remove main vignette as outdated, increment version

ropensci · May 27, 2024 · 366c087 · 366c087
1 parent 198c889
commit 366c087
Show file tree

Hide file tree

Showing 15 changed files with 53 additions and 1,188 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dynamite
 Title: Bayesian Modeling and Causal Inference for Multivariate
     Longitudinal Data
-Version: 1.5.1
+Version: 1.5.2
 Authors@R: c(
     person("Santtu", "Tikka", email = "santtuth@gmail.com", 
            role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4039-4342")),
@@ -18,7 +18,7 @@ Description: Easy-to-use and efficient interface for
   effects, and a wide range of discrete and continuous distributions. 
   Estimation of these dynamic multivariate panel models is carried out via 
   'Stan'. For an  in-depth tutorial of the package, see 
-  (Tikka and Helske, 2023) <arxiv:2302.01607>.
+  (Tikka and Helske, 2024) <arxiv:2302.01607>.
 License: GPL (>= 3)
 URL: https://docs.ropensci.org/dynamite/, https://github.com/ropensci/dynamite/
 BugReports: https://github.com/ropensci/dynamite/issues/

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# dynamite 1.5.2
+
+  * The main package vignette has been temporarily removed as it contained out-of-date information. Please see the arXiv preprint for up-to-date information instead: https://arxiv.org/abs/2302.01607
+
 # dynamite 1.5.1
 
   * The `type` argument of `coef()` and `plot()` has been replaced by `types` accepting multiple types simultaneously, similar to `as.data.table()` and `as.data.frame()`.
@@ -9,7 +13,7 @@
   * Priors of the cutpoint parameters of the `cumulative` family are now customizable.
   * Both `factor` and `ordered factor` responses are now supported for `categorical` and `cumulative` families. In addition, `ordered factor` columns of `data` are no longer converted to `factor` columns.
   * Arguments that have the different names but the same functionality between `rstan` and `cmdstanr` can now be used interchangeably for either backend, such as `iter` and `iter_samples`.
-  * The latent factor component was reparameterized for additional robustness. User-visible changes are related to priors: Instead of prior on the standard deviations `sigma_lambda` and `tau_psi`, prior is now defined on `zeta`, the sum of these, as well as on `kappa`, which is the proportion of `zeta` attributable to `sigma_lambda`.
+  * The latent factor component was reparametrized for additional robustness. User-visible changes are related to priors: Instead of prior on the standard deviations `sigma_lambda` and `tau_psi`, prior is now defined on `zeta`, the sum of these, as well as on `kappa`, which is the proportion of `zeta` attributable to `sigma_lambda`.
 
 # dynamite 1.5.0
 

diff --git a/R/dynamite-package.R b/R/dynamite-package.R
@@ -8,7 +8,7 @@
 #'
 #' # See Also
 #'
-#' * The package vignette.
+#' * The package vignettes
 #' * [dynamite::dynamiteformula()] for information on defining models.
 #' * [dynamite::dynamite()] for information on fitting models.
 #' * \url{https://github.com/ropensci/dynamite/issues/} to submit a bug report

diff --git a/R/dynamiteformula.R b/R/dynamiteformula.R
@@ -2,7 +2,7 @@
 #'
 #' Defines a new observational or a new auxiliary channel for the model using
 #' standard \R formula syntax. Formulas of individual response variables can be
-#' joined together via `+`. See 'Details' and the package vignette for more
+#' joined together via `+`. See 'Details' and the package vignettes for more
 #' information. The function `obs` is a shorthand alias for `dynamiteformula`,
 #' and `aux` is a shorthand alias for
 #' `dynamiteformula(formula, family = "deterministic")`.

