Create index of definitions / theorems at end of bookdown book

Question

For reader convenience, I'd like to include, at the end of my bookdown book, written in markdown, a simple list or index of definitions from the body of the book. i.e. ones created using custom blocks, like this:

```{definition, bar, echo=T}
A bar is defined here as a foo-like thing.
```

(My need is for definitions, but others might like lists of theorems, etc. Don't know if lists of figures and tables could be covered in the same way?)

Thanks to @yihui I know that knitr::all_labels(engine == 'definition') is my friend.

So I can do this anywhere in the end of the book, usually at the end:

```{r comment="",results="asis",echo=FALSE}
knitr::all_labels(engine == 'definition') %>% unlist %>% paste0("\n\n","\\@ref(def:",.,"): ",.,"\n\n",collapse="\n\n") %>% cat

```

Which prints this:

1: bar

2: foobar

With clickable numbers. Which is OK. But wouldn't it be nice if, after each label, the actual definition could be printed too? (The content of the blocks is not available in knitr::all_labels(engine == 'definition'))

score 11 · Accepted Answer · answered Nov 24 '16 at 05:34

11

Here is an example using the output format bookdown::html_document2, and it should also work for any other book output formats:

---
title: "Test Definitions"
output: bookdown::html_document2
---

```{r setup, include=FALSE}
def_list = list()
knitr::knit_hooks$set(engine = function(before, options) {
  if (before && options$engine == 'definition') {
    # collect definition terms from options$name
    def_list[[options$label]] <<- options$name
  }
  NULL
})
```

```{definition, d1, name='Foo'}
Foo is defined as ...
```

```{definition, d2, name='Bar'}
Bar is defined as ...
```

All definitions in this document:

```{r echo=FALSE, results='asis'}
def_list = unlist(def_list)
cat(sprintf('- \\@ref(def:%s) %s', names(def_list), def_list), sep = '\n')
```

Output:

The basic idea is to use a chunk hook to collect definition labels and names, and print them at the end. You do not have to use the chunk option name. It can be an arbitrary option, e.g., term. The option name is special because the name of the definition will be printed in the output. If you don't like that, you can use, for example, term:

```{definition, d2, term='Bar'}
Bar is defined as ...
```

answered Nov 24 '16 at 05:34

Yihui Xie

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great ... so is it possible to use the same kind of hook to also collect the *contents* of the chunk to be able to print the contents of the definitions in the definition list at the end, not just the name and link? I guess I could try instead using something like ref.label at the end of the doc, to re-use the definition chunk contents – Steve Powell Nov 24 '16 at 08:45
The content of a chunk is not accessible from a chunk hook, but you can obtain it from `knitr:::knit_code$get(a_vector_of_chunk_labels)` – Yihui Xie Nov 25 '16 at 02:55
Is there a way to access the contents of empty chunks that are filled with `code` using `all_labels()`? Something like `knitr::opts_chunk$get("code")`? – HBat Feb 15 '19 at 05:55
This code example works for me only with one list, say `options$engine` = 'definition'. But how to add another list, say 'theorem'? Changing list to thm_list() and options$engine == 'theorem' and changing the last chunk accordingly did not work for me. – petzi Sep 19 '19 at 20:06

score 2 · Answer 2 · answered Nov 25 '16 at 08:42

Perfect, so adding on from Yihui's suggestion, this prints out the definitions as well, and no need to bother with names, just labels will do:

```{definition, 'Bar',echo=T,cache=F}
Bar is defined as something
```

```{definition, 'Bar2',echo=T,cache=F}
Bar2 is defined as something else.
```

Here are all the definitions in this book.

```{r comment="",results="asis",echo=FALSE,cache=F}


for(x in knitr::all_labels(engine == 'definition')){
   paste0("\n\n","\\@ref(def:",x,"): ",x,"\n\n>",knitr:::knit_code$get(x),collapse="\n\n") %>% cat
} 

```

... produces this:

Here are all the definitions in this book.

1: Bar

Bar is defined as something

2: Bar2

Bar2 is defined as something else.

Create index of definitions / theorems at end of bookdown book

2 Answers2

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