README.qmd

---
format: 
  gfm:
    toc: true
    include-before-body: 
      text: |
        # Quarto word count
---

<!-- README.md is generated from README.qmd. Please edit that file -->

```{r, include=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.retina = 3
)
```

## Experimental new feature!

::: {.callout-tip}
I've added an experimental new feature that lets you add a sticky status bar at the top of HTML documents to show the word count. I've found that this is *super helpful* when writing, since I don't need to constantly check the terminal output.

I haven't figured out the best way to work with Lua filters and Quarto shortcodes (and getting filters/shortcodes to run in the right order), so for now the process is a little convoluted.

1. Enable `wordcount-banner: true` in the YAML front matter

2. Specify the content of the banner using the different shortcodes in `params: wordcount: `

3. Include an HTML file that uses Javascript to inject the status banner into the document.

Here's a minimal example:

````qmd
---
title: Something
format:
  wordcount-html: 
    wordcount-banner: true
params:
  wordcount: |
    <strong>{{{< words-sum body-note-ref >}}} total words</strong>: {{{< words-body >}}} in the body • {{{< words-ref >}}} in the references • {{{< words-note >}}} in the notes
---

::: {.content-visible when-meta="wordcount-banner"}
{{{< include _extensions/andrewheiss/wordcount/banner.html >}}}
:::

Actual text stuff goes here.
````
:::

## Why counting words is hard

In academic writing and publishing, word counts are important, since many journals specify word limits for submitted articles. Counting how many words you have in a Quarto Markdown file is tricky, though, for a bunch of reasons:

1. **Compatibility with Word**: Academic publishing portals tend to care about Microsoft Word-like counts, but lots of R and Python functions for counting words in a document treat word boundaries differently. 

   For instance, Word considers hyphenated words to be one word (e.g., "A super-neat kick-in-the-pants example" is 4 words in Word), while `stringi::stri_count_words()` counts them as multiple words (e.g. "A super-neat kick-in-the-pants example" is 8 words with {stringi}). Making matters worse, {stringi} counts "/" as a word boundary, so URLs can severely inflate your actual word count.
   
2. **Extra text elements**: Academic writing typically doesn't count the title, abstract, table text, table and figure captions, or equations as words in the manuscript. 

   In computational documents like Quarto Markdown, these often don't appear until the document is rendered, so simply running a word-counting function on a `.qmd` file will count the code generating tables and figures, again inflating the word count.

3. **Citations and bibliography**: Academic writing typically counts references as part of the word count (even though IT SHOULDN'T). However, in Quarto Markdown (and all other flavors of pandoc-based markdown), citations don't get counted until the bibliography is generated, which only happens when the document is rendered. 

   Simply running a word-counting function on a `.qmd` file (or something like the super neat [{wordcountaddin}](https://github.com/benmarwick/wordcountaddin)) will see citekeys in the document like `@Lovelace1842`, but it will only count them as individual words (e.g. not "(Lovelace 1842)" in in-text styles or 'Ada Augusta Lovelace, “Sketch of the Analytical Engine…,” *Taylor’s Scientific Memoirs* 3 (1842): 666–731.' in footnote styles), and more importantly, it will not count any of the automatically generated references in the final bibliography list.

This extension fixes all three of these issues by relying on a [Lua filter](_extensions/wordcount/wordcount.lua) to count the words after the document has been rendered and before it has been converted to its final output format. [Frederik Aust (@crsh)](https://github.com/crsh) uses the same Lua filter for counting words in R Markdown documents with the [{rmdfiltr}](https://github.com/crsh/rmdfiltr) package (I actually just copied and slightly expanded [that package's `inst/wordcount.lua`](https://github.com/crsh/rmdfiltr/blob/master/inst/wordcount.lua)). The filter works really well and [is generally comparable to Word's word count](https://cran.r-project.org/web/packages/rmdfiltr/vignettes/wordcount.html). You should definitely glance through the ["How this all works" section](#how-this-all-works) to understand… um… how it works.


## Using the word count script

### Installing

```bash
quarto add andrewheiss/quarto-wordcount
```

{quarto-wordcount} requires Quarto version >= 1.4.551

This will install the extension under the `_extensions` subdirectory. If you're using version control, you will want to check in this directory.

### Usage

There are two ways to enable the extension: (1) as an output format and (2) as a filter.

