Generate Manual Table of Contents in (R)Markdown Documents

render_toc.R

#' Render Table of Contents
#' 
#' A simple function to extract headers from an RMarkdown or Markdown document
#' and build a table of contents. Returns a markdown list with links to the 
#' headers using 
#' [pandoc header identifiers](http://pandoc.org/MANUAL.html#header-identifiers).
#' 
#' WARNING: This function only works with hash-tag headers.
#' 
#' Because this function returns only the markdown list, the header for the
#' Table of Contents itself must be manually included in the text. Use
#' `toc_header_name` to exclude the table of contents header from the TOC, or
#' set to `NULL` for it to be included.
#' 
#' @section Usage:
#' Just drop in a chunk where you want the toc to appear (set `echo=FALSE`):
#' 
#'     # Table of Contents
#' 
#'     ```{r echo=FALSE}
#'     render_toc("/path/to/the/file.Rmd")
#'     ```
#' 
#' @param filename Name of RMarkdown or Markdown document
#' @param toc_header_name The table of contents header name. If specified, any
#'   header with this format will not be included in the TOC. Set to `NULL` to
#'   include the TOC itself in the TOC (but why?).
#' @param base_level Starting level of the lowest header level. Any headers 
#'   prior to the first header at the base_level are dropped silently.
#' @param toc_depth Maximum depth for TOC, relative to base_level. Default is
#'   `toc_depth = 3`, which results in a TOC of at most 3 levels.
render_toc <- function(
  filename, 
  toc_header_name = "Table of Contents",
  base_level = NULL,
  toc_depth = 3
) {
  x <- readLines(filename, warn = FALSE)
  x <- paste(x, collapse = "\n")
  x <- paste0("\n", x, "\n")
  for (i in 5:3) {
    regex_code_fence <- paste0("\n[`]{", i, "}.+?[`]{", i, "}\n")
    x <- gsub(regex_code_fence, "", x)
  }
  x <- strsplit(x, "\n")[[1]]
  x <- x[grepl("^#+", x)]
  if (!is.null(toc_header_name)) 
    x <- x[!grepl(paste0("^#+ ", toc_header_name), x)]
  if (is.null(base_level))
    base_level <- min(sapply(gsub("(#+).+", "\\1", x), nchar))
  start_at_base_level <- FALSE
  x <- sapply(x, function(h) {
    level <- nchar(gsub("(#+).+", "\\1", h)) - base_level
    if (level < 0) {
      stop("Cannot have negative header levels. Problematic header \"", h, '" ',
           "was considered level ", level, ". Please adjust `base_level`.")
    }
    if (level > toc_depth - 1) return("")
    if (!start_at_base_level && level == 0) start_at_base_level <<- TRUE
    if (!start_at_base_level) return("")
    if (grepl("\\{#.+\\}(\\s+)?$", h)) {
      # has special header slug
      header_text <- gsub("#+ (.+)\\s+?\\{.+$", "\\1", h)
      header_slug <- gsub(".+\\{\\s?#([-_.a-zA-Z]+).+", "\\1", h)
    } else {
      header_text <- gsub("#+\\s+?", "", h)
      header_text <- gsub("\\s+?\\{.+\\}\\s*$", "", header_text) # strip { .tabset ... }
      header_text <- gsub("^[^[:alpha:]]*\\s*", "", header_text) # remove up to first alpha char
      header_slug <- paste(strsplit(header_text, " ")[[1]], collapse="-")
      header_slug <- tolower(header_slug)
    }
    paste0(strrep(" ", level * 4), "- [", header_text, "](#", header_slug, ")")
  })
  x <- x[x != ""]
  knitr::asis_output(paste(x, collapse = "\n"))
}

render_toc_example.Rmd

---
title: "blogdown toc example"
author: '@gadenbuie'
date: "2/28/2018"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source("render_toc.R")
```

## Table of Contents {#crazy-slug-here}

```{r toc, echo=FALSE}
render_toc("blogdown-toc-example.Rmd")
```

### WONT BE INCLUDED IN TOC

# Writing

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
# This is not a header
summary(cars)
```

## Regular Code

```r
# Regular markdown code (not run)
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point()
```

# Plots

## Including Plots {#plots-are-here .class-foo}

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

# More

## Level 1

### Level 1.a

#### Level 1.a.i

### Level 1.b

Is there a way to enable automatic chapter numbering comparable to the suboption 'numbered_section=true' in the normal toc-command of the yaml-header? Instead of having a bullet-point list as the TOC, maybe is it possible to recreate this with a numbered list instead?

I can't test anything right now because my system is bricked, and this is beyond my capabilities anyways. However this would be a great addition to get rid of the pesky standard TOC...

Edit 1 17.08.2021 22:00:16:
I tested it on a friend's computer, and got some weird results. Aside from the fact that numbering doesn't seem to be possible (both automatic and in-header manual numbering, surprisingly, don't show up so far), the subsections of "Methods" are not listed beneath and indented to each other as they would be in a normal toc. I don't know why this is the case. I am running Win10, tested for word, pdf and html output respectively. Not sure why this is the case.

Is there a way to fix this, and possibly add a method of converting to numbered sections? Especially the first one is an absolute dealbreaker right now, but judging from other people's screenshots I might be encountering a bug or I am doing some stupid mistake I am not aware of.

Thank you for this gist.
It seems that blogdown is removing special characters from id in title sections, then !@:? need to be removed.
According to my test, I think this will do the trick:

h <- "éà@ù ?!: tot%" # expected: "[éà@ù ?!: tot%](éàù-tot)"

header_text <- gsub("#+\\s+?", "", h)
header_text <- gsub("\\s+?\\{.+\\}\\s*$", "", header_text) # strip { .tabset ... }
header_text <- gsub("^[^[:alpha:]]*\\s*", "", header_text) # remove up to first alpha char

# Remove special characters from slug
header_slug <- gsub("(\\W*)", "",
       strsplit(header_text, " |-")[[1]] # keep `-` if exists
  )
# Remove empty words
header_slug <- header_slug[header_slug != ""]
header_slug <- paste(header_slug, collapse = "-")
header_slug <- tolower(header_slug)

Nice work! Wondering if there is anyway to change the color of the toc titles?

Hi, this is a very useful function. Thanks. But is there a way to keep the original chapter numbers instead of bullets?