I have this code from an R markdown file which generates a popover. And it's working as expected:

For the R markdown document you need library(rmarkdown), library(pandoc) and pandoc_activate(). You render it with: rmarkdown::render("C:/YourPath/Popover.Rmd")

Popover.Rmd

---
title: "Test Popover"
date: "Last edited: `r format(Sys.time(), '%d.%m.%Y')`"
output: html_document
---

<script>
    $(document).ready(function(){
        // Get the text from the other element
        var textTag_1 = $('#Tag_1-source').text();
        var textTag_2 = $('#Tag_2-source').text();
        
        // Set the popover content dynamically
        $('#Tag_1').attr('data-content', textTag_1);
        $('#Tag_2').attr('data-content', textTag_2);

        // Initialize popover
        $('[data-toggle="popover"]').popover({ trigger: "hover" });
    });
</script>


# Tag definition


I want to define my tags, which I want to use:

- Keyword_Tag_1
    - <p id="Tag_1-source">
            Tag 1 describes...</p>
- Keyword_Tag_2
    - <p id="Tag_2-source">
            Tag 2 is all about...</p>

# Flowers

Flowers are ...


This section is taged with the following tags:
<a  id="Tag_1"
            data-toggle="popover" 
            data-placement="top"   
            data-content="Initial">
            Keyword_Tag_1</a>, 
<a  id="Tag_2"
            data-toggle="popover" 
            data-placement="top"   
            data-content="Initial">
            Keyword_Tag_2</a>

See the rendered result:

Challenge: Now I want the same in a bookdown document, but it's not working. I want to define the Keyword_Tag_1, Keyword_Tag_2... in file index.Rmd and in file section1.Rmd I have some text where I want to add my tags.

Question: Perhaps you can use my skeleton and figure out what has to be added / corrected.

Here you need additional packages: library(bookdown), library(knitr), library(markdown) and library(tinytex)

You render it with: bookdown::render_book("C:/YourPath/index.Rmd", output_format = "bookdown::gitbook")

index.Rmd

---
title: "Popover in Bookdown"
date: "Last edited: `r format(Sys.time(), '%d.%m.%Y')`"
output: bookdown::gitbook
---

<script>
    $(document).ready(function(){
        // Get the text from the other element
        var textTag_1 = $('#Tag_1-source').text();
        var textTag_2 = $('#Tag_2-source').text();
        
        // Set the popover content dynamically
        $('#Tag_1').attr('data-content', textTag_1);
        $('#Tag_2').attr('data-content', textTag_2);
    
        // Initialize popover
        $('[data-toggle="popover"]').popover({ trigger: "hover" });
    });
</script>
    
    
# Tag definition
    
    
I want to define my tags, which I want to use:
    
- Keyword_Tag_1
    - <p id="Tag_1-source">
            Tag 1 describes...</p>
- Keyword_Tag_2
    - <p id="Tag_2-source">
            Tag 2 is all about...</p>

section1.Rmd

# Flowers
    
Flowers are ...
    
    
This section is taged with the following tags:
<a  id="Tag_1"
    data-toggle="popover" 
    data-placement="top"   
    data-content="Initial">
    Keyword_Tag_1</a>, 
<a  id="Tag_2"
    data-toggle="popover" 
    data-placement="top"   
    data-content="Initial">
    Keyword_Tag_2</a>