#### Output format

You can specify one of four different output formats in your YAML settings: `wordcount-html`, `wordcount-pdf`, `wordcount-docx`:

```yaml
title: Something
format:
  wordcount-html: default
```

The `wordcount-FORMAT` format type is really just a wrapper for each base format (HTML, PDF, Word, and Markdown), so all other HTML-, PDF-, Word-, and Markdown-specific options work like normal: 

```yaml
title: Something
format:
  wordcount-html:
    toc: true
    fig-align: center
    cap-location: margin
```

#### Filter

If you're using a [custom output format](https://quarto.org/docs/extensions/listing-formats.html) like [{hikmah-academic-quarto}](https://github.com/andrewheiss/hikmah-academic-quarto) or a [journal article format](https://quarto.org/docs/extensions/listing-journals.html) like [{jss}](https://github.com/quarto-journals/jss), you can't use the `wordcount-html` format, since you can't combine output formats.

To enable word counting for *any* format, including custom formats, you can add the extension Lua scripts as filters. You need to specify three settings:

1. `citeproc: false` must be set so that Quarto doesn't try to process citations
2. The path to `citeproc.lua` so that citations are processed before counting words---[this must come *before* `wordcount.lua`](#how-this-all-works)
3. The path to `wordcount.lua` so that words are counted

```yaml
title: Something
format:
  html:  # Regular built-in format
    citeproc: false
    filters:
      - at: pre-quarto
        path: _extensions/andrewheiss/wordcount/citeproc.lua
      - at: pre-quarto
        path: _extensions/andrewheiss/wordcount/wordcount.lua
  jss-pdf:  # Custom third-party format
    citeproc: false
    filters:
      - at: pre-quarto
        path: _extensions/andrewheiss/wordcount/citeproc.lua
      - at: pre-quarto
        path: _extensions/andrewheiss/wordcount/wordcount.lua
```

### Terminal output

The word count will appear in the terminal output when rendering the document. It shows multiple values: 

- **Overall totals**: (1) the total count of everything, including the body, notes, references, and appendix sections, and (2) the count for just the body and notes. 

  The journals I typically work with count the body + notes + references towards the total word count. When shrinking manuscripts to fit word limits, I find it helpful to split the references count off from the body + notes so I can more easily see where edits might be most efficient (e.g. re-word sentences vs. remove references)

- **Individual section totals**: counts for the (1) text body, (2) notes, (3) references, and (4) appendix

```text
Overall totals:
--------------------------------
- 451 total words
- 378 words in body and notes

Section totals:
--------------------------------
- 315 words in text body
- 63 words in notes
- 53 words in reference section
- 20 words in appendix section
```

### Shortcodes

There are also multiple shortcodes you can use to include different word counts directly in the document:

- Use `{{{< words-total >}}}` to include a count of all words

- Use `{{{< words-body >}}}` to include a count of the words in the text body only, omitting the references, notes, and appendix

- Use `{{{< words-ref >}}}` to include a count of the words in the reference section

- Use `{{{< words-append >}}}` to include a count of the words in the appendix, which must be wrapped in a div with the `#appendix-count` id ([see below for more details](#appendices))

- Use `{{{< words-note >}}}` to include a count of the words in the notes

- Use `{{{< words-sum ARG >}}}` where `ARG` is some concatenation of the four countable areas: `body`, `ref`, `append`, and `note`

  For example, `{{{< words-sum body-note >}}}` includes a count of the words in the body and notes; `{{{< words-sum ref-append >}}}` includes a count of the words in the references and appendix

You can use shortcodes in your YAML metadata too:

```yaml
title: Something
subtitle: "{{{< words-sum body-note-ref >}}} words"
```

### No counting

If you want to omit text from the word count, you can include it in a [fenced div](https://quarto.org/docs/authoring/markdown-basics.html#sec-divs-and-spans) with the `{.no-count}` class:

````markdown
::: {.no-count}

These words don't count.

:::
````

### Code blocks

By default, text inside code blocks ***is*** counted. For example, this:

````qmd
---
title: "Code counting"
format: wordcount-html
---

This sentence has seven words in it.

```{{r}}
# Here is some code

numbers <- 1:10
mean(numbers)
```
````

…will result in these counts:

```text
Overall totals:
-----------------------------
- 16 total words
- 16 words in body and notes

Section totals:
-----------------------------
- 16 words in text body
```

…with 7 words from the sentence and 9 from the code.

Code block counting can be disabled with the YAML option `count-code-blocks`:

````qmd
---
title: "Code counting"
format: 
  wordcount-html:
    count-code-blocks: false
---

This sentence has seven words in it.

