commit of the package

kdgosik · Jan 5, 2018 · 5459439 · 5459439
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diff --git a/.Rbuildignore b/.Rbuildignore
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+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
diff --git a/DESCRIPTION b/DESCRIPTION
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+Package: NotebookToSite
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <yourself@somewhere.net>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.0.1
diff --git a/NAMESPACE b/NAMESPACE
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+exportPattern("^[[:alpha:]]+")
diff --git a/NotebookToSite.Rproj b/NotebookToSite.Rproj
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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/R/create_site.R b/R/create_site.R
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+#' create_site
+#'
+#' The function create_site is meant to make reporducible workflows easier and more standardized.  It
+#' many folders commonly used in projects suchs as docs, src and references.  It also creates an
+#' Rmarkdown file for a notebook as well as uses knitr to spin it into a static website.  This html
+#' file can be easily shared with collaborators or posted on github pages.  It is already placed in
+#' the docs folder, which the user can enable a github pages website to be created from that folder
+#' under the repository director.
+#'
+#' @seealso knitr
+#' @export
+#' @param github_username string of your github username to create a button to direct to your page.
+#' @keywords knitr
+#' @keywords purl
+#' @import utils
+#' @import rmarkdown
+#' @importFrom knitr purl
+#' @importFrom knitr spin
+#' @author Kirk Gosik <kdgosik@gmail.com>
+
+
+
+create_site <- function(github_username = "kdgosik") {
+
+  create_these <- c("src", "references", "docs", "results",
+                    "src/images", "src/html", "src/chunks")
+  for( d in create_these ) dir.create(d, showWarnings = FALSE)
+
+  try({
+    ## reproducible workflow image backgroud found at the ebook The Practice of Reproducible Research
+    download.file(url = "github.com/kdgosik/NotebookToSite/inst/images/cboettig.png",
+                  destfile = "src/images/cboettig.png")
+  })
+
+  ## writing a simple html button file that references my github page
+  html_lines <- c("<!DOCTYPE html>",
+                  "<html>",
+                  paste0('<a href="https://github.com/', github_username, '"><button>My Github</button></a>'),
+                  "</html>")
+  writeLines(html_lines, con = "src/html/github_button.html")
+
+  ## custom css included in the Notebook file to set backgroud of downloaded image above
+  customcss_lines <- c("body{",
+                       " background-image: url('images/cboettig.png');",
+                       "min-height: 500px;",
+                       " /* Set background image to fixed (don't scroll along with the page) */",
+                       " background-attachment: fixed;",
+                       "background-position: right top;",
+                       "/* Set the background image to no repeat */",
+                       "background-repeat: no-repeat;",
+                       "/* Scale the background image to be as large as possible */",
+                       "background-size: cover;",
+                       "}")
+  writeLines(customcss_lines, "src/custom.css")
+
+  # writes the site yaml file
+  site_lines <- c('name: "Reproducible Workflows"',
+                  'output_dir: "../docs"',
+                  'navbar:',
+                  '  title: "Reproducible Workflows"',
+                  '  left:',
+                  '    - text: "Home"',
+                  '      href: index.html',
+                  '    - text: "Notebook"',
+                  '      href: Notebook.html')
+  writeLines(site_lines, "src/_site.yml")
+
+  ## create index file for website
+  index_lines <- c('---',
+                   'title: "Index"',
+                   'output:',
+                   '  html_document:',
+                   '    toc: true',
+                   '    toc_float: true',
+                   '---')
+  index_lines <- paste0("#'", index_lines)
+  writeLines(index_lines, con = "src/index.R")
+  spin("src/index.R", knit = FALSE, format = "Rmd")
+
+
+  ## creating Notebook Rmarkdown file
+  template_lines <- c('---',
+                      'title: "Notebook"',
+                      'output:',
+                      '  html_document:',
+                      '    toc: true',
+                      '    toc_float: true',
+                      '    css: custom.css',
+                      '    includes:',
+                      '      in_header: html/github_button.html',
+                      '---',
+                      '',
+                      '## Comments',
+                      'I need to add markdown comments here',
+                      '[Picture Credit](https://www.practicereproducibleresearch.org/case-studies/cboettig.html)',
+                      '')
+
+  template_lines <- paste0("#'", template_lines)
+  code_lines <- c('```{r NotebookSetup, include=FALSE}',
+                  'knitr::opts_chunk$set(echo = TRUE)')
+  template_lines <- c(template_lines, code_lines)
+  writeLines(template_lines, con = "src/Notebook.R")
+  spin("src/Notebook.R", knit = FALSE, format = "Rmd")
+
+
+  ## output a purl version of the notebook at each documentation level
+  lapply(0:2, function(i){
+    new_file <- paste0("src/Notebook_DocLevel",i,".Rmd")
+    file.copy("src/Notebook.Rmd", new_file, overwrite = TRUE)
+    purl(new_file, documentation = i)
+    r_file <- paste0("Notebook_DocLevel", i, ".R")
+    file.rename(r_file, paste0("src/", r_file))
+  })
+
+  ## copy and rename the documentation 2 level R file to the Final Notebook version
+  file.copy("src/Notebook_DocLevel2.R", "src/FinalNotebook.R", overwrite = TRUE)
+
+  ## spin Final Notebook version R file into and .Rmd file
