#' Renders and Rmarkdown file
#' @param Rmd.file Filename of .Rmd file within the R Markdown directory (source_info$markdown.dir)
#' @param description of rendered file
#' @param ... extra arguments for rmarkdown::render
#' @return Rendered output file information
#' @details Not for direct use. Uses rmarkdown library to access objects in the R script. Will track dependencies for objects used within Rmd file.
#' @export
#' @examples
#'\dontrun{
#' source_info <- create_source_file_dir("adaprHome","read_data.R")
#' renderRmd("read_data.Rmd")
#'}
renderRmd <- function(Rmd.file,description="Rmarkdown",...){
#equire(rmarkdown)
if(!exists("source_info")){
source_info <- list()
stop("Render (adapr) error: source_info not found")
}
mdfile <- createFileInfo(source_info$markdown.dir,Rmd.file,description)
Read.cap(mdfile,I,source_info)#,envir=parent.frame())
shiftmdfile <- file.path(source_info$results.dir,Rmd.file)
file.copy(mdfile$fullname,shiftmdfile,overwrite=TRUE)
outputfile <- rmarkdown::render(shiftmdfile,...)
file.remove(shiftmdfile)
outfile <- createFileInfo(source_info$results.dir,basename(outputfile),paste("rendered Rmarkdown of",description))
Write.cap(NULL,outfile,I,source_info)#,envir=parent.frame())
file.remove(shiftmdfile)
return(outfile)
}
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