Preparing CRAN submission.

crsh · crsh · commit 9572de846d00 · 2016-09-20T15:53:56.000+02:00
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,4 +3,5 @@
 
 ^.travis.yml
 ^cran-comments.md
-^README.Rmd
+^README.Rmd
+^README_files$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,19 +1,19 @@
 Package: prereg
 Type: Package
-Title: R Markdown Template to Preregister Scientific Studies
-Version: 0.1.0.9002
-Date: 2016-2-15
+Title: R Markdown Templates to Preregister Scientific Studies
+Version: 0.2.0
+Date: 2016-9-20
 Authors@R: c(person("Frederik", "Aust", email = "frederik.aust@uni-koeln.de", role = c("aut", "cre")))
 Description: The R Markdown templates in this package are based on the Center
-    for Open Science Preregistration Challenge and the AsPredicted.org questions.
+    for Open Science Preregistration Challenge and the 'AsPredicted.org' questions.
     They are, thus, particularly suited to draft preregistration documents for
-    studies these programs but can also be used for internal preregistrations.
+    these programs but can also be used for internally.
 URL: https://github.com/crsh/prereg
 BugReports: https://github.com/crsh/prereg/issues
 Depends:
-  R (>= 3.2.3)
+  R (>= 3.0.0)
 Imports:
-  rmarkdown (>= 0.9.2)
+  rmarkdown (>= 1.0)
 Suggests:
   testthat
 License: GPL-3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# prereg 0.2.0
+
+- New template based on AsPredicted.org questions. See `?aspredicted_prereg`.
+
 # prereg 0.1.0
 
 Initial release.
diff --git a/R/aspredicted_prereg.R b/R/aspredicted_prereg.R
@@ -1,6 +1,6 @@
 #' AsPredicted.org template
 #'
-#' Knit a PDF document using the AsPredicted.org template
+#' Knit a PDF document using the AsPredicted.org questions
 #'
 #' @param ... additional arguments to \code{\link[rmarkdown]{pdf_document}}; \code{template} is ignored.
 #' @examples
@@ -23,33 +23,33 @@
 aspredicted_prereg <- function(...) {
   ellipsis <- list(...)
   if(!is.null(ellipsis$template)) ellipsis$template <- NULL
-  
+
   # Get cos_prereg template
   template <- system.file(
     "rmarkdown", "templates", "aspredicted_prereg", "resources"
     , "aspredicted_prereg.tex"
     , package = "prereg"
   )
   if(template == "") stop("No LaTeX template file found.") else ellipsis$template <- template
-  
+
   # Create format
   aspredicted_prereg_format <- do.call(rmarkdown::pdf_document, ellipsis)
-  
+
   ## Overwrite preprocessor to set correct margin and CSL defaults
   saved_files_dir <- NULL
-  
+
   # Preprocessor functions are adaptations from the RMarkdown package
   # (https://github.com/rstudio/rmarkdown/blob/master/R/pdf_document.R)
   # to ensure right geometry defaults in the absence of user specified values
   pre_processor <- function(metadata, input_file, runtime, knit_meta, files_dir, output_dir) {
     # save files dir (for generating intermediates)
     saved_files_dir <<- files_dir
-    
+
     aspredicted_pdf_pre_processor(metadata, input_file, runtime, knit_meta, files_dir, output_dir)
   }
-  
+
   aspredicted_prereg_format$pre_processor <- pre_processor
-  
+
   aspredicted_prereg_format
 }
 
@@ -59,7 +59,7 @@ aspredicted_prereg <- function(...) {
 
 aspredicted_pdf_pre_processor <- function(metadata, input_file, runtime, knit_meta, files_dir, output_dir) {
   args <- c()
-  
+
   # Set margins if no other geometry options specified
   has_geometry <- function(text) {
     length(grep("^geometry:.*$", text)) > 0
@@ -71,7 +71,7 @@ aspredicted_pdf_pre_processor <- function(metadata, input_file, runtime, knit_me
       , "--variable", "geometry:top=1.25in"
       , "--variable", "geometry:right=1in"
     )
-  
+
   # Use APA6 CSL citations template if no other file is supplied
   has_csl <- function(text) {
     length(grep("^csl:.*$", text)) > 0
@@ -84,6 +84,6 @@ aspredicted_pdf_pre_processor <- function(metadata, input_file, runtime, knit_me
     if(csl_template == "") stop("No CSL template file found.")
     args <- c(args, c("--csl", rmarkdown::pandoc_path_arg(csl_template)))
   }
-  
+
   args
 }
diff --git a/R/cos_prereg.R b/R/cos_prereg.R
@@ -1,6 +1,6 @@
 #' COS Preregistration Challenge template
 #'
-#' Knit a PDF document using the COS Preregistration Challenge template
+#' Knit a PDF document using the COS Preregistration Challenge questions
 #'
 #' @param ... additional arguments to \code{\link[rmarkdown]{pdf_document}}; \code{template} is ignored.
 #' @examples
@@ -60,7 +60,7 @@ cos_prereg <- function(...) {
 