+  spin("src/FinalNotebook.R", knit = FALSE, format = "Rmd")
+
+  ## purl individual chunks of the final notbook into separate R files
+  purl_chunks("src/FinalNotebook.Rmd")
+
+  ## render all markdown files in the src folder into html files for the website
+  rmarkdown::render_site(input = "src")
+
+}
diff --git a/R/purl_chunks.R b/R/purl_chunks.R
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+#' purl_chunks
+#'
+#' The function purl_chunks takes an Rmarkdown file and returns each chunk as a
+#' seperate R file.  It was found on stackoverflow at
+#' (https://stackoverflow.com/questions/35855837/with-knitr-preserve-chunk-options-when-purling-chunks-into-separate-files)
+#'
+#' @seealso knitr
+#' @export
+#' @param input_file String of the input file name to the Rmarkdown file that will be purlled into seperate chunks
+#' @param input_path String of the path where to place the R files of each of the chunks
+#' @keywords knitr
+#' @keywords purl
+#' @importFrom knitr purl
+#' @author Kirk Gosik <kdgosik@gmail.com>
+
+
+purl_chunks <- function(input_file, input_path = "src/chunks"){
+
+  purled <- knitr::purl(input_file)    # purl original file; save name to variable
+  lines <- readLines(purled)    # read purled file into a character vector of lines
+  starts <- grep('^## ----.*-+', lines)    # use grep to find header row indices
+  stops <- c(starts[-1] - 1L, length(lines))   # end row indices
+  # extract chunk names from headers
+  names <- sub('^## ----([^-]([^,=]*[^,=-])*)[,-][^=].*', '\\1', lines[starts])
+  names <- ifelse(names == lines[starts], '', paste0(names)) # clean if no chunk name
+  # make nice file names with chunk number and name (if exists)
+  file_names <- file.path(input_path,
+                          paste0(names, '.R'))
+  for(chunk in seq_along(starts)){    # loop over header rows
+    # save the lines in the chunk to a file
+    writeLines(append("#!/usr/bin/env Rscript",
+                      lines[starts[chunk]:stops[chunk]]),
+               con = file_names[chunk])
+  }
+  unlink(purled)    # delete purled file of entire document
+
+}
+
diff --git a/R/update_site.R b/R/update_site.R
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+#' update_site
+#'
+#' The function create_site is meant to make reporducible workflows easier and more standardized.  It
+#' many folders commonly used in projects suchs as docs, src and references.  It also creates an
+#' Rmarkdown file for a notebook as well as uses knitr to spin it into a static website.  This html
+#' file can be easily shared with collaborators or posted on github pages.  It is already placed in
+#' the docs folder, which the user can enable a github pages website to be created from that folder
+#' under the repository director.
+#'
+#' @seealso knitr
+#' @export
+#' @keywords knitr
+#' @keywords purl
+#' @import utils
+#' @import rmarkdown
+#' @importFrom knitr purl
+#' @importFrom knitr spin
+#' @author Kirk Gosik <kdgosik@gmail.com>
+
+
+## This will be a seperate function to update the site
+
+## needs updated!!!
+
+update_site <- function() {
+
+  ## check if an index file exists for the website, if not create one
+  if( !{file.exists("src/index.Rmd")} ) {
+    index_lines <- c('---',
+                     'title: "Index"',
+                     'output:',
+                     '  html_document:',
+                     '    toc: true',
+                     '    toc_float: true',
+                     '---')
+    index_lines <- paste0("#'", index_lines)
+    writeLines(index_lines, con = "src/index.R")
+    spin("src/index.R", knit = FALSE, format = "Rmd")
+  }
+
+
+  ## check if a Notebook exists for website, if not creat one
+  if( !{file.exists("src/Notebook.Rmd")} ) {
+    template_lines <- c('---',
+                        'title: "Notebook"',
+                        'output:',
+                        '  html_document:',
+                        '    toc: true',
+                        '    toc_float: true',
+                        '    css: custom.css',
+                        '    includes:',
+                        '      in_header: html/github_button.html',
+                        '---',
+                        '',
+                        '## Comments',
+                        'I need to add markdown comments here',
+                        '[Picture Credit](https://www.practicereproducibleresearch.org/case-studies/cboettig.html)',
+                        '')
+
+    template_lines <- paste0("#'", template_lines)
+    code_lines <- c('```{r NotebookSetup, include=FALSE}',
+                    'knitr::opts_chunk$set(echo = TRUE)')
+    template_lines <- c(template_lines, code_lines)
+    writeLines(template_lines, con = "src/Notebook.R")
+    spin("src/Notebook.R", knit = FALSE, format = "Rmd")
+  }
+
+  ## output a purl version of the notebook at each documentation level
+  lapply(0:2, function(i){
+    new_file <- paste0("src/Notebook_DocLevel",i,".Rmd")
+    file.copy("src/Notebook.Rmd", new_file, overwrite = TRUE)
+    purl(new_file, documentation = i)
+    r_file <- paste0("Notebook_DocLevel", i, ".R")
+    file.rename(r_file, paste0("src/", r_file))
+  })
+
+  ## copy and rename the documentation 2 level R file to the Final Notebook version
+  file.copy("src/Notebook_DocLevel2.R", "src/FinalNotebook.R", overwrite = TRUE)
+
+  ## spin Final Notebook version R file into and .Rmd file
+  spin("src/FinalNotebook.R", knit = FALSE, format = "Rmd")
+
+  ## purl individual chunks of the final notbook into separate R files
+  purl_chunks("src/FinalNotebook.Rmd")
+
+  ## render all markdown files in the src folder into html files for the website
+  rmarkdown::render_site(input = "src")
+
+}
diff --git a/inst/images/cboettig.png b/inst/images/cboettig.png
diff --git a/man/create_site.Rd b/man/create_site.Rd
diff --git a/man/purl_chunks.Rd b/man/purl_chunks.Rd
diff --git a/man/update_site.Rd b/man/update_site.Rd