CRAN release.

crsh · Dec 23, 2020 · fa449db · fa449db
1 parent 0b98703
commit fa449db
Show file tree

Hide file tree

Showing 12 changed files with 178 additions and 73 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,11 @@
 Package: prereg
 Type: Package
 Title: R Markdown Templates to Preregister Scientific Studies
-Version: 0.4.0
-Date: 2019-1-9
-Authors@R: c(person("Frederik", "Aust", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4900-788X")), person("Lisa", "Spitzer", email = "[email protected]", role = "aut"))
+Version: 0.5.0
+Authors@R: c(
+    person("Frederik", "Aust", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4900-788X")),
+    person("Lisa", "Spitzer", email = "[email protected]", role = "aut")
+  )
 Description: Provides a collection of templates to author preregistration documents for scientific studies in PDF format.
 URL: https://github.com/crsh/prereg
 BugReports: https://github.com/crsh/prereg/issues
@@ -14,5 +16,7 @@ Imports:
 Suggests:
   testthat
 License: GPL-3
+Encoding: UTF-8
 LazyData: TRUE
-RoxygenNote: 6.1.1
+Language: en-US
+RoxygenNote: 7.1.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,5 +3,6 @@
 export(aspredicted_prereg)
 export(brandt_prereg)
 export(cos_prereg)
+export(psyquant_prereg)
 export(rr_prereg)
 export(vantveer_prereg)
diff --git a/R/prereg.R b/R/prereg.R
@@ -1,7 +1,7 @@
 #' R Markdown Templates to Preregister Scientific Studies
 #'
-#' The provided \href{http://rmarkdown.rstudio.com/}{R Markdown} templates are based
-#' on the \href{https://cos.io/prereg/}{Center for Open Science Preregistration Challenge},
+#' The provided \href{https://rmarkdown.rstudio.com/}{R Markdown} templates are based
+#' on the \href{https://osf.io/x5w7h/}{Center for Open Science Preregistration Challenge},
 #' the \href{https://aspredicted.org/}{AsPredicted.org} questions, a template suggested
 #' for social psychology by van 't Veer and Giner-Sorolla (2016), and the replication recipe
 #' suggested by Brandt et al. (2013).
@@ -11,11 +11,11 @@
 #'    software is installed on your computer:
 #'
 #'    \itemize{
-#'        \item{\href{http://www.rstudio.com/}{RStudio} (>= 0.98.932); if you don't use RStudio
-#'            , you need to install \href{http://johnmacfarlane.net/pandoc/}{pandoc} using the
-#'            \href{https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md}{instructions for your operating system}}
-#'        \item{A \href{http://de.wikipedia.org/wiki/TeX}{TeX} distribution (2013 or later; e.g., \href{http://miktex.org/}{MikTeX}
-#'            for Windows, \href{https://tug.org/mactex/}{MacTeX} for Mac, obviously, or \href{http://www.tug.org/texlive/}{TeX Live}
+#'        \item{\href{https://rstudio.com/}{RStudio} (>= 0.98.932); if you don't use RStudio
+#'            , you need to install \href{https://pandoc.org/}{pandoc} using the
+#'            \href{https://pandoc.org/installing.html}{instructions for your operating system}}
+#'        \item{A \href{https://de.wikipedia.org/wiki/TeX}{TeX} distribution (2013 or later; e.g., \href{https://miktex.org/}{MikTeX}
+#'            for Windows, \href{https://tug.org/mactex/}{MacTeX} for Mac, obviously, or \href{https://www.tug.org/texlive/}{TeX Live}
 #'            for Linux)}
 #'    }
 #'

diff --git a/README.Rmd b/README.Rmd
@@ -3,23 +3,19 @@ title: "prereg: R Markdown Templates for Preregistrations of Scientific Studies"
 output: github_document
 ---
 