 cos_pdf_pre_processor <- function(metadata, input_file, runtime, knit_meta, files_dir, output_dir) {
   args <- c()
-  
+
   # Set margins if no other geometry options specified
   has_geometry <- function(text) {
     length(grep("^geometry:.*$", text)) > 0
@@ -72,7 +72,7 @@ cos_pdf_pre_processor <- function(metadata, input_file, runtime, knit_meta, file
       , "--variable", "geometry:top=1.25in"
       , "--variable", "geometry:right=1in"
     )
-  
+
   # Use APA6 CSL citations template if no other file is supplied
   has_csl <- function(text) {
     length(grep("^csl:.*$", text)) > 0
@@ -85,6 +85,6 @@ cos_pdf_pre_processor <- function(metadata, input_file, runtime, knit_meta, file
     if(csl_template == "") stop("No CSL template file found.")
     args <- c(args, c("--csl", rmarkdown::pandoc_path_arg(csl_template)))
   }
-  
+
   args
 }
diff --git a/R/prereg.R b/R/prereg.R
@@ -1,8 +1,11 @@
-#' R Markdown Template for Preregistrations of Scientific Studies
+#' R Markdown Templates to Preregister Scientific Studies
 #'
-#' The \href{http://rmarkdown.rstudio.com/}{R Markdown} template in the prereg package is based
+#' 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} and
-#' is, thus, particularly suited to draft preregistrations that enter the challenge.
+#' the \href{https://aspredicted.org/}{AsPredicted.org} questions. They are, thus, particularly
+#' suited to draft preregistration documents for these programs but can also be used for internal
+#' preregistrations.
+#'
 #' @section System requirements:
 #'    Before using \pkg{prereg} to create a preregistration document, make sure the following
 #'    software is installed on your computer:
diff --git a/README.Rmd b/README.Rmd
@@ -3,13 +3,13 @@ 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/web/packages/prereg/index.html)
-[![Download counter](http://cranlogs.r-pkg.org/badges/prereg)](https://cran.r-project.org/web/packages/prereg/index.html)
+[![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/) template and the [AsPredicted.org](http://aspredicted.org) questions.
+The templates are based on the [Center for Open Science Preregistration Challenge](https://cos.io/prereg/) and the [AsPredicted.org](http://aspredicted.org) questions.
 They are, thus, particularly suited to draft preregistration documents for studies these programs but can also be used for internal preregistrations.
 
 If you experience any problems or have suggestions for improvements, please [open an issue](https://github.com/crsh/prereg/issues).
@@ -57,9 +57,27 @@ The template file contains comments that provide further details on how to fill
 If you want to use `prereg` without RStudio you can use the `rmarkdown::render` function to create preregistration documents:
 
 ```S
-rmarkdown::render("mymanuscript.Rmd")
+# Create new COS preregistration challenge R Markdown file
+rmarkdown::draft(
+  "my_preregistration.Rmd"
+  , "cos_prereg"
+  , package = "prereg"
+  , create_dir = FALSE
+  , edit = FALSE
+)
+
+# Render document
+rmarkdown::render("my_preregistration.Rmd")
 ```
 
 ## Acknowledgements
 The templates for the preregistrations were developed by the [Center for Open Science](https://cos.io/prereg/) and [AsPredicted.org](http://aspredicted.org), respectively.
 I thank both for their permission to use their material in this package.
+
+## Package dependencies
+
+```{r echo = FALSE, message = FALSE}
+source("https://gist.githubusercontent.com/crsh/c906e93c260488e7363ea606243057c2/raw/5243c091d5809cb71473c4ef3f926065e9e2532d/plot_dependencies.R")
+
+plot_dependencies()
+```
diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
 prereg: R Markdown Templates for Preregistrations of Scientific Studies
 ================
 
-[![CRAN status](http://www.r-pkg.org/badges/version/prereg)](https://cran.r-project.org/web/packages/prereg/index.html) [![Download counter](http://cranlogs.r-pkg.org/badges/prereg)](https://cran.r-project.org/web/packages/prereg/index.html) [![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 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/) template and the [AsPredicted.org](http://aspredicted.org) questions. They are, thus, particularly suited to draft preregistration documents for studies these programs but can also be used for internal preregistrations.
+`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/) and the [AsPredicted.org](http://aspredicted.org) questions. They are, thus, particularly suited to draft preregistration documents for studies these programs but can also be used for internal preregistrations.
 
 If you experience any problems or have suggestions for improvements, please [open an issue](https://github.com/crsh/prereg/issues).
 
