R/reviewer_comment.R

In revise: Dynamic Revision Letters for 'Rmarkdown' Manuscripts

#' reviewer_comment
#'
#' A comment to style chunks for reviewer comments

reviewer_comment <- function() {
  context <- rstudioapi::getActiveDocumentContext()

  # assign("context", context, envir = globalenv())

  if (length(context$selection) == 0) {
    return(rstudioapi::showDialog(title = ":'(", message = "The ReviewerComment addin will not work in the visual markdown editor. Please switch to the source editor."))
  }

  contents <- context$contents

  if (!any(grepl("^---$", contents))) {
    append_to_front <- rnr_header(detect_primary_file())
    append_to_rear <- '\\clearpage

# References

\\begingroup

<div id="refs"></div>

\\endgroup
'
    output_format <- "pdf"
  } else {
    append_to_front <- NULL
    append_to_rear <- NULL
    output_format <- NULL
  }


  selection <- context$select[[1]]$range
  start <- selection$start[[1]]
  end <- selection$end[[1]]
  document_end <- length(context$contents)

  comment_n <- stringr::str_extract_all(contents, r"(\\reviewerid\{c[0-9]*\})", simplify = TRUE)
  if (length(comment_n) == 0) {
    comment_n <- 1
  } else {
    comment_n <- max(as.numeric(stringr::str_extract_all(comment_n, "\\d*", simplify = TRUE)), na.rm = TRUE)
    comment_n <- comment_n + 1
  }

  if (is.null(output_format)) {
    output_format <- rmarkdown::yaml_front_matter(context$path)$output
    output_format <- tools::file_ext(output_format)
  }

  start_content <- paste0("```{", getOption("reviewer_chunkname")[[1]], "}")
  end_content <- "
```"

  before <- contents[1:start - 1]

  middle <- contents[start:end]
  if (document_end != end) {
    after <- contents[(end + 1):length(contents)]
  } else {
    after <- ""
  }

  new <- c(append_to_front, before, start_content, middle, end_content, after, append_to_rear)

  rstudioapi::setDocumentContents(paste(new, collapse = "\n"), id = context$id)
}


rnr_header <- function(file) {
  yaml <- tryCatch(rmarkdown::yaml_front_matter(file), error = function(e) {
    return(NA)
  })

  title <- tryCatch(yaml["title"][[1]], error = function(e) {
    return("paper title")
  })
  author <- tryCatch(yaml["author"][[1]][[1]]$name, error = function(e) {
    return("Author name")
  })
  bibliography <- tryCatch(yaml["bibliography"][[1]], error = function(e) {
    return("bibliography.json")
  })

  csl <- yaml["csl"][[1]]

  if (!is.null(csl)) {
    csl <- paste0("csl               : ", '"', csl, '"')
  }

  if (!is.null(bibliography)) {
    bibliography <- paste0("bibliography      : ", '"', bibliography, '"')
  }

  if (is.null(title)) title <- "paper title"
  if (is.null(author)) author <- "Author name"
  if (is.null(bibliography)) bibliography <- ""
  if (is.null(csl)) csl <- ""
  if (length(bibliography) > 1) bibliography <- glue::glue("[{paste(bibliography, collapse = ', ')}]")

  header <- glue::glue(r'(---
title             : "!!<title>!!"
authors           : "!!<author>!! on behalf of co-authors"
journal           : "your journal"
manuscript        : "MANUSCRIPT-ID"
handling_editor   : ""

class             : "draft"
!!<bibliography>!!
!!<csl>!!
output            : revise::revise_letter_pdf
---

Dear Dr `r rmarkdown::metadata$handling_editor`,

Thank you for considering our manuscript for publication at _`r rmarkdown::metadata$journal`_. We appreciate the feedback that you, and the reviewers have provided. In the following itemised list we respond to each comment point-by-point.

```{r setup-chunk, include = FALSE}
manuscript <- revise::read_manuscript("!!<file>!!", PDF = TRUE)
```

)', .open = "!!<", .close = ">!!")

  header <- gsub("csl\\s*:\\s*\"NA\"", "", header)
  header <- gsub("bibliography\\s*:\\s*NA", "", header)
  header
}

detect_primary_file <- function() {
  files <- list.files(pattern = ".rmd$", ignore.case = TRUE)
  contents <- suppressWarnings(lapply(files, readLines))

  out <- data.frame(
    files = files,
    has_papaja = sapply(contents, function(x) {
      any(grepl("papaja::apa", x, fixed = TRUE))
    }),
    filesize = sapply(files, file.size)
  )
  if (nrow(out) == 0) {
    return(NA)
  }

  out[order(-out$has_papaja, -out$filesize), "files"][[1]]
}