Ensure example is up to date (#3)

* New .Rproj format

* Use MIT License

* Update author

* Add pkg website link

* Update _pkgdown.yml

* Update docs

* Render site

.Rbuildignore

@@ -8,3 +8,4 @@
 ^pkgdown$
 ^references\.bib$
 ^vignettes/Example-article\.Rmd$
+^LICENSE\.md$

DESCRIPTION

@@ -1,18 +1,22 @@
 Package: exampleRPackage
-Type: Package
 Title: An example R package
-Version: 0.2.0
+Version: 0.2.1
 Date: 2017-12-14
-Authors@R: person("Matti", "Vuorre", email = "mv2521@columbia.edu",
-                  role = c("aut", "cre"))
+Authors@R: 
+    person(
+        "Matti", "Vuorre", 
+        email = "m.j.vuorre@tilburguniversity.edu", 
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0001-5052-066X")
+    )
 Description: This package is an example R package.
-URL: https://github.com/mvuorre/exampleRPackage/
+URL: https://github.com/mvuorre/exampleRPackage/, http://mvuorre.github.io/exampleRPackage
 BugReports: http://github.com/mvuorre/exampleRPackage/issues/
 License: MIT + file LICENSE
 Depends: R (>= 3.1)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.0.2
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Suggests: 
     knitr,

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2017
-COPYRIGHT HOLDER: Matti Vuorre
+YEAR: 2025
+COPYRIGHT HOLDER: exampleRPackage authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2025 exampleRPackage authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NEWS.md

@@ -1,3 +1,8 @@
+# exampleRPackage 0.2.1
+
+* Minor updates to ensure current best practices
+* Updated author metadata
+
 # exampleRPackage 0.2.0
 
 * Changed name from exampleDataPackage to exampleRPackage

README.Rmd

@@ -20,6 +20,8 @@ library(knitr)
 
 exampleRPackage shows how R packages can be used to store and communicate scientific research products and metadata. Browse its [source code](https://github.com/mvuorre/exampleRPackage), or read this document for a tutorial on creating R packages.
 
+Note: This aims to be a concise example and introduction, consult **<https://r-pkgs.org/>** for the definitive guide on R package development.
+
 # Introduction
 
 Research projects produce experiments, data, analyses, manuscripts, posters, slides, stimuli and materials, computational models, and more. However, the potential added value of these products is not fully realized due to limited sharing and curating practices. Although more transparent communication of these research products has recently been encouraged [@HoutkoopDataSharingPsychology2018; @LindsaySharingDataMaterials2017; @VanpaemelAreWeWasting2015; @Wichertspooravailabilitypsychological2006; @KleinPracticalGuideTransparency2018; @MartoneDatasharingpsychology2018; @RouderMinimizingMistakesPsychological2019; @Rouderwhatwhyhow2016], these efforts often focus narrowly on sharing data (and sometimes analysis code). Further, the practical value of sharing is often limited by poor documentation, incompatible file formats, and lack of organization, resulting in low rates of reproducibility [@HardwickeDataavailabilityreusability2018]. Standardization of protocols for sharing would be beneficial; but, such standards have not yet emerged. Instead of developing another standard, we suggest borrowing existing standards and practices from software engineering. Specifically, the R package standard, with additional R authoring tools, provides a robust framework for organizing and sharing reproducible research products.

README.md

@@ -8,6 +8,10 @@ communicate scientific research products and metadata. Browse its
 [source code](https://github.com/mvuorre/exampleRPackage), or read this
 document for a tutorial on creating R packages.
 