@@ -55,10 +55,25 @@ The template file contains comments that provide further details on how to fill
 If you want to use `prereg` without RStudio you can use the `rmarkdown::render` function to create preregistration documents:
 
 ``` s
-rmarkdown::render("mymanuscript.Rmd")
+# Create new COS preregistration challenge R Markdown file
+rmarkdown::draft(
+  "my_preregistration.Rmd"
+  , "cos_prereg"
+  , package = "prereg"
+  , create_dir = FALSE
+  , edit = FALSE
+)
+
+# Render document
+rmarkdown::render("my_preregistration.Rmd")
 ```
 
 Acknowledgements
 ----------------
 
 The templates for the preregistrations were developed by the [Center for Open Science](https://cos.io/prereg/) and [AsPredicted.org](http://aspredicted.org), respectively. I thank both for their permission to use their material in this package.
+
+Package dependencies
+--------------------
+
+![](README_files/figure-markdown_github/unnamed-chunk-1-1.png)
diff --git a/README_files/figure-markdown_github/unnamed-chunk-1-1.png b/README_files/figure-markdown_github/unnamed-chunk-1-1.png
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,11 +1,28 @@
-## Test environments
-* local OS X 10.11 install, R 3.2.3
-* local Ubuntu 14.04 install, R 3.2.3
-* Ubuntu 12.04 (on travis-ci), R 3.2.3
+# Test environments
+
+* local OS X 10.11 install, R 3.3.1
+* local Ubuntu 14.04 install, R 3.3.1
+* Ubuntu 12.04 (old release, release, and devel; on travis-ci)
 * win-builder (devel and release)
 
-## R CMD check results
-There were no ERRORs, WARNINGs or NOTEs.
+# R CMD check results
+
+There were no ERRORs or WARNINGs but one NOTE:
+
+* Found the following (possibly) invalid URLs:
+  URL: http://cos.io/prereg/
+    From: README.md
+    Status: Error
+    Message: libcurl error code 35
+    	Unknown SSL protocol error in connection to cos.io:443
+  URL: https://cos.io/prereg/
+    From: man/prereg.Rd
+    Status: Error
+    Message: libcurl error code 35
+    	Unknown SSL protocol error in connection to cos.io:443
+
+The URL is correct and the web page displays correctly in a web browser.
+
+# Downstream dependencies
 
-## Downstream dependencies
-There are no downstream dependencies.
+There are no downstream dependencies.
diff --git a/inst/rmarkdown/templates/aspredicted_prereg/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/aspredicted_prereg/skeleton/skeleton.Rmd
@@ -73,14 +73,6 @@ output: prereg::aspredicted_prereg
 > Example: We will include a battery of questions for exploratory purposes, including life satisfaction, amount of videogame playing, and family activity. We will also provide an additional survey with 24 questions assessing achievement orientation.We will not report the results of those analyses for the project being pre-registered.
 
 
-## Name
-<!-- Give a title for this AsPredicted pre-registration. Suggestion: use the name of the project, followed by study description. -->
-
-> Example: SUMMER PROGRAMS - GPA performance, Chicago, July 2016
-
-`r rmarkdown::metadata$title`
-
-
 # References
 ## 
 \vspace{-2pc}
diff --git a/inst/rmarkdown/templates/cos_prereg/template.yaml b/inst/rmarkdown/templates/cos_prereg/template.yaml
@@ -1,4 +1,4 @@
 name: COS Preregistration Challenge
 description: >
-  This template is based on the Center for Open Science Preregistration Challenge template and is, thus, particularly suited to draft preregistrations that enter the challenge.
+  This template is based on the Center for Open Science Preregistration Challenge questions and is, thus, particularly suited to draft preregistrations that enter the challenge.
 create_dir: false
diff --git a/man/aspredicted_prereg.Rd b/man/aspredicted_prereg.Rd
diff --git a/man/cos_prereg.Rd b/man/cos_prereg.Rd
diff --git a/man/prereg.Rd b/man/prereg.Rd
diff --git a/tests/testthat/test_skeletons.R b/tests/testthat/test_skeletons.R
@@ -2,38 +2,38 @@ test_that(
   "Knit COS skeleton"
   , {
     skip_on_cran()
-      
+
     # Render skeleton
     rmarkdown::draft(
-      "bare_skeleton.Rmd"
+      "cos_skeleton.Rmd"
       , "cos_prereg"
       , package = "prereg"
       , create_dir = FALSE
       , edit = FALSE
     )
-    rmarkdown::render("bare_skeleton.Rmd")
+    rmarkdown::render("cos_skeleton.Rmd")
 
     # Clean up
-    file.remove(list.files(pattern = "bare"))
+    file.remove(list.files(pattern = "cos"))
   }
 )
 
 test_that(
   "Knit AsPredicted skeleton"
   , {
     skip_on_cran()
-    
+
     # Render skeleton
     rmarkdown::draft(
-      "bare_skeleton.Rmd"
+      "aspredicted_skeleton.Rmd"
       , "aspredicted_prereg"
       , package = "prereg"
       , create_dir = FALSE
       , edit = FALSE
     )
-    rmarkdown::render("bare_skeleton.Rmd")
-    
+    rmarkdown::render("aspredicted_skeleton.Rmd")
+
     # Clean up
-    file.remove(list.files(pattern = "bare"))
+    file.remove(list.files(pattern = "aspredicted"))
   }
 )
