revise vignettes, drop pryr/pder/rmarkdown, increment version, run-ex…

…tended

.Rbuildignore

@@ -9,3 +9,6 @@
 ^_pkgdown.yml$
 ^doc$
 ^Meta$
+^vignettes/.*\.qmd\.orig$
+^vignettes/rebuild_vignettes\.R$
+^vignettes/*_files$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynamite
 Title: Bayesian Modeling and Causal Inference for Multivariate
     Longitudinal Data
-Version: 1.5.4
+Version: 1.5.5
 Authors@R: c(
     person("Santtu", "Tikka", email = "santtuth@gmail.com", 
            role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4039-4342")),
@@ -40,20 +40,17 @@ Imports:
     tibble (>= 2.0.0),
     utils
 Suggests:
-    bookdown,
     cmdstanr,
     covr,
     dplyr,
     knitr,
     mice,
     mockthat,
-    pder,
-    pryr,
-    rmarkdown,
+    quarto,
     testthat (>= 3.0.0),
     tidyr
 VignetteBuilder: 
-    knitr
+    quarto
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd",

NEWS.md

@@ -1,3 +1,9 @@
+# dynamite 1.5.5
+
+  * The package vignettes are now prerendered as some of them took a long time to build.
+  * The vignette builder has been switched to `quarto`.
+  * The package no longer depends on `prder`, `pryr`, and `rmarkdown`.
+
 # dynamite 1.5.4
 
   * Obtaining the model parameter dimensions via `get_parameter_dims()` no longer requires a compiled Stan model. This leads to a significant performance improvement when applied to `dynamiteformula` objects.

R/dynamite.R

@@ -135,13 +135,14 @@
 #'   based on Stan, the  scalability of the package depends directly on the
 #'   scalability of Stan.
 #' @references
-#' Santtu Tikka and Jouni Helske (2023). \pkg{dynamite}: An \R Package for
+#' Santtu Tikka and Jouni Helske (2024). \pkg{dynamite}: An \R Package for
 #' Dynamic Multivariate Panel Models. arXiv preprint,
 #' <https://arxiv.org/abs/2302.01607>.
 #'
 #' Jouni Helske and Santtu Tikka (2022). Estimating Causal Effects
-#' from Panel Data with Dynamic Multivariate Panel Models. SocArxiv preprint,
-#' <https://osf.io/preprints/socarxiv/mdwu5/>.
+#' from Panel Data with Dynamic Multivariate Panel Models.
+#' *Advances in Life Course Research*, 60, 100617.
+#' <https://doi.org/10.1016/j.alcr.2024.100617>.
 #' @examples
 #' data.table::setDTthreads(1) # For CRAN
 #' \donttest{

codemeta.json

@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ropensci/dynamite/",
   "issueTracker": "https://github.com/ropensci/dynamite/issues/",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "1.5.3",
+  "version": "1.5.5",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.0 (2023-04-21 ucrt)",
+  "runtimePlatform": "R version 4.4.2 (2024-10-31 ucrt)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -47,18 +47,6 @@
     }
   ],
   "softwareSuggestions": [
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "bookdown",
-      "name": "bookdown",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=bookdown"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "cmdstanr",
@@ -126,39 +114,15 @@
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "pder",
-      "name": "pder",
+      "identifier": "quarto",
+      "name": "quarto",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=pder"
-    },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "pryr",
-      "name": "pryr",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=pryr"
-    },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "rmarkdown",
-      "name": "rmarkdown",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
+      "sameAs": "https://CRAN.R-project.org/package=quarto"
     },
     {
       "@type": "SoftwareApplication",
@@ -279,11 +243,6 @@
       "sameAs": "https://CRAN.R-project.org/package=loo"
     },
     "9": {
-      "@type": "SoftwareApplication",
-      "identifier": "methods",
-      "name": "methods"
-    },
-    "10": {
       "@type": "SoftwareApplication",
       "identifier": "patchwork",
       "name": "patchwork",
@@ -295,7 +254,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=patchwork"
     },
-    "11": {
+    "10": {
       "@type": "SoftwareApplication",
       "identifier": "posterior",
       "name": "posterior",
@@ -307,7 +266,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=posterior"
     },
-    "12": {
+    "11": {
       "@type": "SoftwareApplication",
       "identifier": "rlang",
       "name": "rlang",
@@ -319,7 +278,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=rlang"
     },
-    "13": {
+    "12": {
       "@type": "SoftwareApplication",
       "identifier": "rstan",
       "name": "rstan",
@@ -331,12 +290,12 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=rstan"
     },
-    "14": {
+    "13": {
       "@type": "SoftwareApplication",
       "identifier": "stats",
       "name": "stats"
     },
-    "15": {
+    "14": {
       "@type": "SoftwareApplication",
       "identifier": "tibble",
       "name": "tibble",
@@ -349,14 +308,14 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=tibble"
     },
-    "16": {
+    "15": {
       "@type": "SoftwareApplication",
       "identifier": "utils",
       "name": "utils"
     },
     "SystemRequirements": null
   },
-  "fileSize": "5071.746KB",
+  "fileSize": "NAKB",
   "citation": [
     {
       "@type": "CreativeWork",
@@ -426,7 +385,7 @@
       ],
       "name": "dynamite: Bayesian Modeling and Causal Inference for Multivariate\n    Longitudinal Data",
       "url": "https://github.com/ropensci/dynamite",
-      "description": "R package version 1.5.3"
+      "description": "R package version 1.5.4"
     }
   ],
   "releaseNotes": "https://github.com/ropensci/dynamite/blob/master/NEWS.md",

vignettes/.gitignore

@@ -1,2 +1,3 @@
 *.html
 *.R
+*_files