diff --git a/codemeta.json b/codemeta.json
@@ -2,13 +2,13 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
   "identifier": "dynamite",
-  "description": "Easy-to-use and efficient interface for Bayesian inference of complex panel (time series) data using dynamic multivariate panel models by Helske and Tikka (2022) <doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple measurements per individual, time-varying and time-invariant effects, and a wide range of discrete and continuous distributions. Estimation of these dynamic multivariate panel models is carried out via 'Stan'. For an in-depth tutorial of the package, see (Tikka and Helske, 2023) <arxiv:2302.01607>.",
+  "description": "Easy-to-use and efficient interface for Bayesian inference of complex panel (time series) data using dynamic multivariate panel models by Helske and Tikka (2024) <doi:10.1016/j.alcr.2024.100617>. The package supports joint modeling of multiple measurements per individual, time-varying and time-invariant effects, and a wide range of discrete and continuous distributions. Estimation of these dynamic multivariate panel models is carried out via 'Stan'. For an in-depth tutorial of the package, see (Tikka and Helske, 2024) <arxiv:2302.01607>.",
   "name": "dynamite: Bayesian Modeling and Causal Inference for Multivariate\n    Longitudinal Data",
-  "relatedLink": "https://docs.ropensci.org/dynamite/",
+  "relatedLink": ["https://docs.ropensci.org/dynamite/", "https://CRAN.R-project.org/package=dynamite"],
   "codeRepository": "https://github.com/ropensci/dynamite/",
   "issueTracker": "https://github.com/ropensci/dynamite/issues/",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "1.5.1",
+  "version": "1.5.2",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -332,11 +332,11 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "5739.626KB",
+  "fileSize": "5946.449KB",
   "citation": [
     {
       "@type": "CreativeWork",
-      "datePublished": "2023",
+      "datePublished": "2024",
       "author": [
         {
           "@type": "Person",
@@ -350,14 +350,14 @@
         }
       ],
       "name": "dynamite: An R Package for Dynamic Multivariate Panel Models",
-      "identifier": "10.48550/ARXIV.2302.01607",
+      "identifier": "10.48550/arXiv.2302.01607",
       "url": "https://arxiv.org/abs/2302.01607",
-      "@id": "https://doi.org/10.48550/ARXIV.2302.01607",
-      "sameAs": "https://doi.org/10.48550/ARXIV.2302.01607"
+      "@id": "https://doi.org/10.48550/arXiv.2302.01607",
+      "sameAs": "https://doi.org/10.48550/arXiv.2302.01607"
     },
     {
-      "@type": "CreativeWork",
-      "datePublished": "2022",
+      "@type": "ScholarlyArticle",
+      "datePublished": "2024",
       "author": [
         {
           "@type": "Person",
@@ -371,11 +371,23 @@
         }
       ],
       "name": "Estimating Causal Effects from Panel Data with Dynamic\n    Multivariate Panel Models",
-      "url": "https://osf.io/preprints/socarxiv/mdwu5/"
+      "identifier": "10.1016/j.alcr.2024.100617",
+      "pagination": "100617",
+      "@id": "https://doi.org/10.1016/j.alcr.2024.100617",
+      "sameAs": "https://doi.org/10.1016/j.alcr.2024.100617",
+      "isPartOf": {
+        "@type": "PublicationIssue",
+        "datePublished": "2024",
+        "isPartOf": {
+          "@type": ["PublicationVolume", "Periodical"],
+          "volumeNumber": "60",
+          "name": "Advances in Life Course Research"
+        }
+      }
     },
     {
       "@type": "SoftwareSourceCode",
-      "datePublished": "2022",
+      "datePublished": "2024",
       "author": [
         {
           "@type": "Person",
@@ -388,9 +400,19 @@
           "familyName": "Helske"
         }
       ],
-      "name": "Bayesian Modeling and Causal Inference for Multivariate\n    Longitudinal Data",
+      "name": "dynamite: Bayesian Modeling and Causal Inference for Multivariate\n    Longitudinal Data",
       "url": "https://github.com/ropensci/dynamite",
-      "description": "R package version 1.0.0"
+      "description": "R package version 1.5.2"
     }
-  ]
+  ],
+  "releaseNotes": "https://github.com/ropensci/dynamite/blob/master/NEWS.md",
+  "readme": "https://github.com/ropensci/dynamite/blob/main/README.md",
+  "contIntegration": ["https://github.com/ropensci/dynamite/actions", "https://app.codecov.io/gh/ropensci/dynamite?branch=main"],
+  "developmentStatus": "https://www.repostatus.org/#active",
+  "review": {
+    "@type": "Review",
+    "url": "https://github.com/ropensci/software-review/issues/554",
+    "provider": "https://ropensci.org"
+  },
+  "keywords": ["bayesian-inference", "panel-data", "r", "r-package", "rstats", "stan", "statistical-models"]
 }
diff --git a/dynamite.Rproj b/dynamite.Rproj
@@ -19,5 +19,6 @@ LineEndingConversion: Posix
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageBuildArgs: --compact-vignettes=both
 PackageCheckArgs: --run-donttest
 PackageRoxygenize: rd,namespace
diff --git a/inst/CITATION b/inst/CITATION
@@ -7,7 +7,7 @@ bibentry(
   url = "https://arxiv.org/abs/2302.01607",
   author = c(person("Santtu", "Tikka"), person("Jouni", "Helske")),
   title = "dynamite: An R Package for Dynamic Multivariate Panel Models",
-  year = "2023"
+  year = "2024"
 )
 bibentry(
   key = "dmpmpaper",
@@ -27,7 +27,7 @@ bibentry(
   title = "dynamite: Bayesian Modeling and Causal Inference for Multivariate
     Longitudinal Data",
   author = c(person("Santtu", "Tikka"), person("Jouni", "Helske")),
-  note = "R package version 1.5.1",
+  note = "R package version 1.5.2",
   year = "2024",
   url = "https://github.com/ropensci/dynamite"
 )
diff --git a/man/dynamite-package.Rd b/man/dynamite-package.Rd
diff --git a/man/dynamiteformula.Rd b/man/dynamiteformula.Rd
diff --git a/vignettes/dag.png b/vignettes/dag.png