NotebookToSite.Rcheck/00_pkg_src/NotebookToSite/R/create_site.R
In kdgosik/NotebookToSite: Cretes a notebook and makes a site out of it.
#' create_site
#'
#' The function create_site is meant to make reporducible workflows easier and more standardized. It creates
#' many folders commonly used in projects suchs as docs, src, results 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 = "https://github.com/kdgosik/NotebookToSite/blob/master/inst/images/cboettig.png?raw=true",
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")
knitr::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")
knitr::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)
knitr::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
knitr::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")
}
kdgosik/NotebookToSite documentation built on May 3, 2019, 1:48 p.m.
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#' create_site
#'
#' The function create_site is meant to make reporducible workflows easier and more standardized. It creates
#' many folders commonly used in projects suchs as docs, src, results 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 = "https://github.com/kdgosik/NotebookToSite/blob/master/inst/images/cboettig.png?raw=true",
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")
knitr::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")
knitr::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)
knitr::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
knitr::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")
}
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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