moveDocs

moveDocs relocates files by renaming with a new file path. Specifically, it scans for md and html files in the docs/Rmd directory and/or pdf files in the docs/Rnw directory. If such files are found in the respective locations, they are moved to docs/md, docs/html, and docs/pdf, respectively.

The intent is to clean up the Rmd and Rnw directories after knitr has been used to knit documents in place. I do this because I have more success knitting documents with the confluence of RStudio, rmarkdown, knitr, pandoc, and LaTeX when the knitting occurs all within the directory of the originating files. The process is more prone to throwing errors when trying to specify alternate locations for outputs.

moveDocs makes a nominal effort to replace a possible relative path with a full file path before proceeding, if the former is supplied. Default arguments include move=TRUE which will call file.rename and copy=FALSE which, if TRUE (and move=FALSE), will alternatively call file.copy. If both are TRUE, any files found are moved.

This function will always overwrite any existing file versions previously moved to the output directories, by way of file.rename. To keep the behavior consistent, when move=FALSE and copy=TRUE, file.copy always executes with its argument, overwrite=TRUE. This should never cause problems because in the context I intend for this function, the types of files being moved or copied from docs/Rmd and docs/Rnw are never used as inputs to other files, functions, or processes, nor are they meant to be edited by hand after being generated.

If there are LaTeX-associated files present (.TeX, .aux, and .txt files with the same file names as local pdf files.), these files will be removed if remove.latex=TRUE (default). If FALSE, the default latexDir="LaTeX" means that these files will be moved to the docs/LaTeX directory rather than deleted. If this directory does not exist, it will be created. An alternate location can be specified, such as “pdf” if you want to keep these files with the related pdf files after those are moved by moveDocs as well to docs/pdf. The directory of supplemental pdf figures, if any, which is creating during knitting, is not included in the file move at this time.

# Organization documentation
moveDocs <- function(path.docs, type = c("md", "html", "pdf"), move = TRUE, 
    copy = FALSE, remove.latex = TRUE, latexDir = "latex") {
    if (any(!(type %in% c("md", "html", "pdf")))) 
        stop("type must be among 'md', 'html', and 'pdf'")
    stopifnot(move | copy)
    if (path.docs == "." | path.docs == "./") 
        path.docs <- getwd()
    if (strsplit(path.docs, "/")[[1]][1] == "..") {
        tmp <- strsplit(path.docs, "/")[[1]][-1]
        if (length(tmp)) 
            path.docs <- file.path(getwd(), paste0(tmp, collapse = "/")) else stop("Check path.docs argument.")
    }
    for (i in 1:length(type)) {
        if (type[i] == "pdf") 
            origin <- "Rnw" else origin <- "Rmd"
        path.i <- file.path(path.docs, origin)
        infiles <- list.files(path.i, pattern = paste0("\\.", type[i], "$"), 
            full = TRUE)
        if (type[i] == "pdf") {
            extensions <- c("tex", "aux", "log")
            all.pdfs <- basename(list.files(path.docs, pattern = ".pdf$", full = T, 
                recursive = T))
            pat <- paste0("^", rep(gsub("pdf", "", all.pdfs), length(extensions)), 
                rep(extensions, each = length(all.pdfs)), "$")
            latex.files <- unlist(sapply(1:length(pat), function(p, path, pat) list.files(path, 
                pattern = pat[p], full = TRUE), path = path.i, pat = pat))
            print(latex.files)
            if (length(latex.files)) {
                if (remove.latex) {
                  unlink(latex.files)
                } else {
                  dir.create(file.path(path.docs, latexDir), showWarnings = FALSE, 
                    recursive = TRUE)
                  file.rename(latex.files, file.path(path.docs, latexDir, basename(latex.files)))
                }
            }
        }
        if (length(infiles)) {
            infiles <- infiles[basename(dirname(infiles)) == origin]
            if (length(infiles)) {
                if (type[i] == "html") {
                  html.dirs <- gsub("\\.html", "_files", infiles)
                  dirs <- list.dirs(path.i, recursive = FALSE)
                  ind <- which(dirs %in% html.dirs)
                  if (length(ind)) {
                    html.dirs <- dirs[ind]
                    html.dirs.recur <- list.dirs(html.dirs)
                    for (p in 1:length(html.dirs.recur)) dir.create(gsub("/Rmd", 
                      "/html", html.dirs.recur[p]), recursive = TRUE, showWarnings = FALSE)
                    subfiles <- unique(unlist(lapply(1:length(html.dirs.recur), 
                      function(p, path) list.files(path[p], full = TRUE), path = html.dirs.recur)))
                    subfiles <- subfiles[!(subfiles %in% html.dirs.recur)]
                    file.copy(subfiles, gsub("/Rmd", "/html", subfiles), overwrite = TRUE)
                    if (move) 
                      unlink(html.dirs, recursive = TRUE)
                  }
                }
                outfiles <- file.path(path.docs, type[i], basename(infiles))
                if (move) 
                  file.rename(infiles, outfiles) else if (copy) 
                  file.copy(infiles, outfiles, overwrite = TRUE)
            }
        }
    }
}