New template: AsPredicted.org questions

Author: crsh

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: prereg
 Type: Package
 Title: R Markdown Template to Preregister Scientific Studies
-Version: 0.1.0.9000
+Version: 0.1.0.9002
 Date: 2016-2-15
 Authors@R: c(person("Frederik", "Aust", email = "frederik.aust@uni-koeln.de", role = c("aut", "cre")))
-Description: The R Markdown template in this package is based on the Center
-    for Open Science Preregistration Challenge and is, thus, particularly suited to
-    draft preregistration documents for studies that enter the challenge.
+Description: The R Markdown templates in this package are based on the Center
+    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.
 URL: https://github.com/crsh/prereg
 BugReports: https://github.com/crsh/prereg/issues
 Depends:

NAMESPACE

@@ -1,3 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
+export(aspredicted_prereg)
 export(cos_prereg)

R/aspredicted_prereg.R

@@ -0,0 +1,89 @@
+#' AsPredicted.org template
+#'
+#' Knit a PDF document using the AsPredicted.org template
+#'
+#' @param ... additional arguments to \code{\link[rmarkdown]{pdf_document}}; \code{template} is ignored.
+#' @examples
+#' \dontrun{
+#' # Create R Markdown file
+#' rmarkdown::draft(
+#'   "my_preregistration.Rmd"
+#'   , "aspredicted_prereg"
+#'   , package = "prereg"
+#'   , create_dir = FALSE
+#'   , edit = FALSE
+#'   )
+#'
+#' # Render file
+#' rmarkdown::render("my_preregistration.Rmd")
+#' }
+#'
+#' @export
+
+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
+}
+
+# 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
+
+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:.*$", text)) > 0
+  }
+  if (!has_geometry(readLines(input_file, warn = FALSE)))
+    args <- c(args
+      , "--variable", "geometry:left=2.5in"
+      , "--variable", "geometry:bottom=1.25in"
+      , "--variable", "geometry:top=1.25in"
+      , "--variable", "geometry:right=1in"
+    )
+  
+  # Use APA6 CSL citations template if no other file is supplied
+  has_csl <- function(text) {
+    length(grep("^csl:.*$", text)) > 0
+  }
+  if (!has_csl(readLines(input_file, warn = FALSE))) {
+    csl_template <- system.file(
+      "rmarkdown", "templates", "aspredicted_prereg", "resources", "apa6.csl"
+      , package = "prereg"
+    )
+    if(csl_template == "") stop("No CSL template file found.")
+    args <- c(args, c("--csl", rmarkdown::pandoc_path_arg(csl_template)))
+  }
+  
+  args
+}

R/cos_prereg.R

@@ -45,7 +45,7 @@ cos_prereg <- function(...) {
     # save files dir (for generating intermediates)
     saved_files_dir <<- files_dir
 
-    pdf_pre_processor(metadata, input_file, runtime, knit_meta, files_dir, output_dir)
+    cos_pdf_pre_processor(metadata, input_file, runtime, knit_meta, files_dir, output_dir)
   }
 
   cos_prereg_format$pre_processor <- pre_processor
@@ -58,9 +58,9 @@ cos_prereg <- function(...) {
 # (https://github.com/rstudio/rmarkdown/blob/master/R/pdf_document.R)
 # to ensure right geometry defaults in the absence of user specified values
 
-pdf_pre_processor <- function(metadata, input_file, runtime, knit_meta, files_dir, output_dir) {
+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:.*$", text)) > 0
@@ -72,20 +72,19 @@ pdf_pre_processor <- function(metadata, input_file, runtime, knit_meta, files_di
       , "--variable", "geometry:top=1.25in"
       , "--variable", "geometry:right=1in"
     )
-
+  
   # Use APA6 CSL citations template if no other file is supplied
   has_csl <- function(text) {
     length(grep("^csl:.*$", text)) > 0
   }
   if (!has_csl(readLines(input_file, warn = FALSE))) {
     csl_template <- system.file(
-      "rmarkdown", "templates", "cos_prereg", "resources"
-      , "apa6.csl"
+      "rmarkdown", "templates", "cos_prereg", "resources", "apa6.csl"
       , package = "prereg"
     )
     if(csl_template == "") stop("No CSL template file found.")
     args <- c(args, c("--csl", rmarkdown::pandoc_path_arg(csl_template)))
   }
-
+  
   args
-}
+}