-[![CRAN status](http://www.r-pkg.org/badges/version/prereg)](https://cran.r-project.org/package=prereg)
-[![Download counter](http://cranlogs.r-pkg.org/badges/prereg)](https://cran.r-project.org/package=prereg)
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![Build status](https://travis-ci.org/crsh/prereg.svg?branch=master)](https://travis-ci.org/crsh/prereg)
+[![CRAN/METACRAN](https://img.shields.io/cran/v/prereg?label=CRAN&logo=r)](https://cran.r-project.org/package=prereg) [![Download counter](https://cranlogs.r-pkg.org/badges/prereg)](https://cran.r-project.org/package=prereg) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org) ![GitHub last commit](https://img.shields.io/github/last-commit/crsh/prereg/master?label=Last commit&logo=github&logoColor=%23FFF) ![Travis build status](https://img.shields.io/travis/crsh/prereg?label=Build&logo=travis-ci&logoColor=%23FFF) [![GitHub bug issues](https://img.shields.io/github/issues/crsh/prereg/bug?label=Bugs&logo=github&logoColor=%23FFF)](https://github.com/crsh/prereg/issues?q=is%3Aopen+is%3Aissue+label%3Abug)
 
-`prereg` provides [R Markdown](http://rmarkdown.rstudio.com/) templates that facilitates authoring preregistrations of scientific studies in PDF format.
-The templates are based on the [Center for Open Science Preregistration Challenge](https://cos.io/prereg/), the [AsPredicted.org](http://aspredicted.org) questions, a template suggested for social psychology by van 't Veer and Giner-Sorolla (2016), and the replication recipe suggested by Brandt et al. (2013).
+`prereg` provides [R Markdown](https://rmarkdown.rstudio.com/) templates that facilitates authoring preregistrations of scientific studies in PDF format.
 
 If you experience any problems or have suggestions for improvements, please [open an issue](https://github.com/crsh/prereg/issues).
 
 ## Setup
 ### Requirements
 To use R Markdown and `prereg` you need the following software on your computer:
 
-- [R](http://www.r-project.org/) (2.11.1 or later)
-- [RStudio](http://www.rstudio.com/) (0.99.441 or later) is optional; if you don't use RStudio, you need to install [pandoc](http://johnmacfarlane.net/pandoc/) using the [instructions for your operating system](https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md)
-- A [TeX](http://de.wikipedia.org/wiki/TeX) distribution (2013 or later; e.g., [MikTeX](http://miktex.org/) for Windows, [MacTeX](https://tug.org/mactex/) for Mac, obviously, or [TeX Live](http://www.tug.org/texlive/) for Linux)
+- [R](https://www.r-project.org/) (2.11.1 or later)
+- [RStudio](https://rstudio.com/) (0.99.441 or later) is optional; if you don't use RStudio, you need to install [pandoc](https://pandoc.org/) using the [instructions for your operating system](https://pandoc.org/installing.html)
+- A [TeX](https://de.wikipedia.org/wiki/TeX) distribution (2013 or later; e.g., [MikTeX](https://miktex.org/) for Windows, [MacTeX](https://tug.org/mactex/) for Mac, obviously, or [TeX Live](https://www.tug.org/texlive/) for Linux)
   - If you are running **Windows**, use MikTex if possible. Currently, pandoc and the Windows version of Tex Live [don't seem to like each other](https://github.com/rstudio/rmarkdown/issues/6). Make sure you install the *complete*---not the basic---version.
 
 ### Install prereg
@@ -77,16 +73,14 @@ Possible repositories for this are:
 - [Open Science Framework](https://osf.io/prereg/): An interdisciplinary platform provided by the Center for Open Science where preregistrations as well as other materials and data can be uploaded
 
 
-## Acknowledgements
-The templates for the preregistrations were developed by the [Center for Open Science](https://cos.io/prereg/), [AsPredicted.org](http://aspredicted.org), Anna Elisabeth van 't Veer and Roger Giner-Sorolla, and a task force composed of members of the American Psychological Association (APA), the British Psychological Society (BPS), the German Psychological Society (DGPs), the Center for Open Science (cos), and the Leibniz Institute for Psychology (ZPID).
+## Acknowledgments
+The templates for the preregistrations were developed by the [Center for Open Science](https://www.cos.io/initiatives/prereg), [AsPredicted.org](https://aspredicted.org/), Anna Elisabeth van 't Veer and Roger Giner-Sorolla, and a task force composed of members of the American Psychological Association (APA), the British Psychological Society (BPS), the German Psychological Society (DGPs), the Center for Open Science (cos), and the Leibniz Institute for Psychology (ZPID).
 I'm thankful for their permission to use their material in this package.
 
