allow colformat_md to offset citation note number

NEWS.md

@@ -4,6 +4,7 @@
 
 * `colformat_md` supports multiple paragprahs by collapsing them with a separator given to the `.sep` argument (default: `"\n\n") (#43).
 * `colformat_md` can now automatically add citations to reference on R Markdown (#48).
+* `colformat_md` gains `.cite_offset` option (default: 0) to offset note number when the citation style such as vancouver requires the number be consistent with the body (#50).
 
 ## Bug fixes
 

R/as-paragraph-md.R

@@ -34,7 +34,11 @@ lua <- function(...) {
   c("--lua-filter", system.file("lua", ..., package = "ftExtra"))
 }
 
-lua_filters <- function(.sep) {
+meta <- function(key, val) {
+  sprintf("--metadata=%s:%s", key, val)
+}
+
+lua_filters <- function(.sep = "\n\n", .cite_offset = 0) {
   if (!rmarkdown::pandoc_available("2")) return(NULL)
 
   c(
@@ -43,33 +47,42 @@ lua_filters <- function(.sep) {
     if (rmarkdown::pandoc_available("2.7.3")) {
       c(
         lua("math.lua"),
-        paste0("--metadata=pandoc-path:", rmarkdown::pandoc_exec()),
+        meta("pandoc_path", rmarkdown::pandoc_exec()),
         if (!rmarkdown::pandoc_available("2.10")) {
-          paste0("--metadata=temporary-directory:", tempdir())
+          meta("temporary-directory", tempdir())
         }
       )
     },
+    if (.cite_offset != 0) {
+      c(
+        rmarkdown::pandoc_citeproc_args(),
+        lua("cite-offset.lua"),
+        meta("citationNoteNumOffset", .cite_offset)
+      )
+    },
     if (rmarkdown::pandoc_available("2.2.3")) {
-      c(lua("blocks-to-inlines.lua"), paste0("--metadata=sep_blocks:", .sep))
+      c(lua("blocks-to-inlines.lua"), meta("sep_blocks", .sep))
     }
   )
 }
 
 
-
+#' @param ...
+#'  parameters passed to lua_filters
+#' @noRd
 parse_md <- function(x,
                      auto_color_link = "blue",
                      pandoc_args = NULL,
                      .from = "markdown",
                      .footnote_options = NULL,
-                     .sep = "\n\n") {
+                     ...) {
   if (!is.character(auto_color_link) || length(auto_color_link) != 1L) {
     stop("`auto_color_link` must be a string")
   }
 
   md_df <- md2df(
     x,
-    pandoc_args = c(lua_filters(.sep = .sep), pandoc_args),
+    pandoc_args = c(lua_filters(...), pandoc_args),
     .from = .from,
     .check = TRUE
   )

R/colformat.R

@@ -10,6 +10,9 @@
 #'   Options for footnotes generated by `footnote_options()`.
 #' @param .sep
 #'   A separator of paragraphs (default: `"\n\n"`)
+#' @param .cite_offset
+#'   A offset value of citation note number (default: 0).
+#'   Use this to start number higher 0 for the consistency with the body text.
 #' @inheritParams as_paragraph_md
 #'
 #' @examples
@@ -30,7 +33,8 @@ colformat_md <- function(x,
                          pandoc_args = NULL,
                          .from = "markdown+autolink_bare_uris",
                          .footnote_options = footnote_options(),
-                         .sep = "\n\n"
+                         .sep = "\n\n",
+                         .cite_offset = 0
 ) {
   .j <- rlang::enexpr(j)
   part <- match.arg(part)
@@ -66,7 +70,8 @@ colformat_md <- function(x,
                              md_extensions = md_extensions,
                              pandoc_args = pandoc_args,
                              .footnote_options = .footnote_options,
-                             .sep = .sep
+                             .sep = .sep,
+                             .cite_offset = .cite_offset
                            ))
 
   structure(

R/md2ast.R

@@ -20,7 +20,11 @@ md2ast <- function(x,
     to = "json",
     from = .from,
     output = tf,
-    citeproc = !is.null(yaml$bibliography) || any(grepl("^--bibliography", pandoc_args)),
+    citeproc = (
+      !all(rmarkdown::pandoc_citeproc_args() %in% pandoc_args) &&
+      !is.null(yaml$bibliography) ||
+      any(grepl("^--bibliography", pandoc_args))
+    ),
     options = pandoc_args,
     wd = getwd()
   )

docs/pkgdown.yml

@@ -5,5 +5,5 @@ articles:
   format_columns: format_columns.html
   group-rows: group-rows.html
   transform-headers: transform-headers.html
-last_built: 2021-03-07T13:23Z
+last_built: 2021-03-11T13:08Z
 

inst/lua/cite-offset.lua

@@ -0,0 +1,15 @@
+function Meta(meta)
+  offset = meta.citationNoteNumOffset or 0
+end
+
+function add(x)
+  return math.floor(tonumber(x) + offset)
+end
+
+function Cite(cite)
+  cite.citations[1].note_num = math.floor(offset + cite.citations[1].note_num)
+  cite.content[1].text = cite.content[1].text:gsub("%d+", add)
+  return cite
+end
+
+return {{Meta = Meta}, {Cite = Cite}}

vignettes/format_columns.Rmd

@@ -265,12 +265,10 @@ knitr::write_bib("ftExtra")
 ```
 
 Second, specify it within the YAML front matter.
-It may also be required to cite references in the `nocite` field.
 
 ```yaml
 ---
 bibliography: ftExtra.bib
-nocite: @R-ftExtra
 ---
 ```
 
@@ -286,10 +284,6 @@ data.frame(
   flextable::autofit(add_w = 0.2)
 ```
 
----
-no-cite: "@R-ftExtra"
----
-
 ```{r, echo=FALSE, warning=FALSE}
 tf <- tempfile(fileext = ".bib")
 knitr::write_bib("ftExtra", tf)
@@ -302,6 +296,9 @@ data.frame(
   flextable::autofit(add_w = 0.2)
 ```
 
+If citation style such as Vancouver requires citations be numbered sequentially and consistently with the body,
+manually offset the number for example by `colformat_md(.cite_offset = 5)`.
+
 # Math
 
 The rendering of math is also possible.