diff --git a/R/deploy_shinystan.R b/R/deploy_shinystan.R index 82a864cb..9cbefb72 100644 --- a/R/deploy_shinystan.R +++ b/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'. #' diff --git a/R/launch_shinystan.R b/R/launch_shinystan.R index 4db64288..3adc249f 100644 --- a/R/launch_shinystan.R +++ b/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. #' diff --git a/R/shinystan-package.R b/R/shinystan-package.R index 3cc003a1..7af62cb3 100644 --- a/R/shinystan-package.R +++ b/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}) #' } #' diff --git a/man-roxygen/reference-bayesvis.R b/man-roxygen/reference-bayesvis.R index df2ff0d1..99b0b12b 100644 --- a/man-roxygen/reference-bayesvis.R +++ b/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)) diff --git a/man/deploy_shinystan.Rd b/man/deploy_shinystan.Rd index eb6a332e..19cd41ed 100644 --- a/man/deploy_shinystan.Rd +++ b/man/deploy_shinystan.Rd @@ -30,7 +30,7 @@ deployment is successful.} } \description{ Requires a (free or paid) 'ShinyApps' account. Visit -\url{http://www.shinyapps.io/} to sign up. +\url{https://www.shinyapps.io/} to sign up. } \details{ In \code{...}, the arguments \code{ppcheck_data} and @@ -62,7 +62,7 @@ deploy_shinystan(sso, appName = "my-model") 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'. } diff --git a/man/launch_shinystan.Rd b/man/launch_shinystan.Rd index f7db09f0..9f2ac0be 100644 --- a/man/launch_shinystan.Rd +++ b/man/launch_shinystan.Rd @@ -79,10 +79,12 @@ User-friendly Bayesian regression modeling: A tutorial with rstanarm and shinyst \emph{The Quantitative Methods for Psychology}. 14(2), 99--119. \url{https://www.tqmp.org/RegularArticles/vol14-2/p099/p099.pdf} -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}. +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)) } \seealso{ \code{\link{as.shinystan}} for creating \code{shinystan} objects. diff --git a/man/launch_shinystan_demo.Rd b/man/launch_shinystan_demo.Rd index 2d1f52ff..7d7115c2 100644 --- a/man/launch_shinystan_demo.Rd +++ b/man/launch_shinystan_demo.Rd @@ -17,7 +17,7 @@ the only option, but additional demos may be available in future releases. \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/}.} }} \item{rstudio}{Only relevant for 'RStudio' users. The default (\code{FALSE}) diff --git a/man/shinystan-package.Rd b/man/shinystan-package.Rd index 86e15272..20a37c21 100644 --- a/man/shinystan-package.Rd +++ b/man/shinystan-package.Rd @@ -21,14 +21,14 @@ ShinyStan app provides interactive plots and tables helpful for analyzing a 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. @@ -68,8 +68,8 @@ higher-level interfaces to Stan that use \pkg{rstan} internally. \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}) } } @@ -80,10 +80,12 @@ User-friendly Bayesian regression modeling: A tutorial with rstanarm and shinyst \emph{The Quantitative Methods for Psychology}. 14(2), 99--119. \url{https://www.tqmp.org/RegularArticles/vol14-2/p099/p099.pdf} -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}. +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)) } \seealso{ \code{\link{as.shinystan}} for creating \code{shinystan} objects.