 ## Package dependencies
 
 ```{r echo = FALSE, message = FALSE, fig.path = "tools/images/", warning = FALSE}
-source("https://gist.githubusercontent.com/crsh/c906e93c260488e7363ea606243057c2/raw/817a8b1304ee6b1b6b149c3e948d8a59550313bd/plot_dependencies.R")
-
-plot_dependencies()
+depgraph::plot_dependency_graph()
 ```
 
 # References

diff --git a/README.md b/README.md
@@ -1,23 +1,47 @@
 prereg: R Markdown Templates for Preregistrations of Scientific Studies
 ================
 
-[![CRAN status](http://www.r-pkg.org/badges/version/prereg)](https://cran.r-project.org/package=prereg) [![Download counter](http://cranlogs.r-pkg.org/badges/prereg)](https://cran.r-project.org/package=prereg) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![Build status](https://travis-ci.org/crsh/prereg.svg?branch=master)](https://travis-ci.org/crsh/prereg)
-
-`prereg` provides [R Markdown](http://rmarkdown.rstudio.com/) templates that facilitates authoring preregistrations of scientific studies in PDF format. The templates are based on the [Center for Open Science Preregistration Challenge](https://cos.io/prereg/), the [AsPredicted.org](http://aspredicted.org) questions, a template suggested for social psychology by van 't Veer and Giner-Sorolla (2016), and the replication recipe suggested by Brandt et al. (2013).
-
-If you experience any problems or have suggestions for improvements, please [open an issue](https://github.com/crsh/prereg/issues).
-
-Setup
------
+[![CRAN/METACRAN](https://img.shields.io/cran/v/prereg?label=CRAN&logo=r)](https://cran.r-project.org/package=prereg)
+[![Download
+counter](https://cranlogs.r-pkg.org/badges/prereg)](https://cran.r-project.org/package=prereg)
+[![Project Status: Active - The project has reached a stable, usable
+state and is being actively
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org)
+![GitHub last
+commit](https://img.shields.io/github/last-commit/crsh/prereg/master?label=Last%20commit&logo=github&logoColor=%23FFF)
+![Travis build
+status](https://img.shields.io/travis/crsh/prereg?label=Build&logo=travis-ci&logoColor=%23FFF)
+[![GitHub bug
+issues](https://img.shields.io/github/issues/crsh/prereg/bug?label=Bugs&logo=github&logoColor=%23FFF)](https://github.com/crsh/prereg/issues?q=is%3Aopen+is%3Aissue+label%3Abug)
+
+`prereg` provides [R Markdown](https://rmarkdown.rstudio.com/) templates
+that facilitates authoring preregistrations of scientific studies in PDF
+format.
+
+If you experience any problems or have suggestions for improvements,
+please [open an issue](https://github.com/crsh/prereg/issues).
+
+## Setup
 
 ### Requirements
 
-To use R Markdown and `prereg` you need the following software on your computer:
-
--   [R](http://www.r-project.org/) (2.11.1 or later)
--   [RStudio](http://www.rstudio.com/) (0.99.441 or later) is optional; if you don't use RStudio, you need to install [pandoc](http://johnmacfarlane.net/pandoc/) using the [instructions for your operating system](https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md)
--   A [TeX](http://de.wikipedia.org/wiki/TeX) distribution (2013 or later; e.g., [MikTeX](http://miktex.org/) for Windows, [MacTeX](https://tug.org/mactex/) for Mac, obviously, or [TeX Live](http://www.tug.org/texlive/) for Linux)
--   If you are running **Windows**, use MikTex if possible. Currently, pandoc and the Windows version of Tex Live [don't seem to like each other](https://github.com/rstudio/rmarkdown/issues/6). Make sure you install the *complete*---not the basic---version.
+To use R Markdown and `prereg` you need the following software on your
+computer:
+
+  - [R](https://www.r-project.org/) (2.11.1 or later)
+  - [RStudio](https://rstudio.com/) (0.99.441 or later) is optional; if
+    you don’t use RStudio, you need to install
+    [pandoc](https://pandoc.org/) using the [instructions for your
+    operating system](https://pandoc.org/installing.html)
+  - A [TeX](https://de.wikipedia.org/wiki/TeX) distribution (2013 or
+    later; e.g., [MikTeX](https://miktex.org/) for Windows,
+    [MacTeX](https://tug.org/mactex/) for Mac, obviously, or [TeX
+    Live](https://www.tug.org/texlive/) for Linux)
+      - If you are running **Windows**, use MikTex if possible.
+        Currently, pandoc and the Windows version of Tex Live [don’t
+        seem to like each
+        other](https://github.com/rstudio/rmarkdown/issues/6). Make sure
+        you install the *complete*—not the basic—version.
 