+Note: This aims to be a concise example and introduction, consult
+**<https://r-pkgs.org/>** for the definitive guide on R package
+development.
+
 # Introduction
 
 Research projects produce experiments, data, analyses, manuscripts,
@@ -59,31 +63,31 @@ analysis code embedded in narrative documents.
 The outline of this tutorial is as follows:
 
 1.  Create a new R package with R Studio
-      - Set up the fundamental package infrastructure
+    - Set up the fundamental package infrastructure
 2.  Describe the package
-      - Edit DESCRIPTION and readme files
+    - Edit DESCRIPTION and readme files
 3.  Add data to package
-      - Add raw data, preprocessing scripts, and an R data object
+    - Add raw data, preprocessing scripts, and an R data object
 4.  Create and add functions
-      - Create and document functions
-      - Dependencies
+    - Create and document functions
+    - Dependencies
 5.  Document the package
-      - Describe the package, its functions, and data, in a machine- and
-        human-readable format
+    - Describe the package, its functions, and data, in a machine- and
+      human-readable format
 
 After these steps, you will have a functional R package on your
 computer. Then, we will talk about sharing and showcasing your package
 online.
 
-  - Sharing the package
-      - Upload to GitHub to make your package (and its source code)
-        available
-      - Connect to Open Science Framework
-  - Create a website for the package
-      - Showcase your R package online with a website
-  - Add narrative documents
-      - Describe how to use your data and functions (e.g. manuscripts,
-        supplementary analysis files)
+- Sharing the package
+  - Upload to GitHub to make your package (and its source code)
+    available
+  - Connect to Open Science Framework
+- Create a website for the package
+  - Showcase your R package online with a website
+- Add narrative documents
+  - Describe how to use your data and functions (e.g. manuscripts,
+    supplementary analysis files)
 
 ## Create a package with R Studio
 
@@ -489,34 +493,35 @@ Markdown](https://rmarkdown.rstudio.com/) websites.
 
 ## Online Resources
 
-  - <http://r-pkgs.had.co.nz/>: Website of Hadley Wickham’s R Packages
-    book (Wickham 2015).
-  - [Writing an R package from
-    scratch](https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/):
-    A short and good blog post on how to create minimal R packages
-  - [Writing R
-    Extensions](https://cran.r-project.org/doc/manuals/r-release/R-exts.html):
-    The official R documentation on writing R packages. This is the
-    complete and definitive set of instructions on how to write R
-    packages. It is almost unreadable in it’s comprehensiveness, and
-    unnecessary for small R packages.
-  - <https://happygitwithr.com/>: A guide for using Git with R and R
-    Studio
+- <http://r-pkgs.had.co.nz/>: Website of Hadley Wickham’s R Packages
+  book (Wickham 2015).
+- [Writing an R package from
+  scratch](https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/):
+  A short and good blog post on how to create minimal R packages
+- [Writing R
+  Extensions](https://cran.r-project.org/doc/manuals/r-release/R-exts.html):
+  The official R documentation on writing R packages. This is the
+  complete and definitive set of instructions on how to write R
+  packages. It is almost unreadable in it’s comprehensiveness, and
+  unnecessary for small R packages.
+- <https://happygitwithr.com/>: A guide for using Git with R and R
+  Studio
 
 ## References
 
-<div id="refs" class="references">
+<div id="refs" class="references csl-bib-body hanging-indent"
+entry-spacing="0">
 
-<div id="ref-allaire_rmarkdown:_2016">
+<div id="ref-allaire_rmarkdown:_2016" class="csl-entry">
 
 Allaire, J. J., Joe Cheng, Yihui Xie, Jonathan McPherson, Winston Chang,
-Jeff Allen, Hadley Wickham, and Rob Hyndman. 2016. *Rmarkdown: Dynamic
-Documents for R* (version 1.3).
+Jeff Allen, Hadley Wickham, and Rob Hyndman. 2016. “Rmarkdown: Dynamic
+Documents for R.”
 <https://cran.r-project.org/web/packages/rmarkdown/index.html>.
 