```{{r}}
# Here is some code

numbers <- 1:10
mean(numbers)
```
````

…which makes these counts:

```text
Overall totals:
----------------------------
- 7 total words
- 7 words in body and notes

Section totals:
----------------------------
- 7 words in text body
```


### Appendices

In academic writing, it's often helpful to have a separate word count for content in the appendices, since things there don't typically count against journal word limits. [Quarto has a neat feature for automatically creating an appendix section](https://quarto.org/docs/authoring/appendices.html) and moving content there automatically as needed. It does this (I think) with a fancy Lua filter.

However, Quarto's appendix-generating process comes *after* any custom Lua filters, so even though the final rendered document creates a div with the id "appendix", that div isn't accessible when counting words (since it doesn't exist yet), so there's no easy way to extract the appendix words from the rest of the text.

So, as a (temporary?) workaround (until I can figure out how to make this Lua filter run after the creation of the appendix div?), you can get a separate word count for the appendix by creating your own fenced div with the id `appendix-count`:

````markdown
# Introduction

Regular text goes here.

::: {#appendix-count}

# Appendix {.appendix}

More words here

:::
````


## Example

You can see a minimal sample document at [`template.qmd`](template.qmd).


## Credits

The original [`wordcount.lua`](_extensions/wordcount/wordcount.lua) filter came from [Frederik Aust's (@crsh)](https://github.com/crsh) [{rmdfiltr}](https://github.com/crsh/rmdfiltr) package.


## How this all works

Behind the scenes, pandoc typically converts a Markdown document to an abstract syntax tree (AST), or an output-agnostic representation of all the document elements. In AST form, it's easy to use the [Lua language](https://pandoc.org/lua-filters.html) to extract or exclude specific elements of the document (i.e. exclude captions or only look at the references).

Quarto was designed to be language-agnostic, so {rmdfiltr}'s approach of using R to dynamically set the path to its Lua filters in YAML front matter does not work with Quarto files. ([See this comment from the Quarto team stating that you cannot use R output in the Quarto YAML header](https://github.com/quarto-dev/quarto-cli/issues/1391#issuecomment-1185348644).)

But it's still possible to use the fancy {rmdfiltr} Lua filter with Quarto with a little trickery!

In order to include citations in the word count, we have to feed the word count filter a version of the document that has been processed with the [`--citeproc` option](https://pandoc.org/MANUAL.html#citation-rendering) enabled. However, in both R Markdown/knitr and in Quarto, the `--citeproc` flag is designed to be the last possible option, resulting in pandoc commands that look something like this:

```sh
pandoc whatever.md --output whatever.html --lua-filter wordcount.lua --citeproc
```

The order of these arguments matters, so having `--lua-filter wordcount.lua` come before `--citeproc` makes it so the words will be counted before the bibliography is generated, which isn't great.

{rmdfiltr} gets around this ordering issue by editing the YAML front matter to (1) disable citeproc in general and (2) specify the `--citeproc` flag before running the filter:

```yaml
output:
  html_document:
    citeproc: false
    pandoc_args:
      - '--citeproc'
      - '--lua-filter'
      - '/path/to/rmdfiltr/wordcount.lua'
```

That generates a pandoc command like this, with `--citeproc` first, so the generated references get counted:

```sh
pandoc whatever.md --output whatever.html --citeproc --lua-filter wordcount.lua
```

Quarto doesn't have a `pandoc_args` option though. Instead, it has a `filters` YAML key that lets you specify a list of Lua filters to apply to the document at specific steps in the rendering process:

```yaml
format:
  html:
    citeproc: false
    filters: 
      - "/path/to/wordcount.lua"
```

However, there's no obvious way to reposition the `--citeproc` argument and it will automatically appear at the end, making it so generated references aren't counted. 

Fortunately, [this GitHub comment](https://github.com/quarto-dev/quarto-cli/issues/2294#issuecomment-1238954661) shows that it's possible to make a Lua filter that basically behaves like `--citeproc` by feeding the whole document to `pandoc.utils.citeproc()`. That means we can create a little Lua script like `citeproc.lua`:

```lua
-- Lua filter that behaves like `--citeproc`
function Pandoc (doc)
  return pandoc.utils.citeproc(doc)
end
```

…and then include *that* as a filter:

```yaml
format:
  html:
    citeproc: false
    filters:
      - at: pre-quarto
        path: "path/to/citeproc.lua"
      - at: pre-quarto
        path: "path/to/wordcount.lua"
```

This creates a pandoc command that looks something like this, feeding the document to the citeproc "filter" first, then feeding that to the word count script:

```sh
pandoc whatever.md --output whatever.html  --lua-filter citeproc.lua --lua-filter wordcount.lua
```