 ### Install prereg
 
@@ -27,7 +51,8 @@ You can install the stable version of `prereg` from CRAN
 install.packages("prereg")
 ```
 
-or the development version from this GitHub repository (you may have to install the `devtools` package first).
+or the development version from this GitHub repository (you may have to
+install the `devtools` package first).
 
 ``` r
 install.packages("devtools")
@@ -36,7 +61,8 @@ devtools::install_github("crsh/prereg")
 
 ### Create a preregistration document
 
-Once you have installed the `prereg` you can select the templates when creating a new R Markdown file through the RStudio menus.
+Once you have installed the `prereg` you can select the templates when
+creating a new R Markdown file through the RStudio menus.
 
 ![](tools/images/template_selection.png)
 
@@ -46,13 +72,15 @@ Once you have installed the `prereg` you can select the templates when creating
 
 ![](tools/images/prereg_page1.png) ![](tools/images/prereg_page2.png)
 
-The template file contains comments that provide further details on how to fill in the form but are invisible in the final PDF document.
+The template file contains comments that provide further details on how
+to fill in the form but are invisible in the final PDF document.
 
 ![](tools/images/prereg_rmd.png)
 
 #### Using prereg without RStudio
 
-If you want to use `prereg` without RStudio you can use the `rmarkdown::render` function to create preregistration documents:
+If you want to use `prereg` without RStudio you can use the
+`rmarkdown::render` function to create preregistration documents:
 
 ``` r
 # Create new COS preregistration challenge R Markdown file
@@ -68,19 +96,44 @@ rmarkdown::draft(
 rmarkdown::render("my_preregistration.Rmd")
 ```
 
-Acknowledgements
-----------------
+## Uploading your preregistration
+
+After knitting your preregistration to a PDF file using this package,
+you may upload this protocol to a trustworthy repository to complete
+your preregistration. Possible repositories for this are:
+
+  - [Preregistration in Psychology](https://prereg-psych.org/): A
+    preregistration platform provided by the Leibniz Institute for
+    Psychology (ZPID) which focuses on psychological research
+  - [Open Science Framework](https://osf.io/prereg/): An
+    interdisciplinary platform provided by the Center for Open Science
+    where preregistrations as well as other materials and data can be
+    uploaded
+
+## Acknowledgments
 
-The templates for the preregistrations were developed by the [Center for Open Science](https://cos.io/prereg/), [AsPredicted.org](http://aspredicted.org), and Anna Elisabeth van 't Veer and Roger Giner-Sorolla, respectively. I'm thankful for their permission to use their material in this package.
+The templates for the preregistrations were developed by the [Center for
+Open Science](https://www.cos.io/initiatives/prereg),
+[AsPredicted.org](https://aspredicted.org/), Anna Elisabeth van ’t Veer
+and Roger Giner-Sorolla, and a task force composed of members of the
+American Psychological Association (APA), the British Psychological
+Society (BPS), the German Psychological Society (DGPs), the Center for
+Open Science (cos), and the Leibniz Institute for Psychology (ZPID). I’m
+thankful for their permission to use their material in this package.
 
-Package dependencies
---------------------
+## Package dependencies
 
-![](tools/images/unnamed-chunk-1-1.png)
+![](tools/images/unnamed-chunk-1-1.png)<!-- -->
 
-References
-==========
+# References
 
-Brandt, M. J., IJzerman, H., Dijksterhuis, A., Farach, F. J., Geller, J., Giner-Sorolla, R., ... van 't Veer, A. (2014). The Replication Recipe: What makes for a convincing replication? *Journal of Experimental Social Psychology*, 50, 217--224. doi: [10.1016/j.jesp.2013.10.005](https://doi.org/10.1016/j.jesp.2013.10.005)
+Brandt, M. J., IJzerman, H., Dijksterhuis, A., Farach, F. J., Geller,
+J., Giner-Sorolla, R., … van ’t Veer, A. (2014). The Replication Recipe:
+What makes for a convincing replication? *Journal of Experimental Social
+Psychology*, 50, 217–224. doi:
+[10.1016/j.jesp.2013.10.005](https://doi.org/10.1016/j.jesp.2013.10.005)
 
-van 't Veer, A. E., & Giner-Sorolla, R. (2016). Pre-registration in social psychology---A discussion and suggested template. *Journal of Experimental Social Psychology*, 67, 2--12. doi: [10.1016/j.jesp.2016.03.004](https://doi.org/10.1016/j.jesp.2016.03.004)
+van ’t Veer, A. E., & Giner-Sorolla, R. (2016). Pre-registration in
+social psychology—A discussion and suggested template. *Journal of
+Experimental Social Psychology*, 67, 2–12. doi:
+[10.1016/j.jesp.2016.03.004](https://doi.org/10.1016/j.jesp.2016.03.004)
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,16 +1,39 @@
-# Test environments
+## Test environments
 
-* local OS X 10.12.6 install, R 3.5.1
-* Fedora Linux, R-devel, clang, gfortran (r-hub)
-* Ubuntu Linux 16.04 LTS, R-release, GCC (r-hub)
+* macOS 10.15.7 Catalina, R 4.0.2 (local)
+* macOS 10.13.6 High Sierra, R-release, brew (r-hub)
+* Ubuntu 16.04.6 Xenial, R-oldrel  (Travis-CI)
+* Ubuntu 16.04.6 Xenial, R-release  (Travis-CI)
+* Ubuntu 16.04.6 Xenial, R-devel  (Travis-CI)
+* Debian Linux, R-devel, GCC (r-hub)
 * Windows Server 2008 R2 SP1, R-devel, 32/64 bit (r-hub)
-* Windows Server 2008, R-oldrelease (win-builder)
+* Windows Server 2008, R-oldrel (win-builder)
 * Windows Server 2008, R-release (win-builder)
 
 ## R CMD check results
-There were no ERRORs, WARNINGs, or NOTEs.
 
-r-hub and win-builder CRAN check notes "Author field differs from that derived from Authors@R" due to the ORCID id auto-expansion to a URL.
+0 errors | 0 warnings | 1 note
 
-## Downstream dependencies
-There are no downstream dependencies.
+## Comments
+
+This is a resubmission. Addresses 1 note:
+
+>   Found the following (possibly) invalid URLs:
+    URL: https://cos.io/prereg/ (moved to https://www.cos.io/initiatives/prereg)
+      From: README.md
+      Status: 200
+      Message: OK
+
+* Followed moved content
+
+I keep seeing one issue:
+
+> Found the following (possibly) invalid URLs
+  
+  Found the following (possibly) invalid URLs:
+    URL: https://aspredicted.org/
+      From: man/prereg.Rd
+      Status: 406
+      Message: Not Acceptable
+
+But URL is valid.
diff --git a/inst/NEWS.md b/inst/NEWS.md
@@ -1,6 +1,7 @@
 # prereg 0.5.0
 
 - New template for preregistration of Registered Reports (based on: https://osf.io/93znh/). See `?rr_prereg`. (suggested by @crsh #4, PR by @LisaSpitzer, #10)
+- New template for preregistration for Quantitative Research in Psychology. See `?psyquant_prereg`. (PR by @LisaSpitzerZPID, #15)
 
 # prereg 0.4.0