 </div>
 
-<div id="ref-gorgolewski_brain_2016">
+<div id="ref-gorgolewski_brain_2016" class="csl-entry">
 
 Gorgolewski, Krzysztof J., Tibor Auer, Vince D. Calhoun, R. Cameron
 Craddock, Samir Das, Eugene P. Duff, Guillaume Flandin, et al. 2016.
@@ -526,7 +531,8 @@ Describing Outputs of Neuroimaging Experiments.” *Scientific Data* 3
 
 </div>
 
-<div id="ref-HardwickeDataavailabilityreusability2018">
+<div id="ref-HardwickeDataavailabilityreusability2018"
+class="csl-entry">
 
 Hardwicke, Tom E., Maya B. Mathur, Kyle MacDonald, Gustav Nilsonne,
 George C. Banks, Mallory C. Kidwell, Alicia Hofelich Mohr, et al. 2018.
@@ -537,7 +543,7 @@ Cognition.” *Royal Society Open Science* 5 (8): 180448.
 
 </div>
 
-<div id="ref-HoutkoopDataSharingPsychology2018">
+<div id="ref-HoutkoopDataSharingPsychology2018" class="csl-entry">
 
 Houtkoop, Bobby Lee, Chris Chambers, Malcolm Macleod, Dorothy V. M.
 Bishop, Thomas E. Nichols, and Eric-Jan Wagenmakers. 2018. “Data Sharing
@@ -547,7 +553,7 @@ Methods and Practices in Psychological Science* 1 (1): 70–85.
 
 </div>
 
-<div id="ref-KleinPracticalGuideTransparency2018">
+<div id="ref-KleinPracticalGuideTransparency2018" class="csl-entry">
 
 Klein, Olivier, Tom E. Hardwicke, Frederik Aust, Johannes Breuer, Henrik
 Danielsson, Alicia Hofelich Mohr, Hans Ijzerman, Gustav Nilsonne, Wolf
@@ -557,23 +563,23 @@ Transparency in Psychological Science.” *Collabra: Psychology* 4 (1):
 
 </div>
 
-<div id="ref-LindsaySharingDataMaterials2017">
+<div id="ref-LindsaySharingDataMaterials2017" class="csl-entry">
 
 Lindsay, D. Stephen. 2017. “Sharing Data and Materials in Psychological
 Science.” *Psychological Science* 28 (6): 699–702.
 <https://doi.org/10.1177/0956797617704015>.
 
 </div>
 
-<div id="ref-MartoneDatasharingpsychology2018">
+<div id="ref-MartoneDatasharingpsychology2018" class="csl-entry">
 
 Martone, Maryann E., Alexander Garcia-Castro, and Gary R. VandenBos.
 2018. “Data Sharing in Psychology.” *American Psychologist* 73 (2):
 111–25. <https://doi.org/10.1037/amp0000242>.
 
 </div>
 
-<div id="ref-morey_peer_2016">
+<div id="ref-morey_peer_2016" class="csl-entry">
 
 Morey, Richard D., Christopher D. Chambers, Peter J. Etchells, Christine
 R. Harris, Rink Hoekstra, Daniël Lakens, Stephan Lewandowsky, et al.
@@ -583,23 +589,25 @@ Research Practices Through Peer Review.” *Royal Society Open Science* 3
 
 </div>
 
-<div id="ref-nosek_promoting_2015">
+<div id="ref-nosek_promoting_2015" class="csl-entry">
 
 Nosek, Brian A., G. Alter, G. C. Banks, D. Borsboom, S. D. Bowman, S. J.
 Breckler, S. Buck, et al. 2015. “Promoting an Open Research Culture.”
-*Science* 348 (6242): 1422–5. <https://doi.org/10.1126/science.aab2374>.
+*Science* 348 (6242): 1422–25.
+<https://doi.org/10.1126/science.aab2374>.
 
 </div>
 
-<div id="ref-Rouderwhatwhyhow2016">
+<div id="ref-Rouderwhatwhyhow2016" class="csl-entry">
 
 Rouder, Jeffrey N. 2016. “The What, Why, and How of Born-Open Data.”
-*Behavior Research Methods* 48 (3): 1062–9.
+*Behavior Research Methods* 48 (3): 1062–69.
 <https://doi.org/10.3758/s13428-015-0630-z>.
 