README.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "prereg: R Markdown Template for Preregistrations of Scientific Studies"
+title: "prereg: R Markdown Templates for Preregistrations of Scientific Studies"
 output: github_document
 ---
 
@@ -8,7 +8,9 @@ output: github_document
 [![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 an [R Markdown](http://rmarkdown.rstudio.com/) template that facilitates authoring preregistrations of scientific studies in PDF format. The template is based on the [Center for Open Science Preregistration Challenge](https://cos.io/prereg/) template and is, thus, particularly suited to draft preregistrations that enter the challenge.
+`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.
 
 If you experience any problems or have suggestions for improvements, please [open an issue](https://github.com/crsh/prereg/issues).
 
@@ -36,7 +38,7 @@ devtools::install_github("crsh/prereg")
 ```
 
 ### Create a preregistration document
-Once you have installed the `prereg` you can select the template 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.
 
 ![](https://www.dropbox.com/s/y39lywyloypuncb/template_selection.png?dl=1)
 
@@ -46,7 +48,7 @@ Once you have installed the `prereg` you can select the template when creating a
 
 ![](https://www.dropbox.com/s/fq6giram61bxe2m/prereg_page1.png?dl=1) ![](https://www.dropbox.com/s/cm64wpnl8la72q0/prereg_page2.png?dl=1)
 
-The template file contains comments, which are invisible in the final PDF document, that provide further details on how to fill in the form.
+The template file contains comments that provide further details on how to fill in the form but are invisible in the final PDF document.
 
 ![](https://www.dropbox.com/s/ylaf6zhxri46w42/prereg_rmd.png?dl=1)
 
@@ -57,3 +59,7 @@ If you want to use `prereg` without RStudio you can use the `rmarkdown::render`
 ```S
 rmarkdown::render("mymanuscript.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.

README.md

@@ -1,9 +1,9 @@
-prereg: R Markdown Template for Preregistrations of Scientific Studies
+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)
 
-`prereg` provides an [R Markdown](http://rmarkdown.rstudio.com/) template that facilitates authoring preregistrations of scientific studies in PDF format. The template is based on the [Center for Open Science Preregistration Challenge](https://cos.io/prereg/) template and is, thus, particularly suited to draft preregistrations that enter the challenge.
+`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.
 
 If you experience any problems or have suggestions for improvements, please [open an issue](https://github.com/crsh/prereg/issues).
 
@@ -36,7 +36,7 @@ devtools::install_github("crsh/prereg")
 
 ### Create a preregistration document
 
-Once you have installed the `prereg` you can select the template 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.
 
 ![](https://www.dropbox.com/s/y39lywyloypuncb/template_selection.png?dl=1)
 
@@ -46,7 +46,7 @@ Once you have installed the `prereg` you can select the template when creating a
 
 ![](https://www.dropbox.com/s/fq6giram61bxe2m/prereg_page1.png?dl=1) ![](https://www.dropbox.com/s/cm64wpnl8la72q0/prereg_page2.png?dl=1)
 
-The template file contains comments, which are invisible in the final PDF document, that provide further details on how to fill in the form.
+The template file contains comments that provide further details on how to fill in the form but are invisible in the final PDF document.
 
 ![](https://www.dropbox.com/s/ylaf6zhxri46w42/prereg_rmd.png?dl=1)
 
@@ -57,3 +57,8 @@ If you want to use `prereg` without RStudio you can use the `rmarkdown::render`
 ``` s
 rmarkdown::render("mymanuscript.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.