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I have the following document.

Everytime I open a new session in RStudio, I'm greeted with the error message:

I'd like to number my tables made with the gt package in rmarkdown rendered pdf.
What I've tried
In a markdown doc, defining a function f that increments a variable every time it is called:

Following the R Markdown Cookbook (along with a number of the posts here) and I'm trying to insert a collection of LaTeX packages in the YAML header for my R Markdown file.

When I copy/paste the header from that website into my file:

Suppose I have the following Rmd file called render-issues.Rmd:

I'm trying to write a distill::distill_article blogpost which requires the use of LaTeX math environments e.g. theorem, lemma, proof etc.

I have tried to follow these instructions and also these instructions but am unable to render the theorem environments whether using LaTeX blocks or rmarkdown blocks.

I also note that a similar question was asked about specifically using distill::distill_article in bookdown. This fix did not work either. Note that my use-case is to use the bookdown theorem environments inside distill::distill_article, not the other way around.

Here is a reprex for the issue:

I am completely new to Rmarkdown and blogdown and I am having a hard time understanding how does .markdown, .Rmarkdown, .Rmd et .md etc... files are produced and, in some ways, are different working with Rstudio.

To be more specific, I am building a website with Hugo Apéro theme in Rstudio, hence with blogdown and Rmarkdown files.

I want to create a series of blogposts related to one another and with the TOC on the left side of the page just like Alison Hill did in her own blog here

In theory, this is not so hard and I managed to write the firsts blog posts in my own series with some math equations and everything that I wanted with some .Rmd files.

This is were it gets tricky, when I knit the said .Rmd files it produces only one .html file. I cannot find a way to produce the .md file necessary for hugo and/or blogdown (I do not really know what does what up to here) to produce the TOC of one specific blogpost. Looking at Alison Hill's blog posts it corresponds to the On this page TOC.

I know that Rstudio v2 need some work around to produce the .html and .md file (see this very specific question here) however, none of the proposed solutions seem to work for me.

I managed to produce an .markdown file from a .Rmarkdown file which render the TOC like I want, however, .Rmarkdown files are not the best for math rendering, (see Creating Websites with R Markdown - Ch1.5), are not created in Rstudio etc... which does not make me want to use this format (maybe that is a mistake ?)

The absence of TOC in the final page seem related to another element : a headers link button. Still, looking at Alison Hill's blog posts I notice a link button next to each headers that I do not have if I work with .Rmd file (which produce only .html file) but they appears with the .Rmarkdown file (which produce only .md file)

So I guess my question is :

1. How can I include a TOC from the .Rmd file ?

2. How can I create a .md file from .Rmd file in Rstudio ? and why none of these solutions work for me :

   • use the argument keep_md = TRUE in html_document()
   • call rmarkdown::render() with clean = FALSE
   • Use md_document as one of your output formats

Also, in working on my blog post I wanted to create pannelsets like in Hugo Apero documentation and it does not work with the first syntax in a .Rmd file :

I was wondering if it's possible to use/readapt Lua filters in r-markdown to get font colours when using citations with r-markdown syntax. For example, when I try to replicate the code from R Markdown Cookbook and add a citation inside the [...] block, I get the following result:

The following R code can be used to replicate the same pdf document:

I am making a book via bookdown. I know it is possible to omit headings from the Table of Contents by adding the attributes {.unlisted .unnumbered}, as shown in Section 4.18 of the R Markdown Cookbook. However, how can I add arbitrary content to the Table of Contents? If I only needed to add this for the PDF output, I could use (e.g.) the LaTeX command \addcontentsline, but I need this to show in the HTML contents sidebar as well.

For example, if you set up a new default bookdown project from RStudio, it includes the file 01-intro.Rmd. The first few lines are