 </div>
 
-<div id="ref-RouderMinimizingMistakesPsychological2019">
+<div id="ref-RouderMinimizingMistakesPsychological2019"
+class="csl-entry">
 
 Rouder, Jeffrey N., Julia M. Haaf, and Hope K. Snyder. 2019. “Minimizing
 Mistakes in Psychological Science.” *Advances in Methods and Practices
@@ -608,7 +616,7 @@ in Psychological Science* 2 (1): 3–11.
 
 </div>
 
-<div id="ref-VanpaemelAreWeWasting2015">
+<div id="ref-VanpaemelAreWeWasting2015" class="csl-entry">
 
 Vanpaemel, Wolf, Maarten Vermorgen, Leen Deriemaecker, and Gert Storms.
 2015. “Are We Wasting a Good Crisis? The Availability of Psychological
@@ -617,7 +625,7 @@ Research Data After the Storm.” *Collabra: Psychology* 1 (1): Art. 3.
 
 </div>
 
-<div id="ref-VuorreCuratingResearchAssets2018">
+<div id="ref-VuorreCuratingResearchAssets2018" class="csl-entry">
 
 Vuorre, Matti, and James P. Curley. 2018. “Curating Research Assets: A
 Tutorial on the Git Version Control System.” *Advances in Methods and
@@ -626,7 +634,8 @@ Practices in Psychological Science* 1 (2): 219–36.
 
 </div>
 
-<div id="ref-Wichertspooravailabilitypsychological2006">
+<div id="ref-Wichertspooravailabilitypsychological2006"
+class="csl-entry">
 
 Wicherts, Jelte M., Denny Borsboom, Judith Kats, and Dylan Molenaar.
 2006. “The Poor Availability of Psychological Research Data for
@@ -635,29 +644,29 @@ Reanalysis.” *American Psychologist* 61 (7): 726–28.
 
 </div>
 
-<div id="ref-wickham_pkgdown:_2017">
+<div id="ref-WickhamPackagesOrganizeTest2015" class="csl-entry">
 
-Wickham, Hadley. 2017. *Pkgdown: Make Static HTML Documentation for a
-Package*. <https://github.com/hadley/pkgdown>.
+Wickham, Hadley. 2015. *R Packages: Organize, Test, Document, and Share
+Your Code*. "O’Reilly Media, Inc.". <http://r-pkgs.had.co.nz/>.
 
 </div>
 
-<div id="ref-WickhamPackagesOrganizeTest2015">
+<div id="ref-wickham_pkgdown:_2017" class="csl-entry">
 
-———. 2015. *R Packages: Organize, Test, Document, and Share Your Code*.
-"O’Reilly Media, Inc.". <http://r-pkgs.had.co.nz/>.
+———. 2017. *Pkgdown: Make Static HTML Documentation for a Package*.
+<https://github.com/hadley/pkgdown>.
 
 </div>
 
-<div id="ref-wickham_roxygen2:_2017">
+<div id="ref-wickham_roxygen2:_2017" class="csl-entry">
 
 Wickham, Hadley, Peter Danenberg, and Manuel Eugster. 2017. *Roxygen2:
 In-Line Documentation for R*.
 <https://CRAN.R-project.org/package=roxygen2>.
 
 </div>
 
-<div id="ref-WilkinsonFAIRGuidingPrinciples2016">
+<div id="ref-WilkinsonFAIRGuidingPrinciples2016" class="csl-entry">
 
 Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg,
 Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al.

_pkgdown.yml

@@ -1,17 +1,17 @@
+home:
+  title: Example R Package
+  description: An example R package with good practices.
 url: http://mvuorre.github.io/exampleRPackage
-title: Example R Package
 destination: docs
 development:
   mode: release
 template:
-  params:
-    bootswatch: spacelab
+  bootstrap: 5
 navbar:
   structure:
     left:  [home, articles, reference, news]
     right: [github]
 components:
-  home: ~
   articles:
     text: Articles
     menu: