rmarkdown.r

In wencke/wencke.github.io: Visualization of Functional Analysis Data

#' This R script will process all R mardown files (those with in_ext file extention,
#' .rmd by default) in the current working directory. Files with a status of
#' 'processed' will be converted to markdown (with out_ext file extention, '.markdown'
#' by default). It will change the published parameter to 'true' and change the
#' status parameter to 'publish'.
#'
#' @param dir the directory to process R Markdown files.
#' @param images.dir the base directory where images will be generated.
#' @param images.url
#' @param out_ext the file extention to use for processed files.
#' @param in_ext the file extention of input files to process.
#' @param recursive should rmd files in subdirectories be processed.
#' @return nothing.
#' @author Jason Bryer <jason@bryer.org>
convertRMarkdown <- function(dir=getwd(), images.dir=dir, images.url='/images/',
out_ext='.markdown', in_ext='.rmd', recursive=FALSE) {
require(knitr, quietly=TRUE, warn.conflicts=FALSE)
files <- list.files(path=dir, pattern=in_ext, ignore.case=TRUE, recursive=recursive)
for(f in files) {
message(paste("Processing ", f, sep=''))
content <- readLines(f)
frontMatter <- which(substr(content, 1, 3) == '---')
if(length(frontMatter) >= 2 & 1 %in% frontMatter) {
statusLine <- which(substr(content, 1, 7) == 'status:')
publishedLine <- which(substr(content, 1, 10) == 'published:')
if(statusLine > frontMatter[1] & statusLine < frontMatter[2]) {
status <- unlist(strsplit(content[statusLine], ':'))[2]
status <- sub('[[:space:]]+$', '', status)
status <- sub('^[[:space:]]+', '', status)
if(tolower(status) == 'process') {
#This is a bit of a hack but if a line has zero length (i.e. a
#black line), it will be removed in the resulting markdown file.
#This will ensure that all line returns are retained.
content[nchar(content) == 0] <- ' '
message(paste('Processing ', f, sep=''))
content[statusLine] <- 'status: publish'
content[publishedLine] <- 'published: true'
outFile <- paste(substr(f, 1, (nchar(f)-(nchar(in_ext)))), out_ext, sep='')
render_markdown(strict=TRUE)
opts_knit$set(out.format='markdown')
opts_knit$set(base.dir=images.dir)
opts_knit$set(base.url=images.url)
try(knit(text=content, output=outFile), silent=FALSE)
} else {
warning(paste("Not processing ", f, ", status is '", status,
"'. Set status to 'process' to convert.", sep=''))
}
} else {
warning("Status not found in front matter.")
}
} else {
warning("No front matter found. Will not process this file.")
}
}
invisible()
}