#'   ([journal version](https://rss.onlinelibrary.wiley.com/doi/full/10.1111/rssa.12378),
+#'    [preprint arXiv:1709.01449](https://arxiv.org/abs/1709.01449),
+#'    [code on GitHub](https://github.com/jgabry/bayes-vis-paper))