_pre_knit.R

library(rmarkdown)
pre_knit <- function(input, ...){
  rd <- readLines(input)
  id <- grep('◊', rd)
  
  rd[id] <- stringr::str_replace_all(rd[id],
                                     "`◊([:alnum:]+)\\((.*?)\\)`",
                                     replacement = '`r \\1("\\2")`')
  file.copy(input, paste0(input, 'original.Rmd'))
  writeLines(text = rd, con = input)
}


custom_format <- rmarkdown::output_format(knitr = rmarkdown::knitr_options(opts_chunk = list(dev = 'png')),
                                          pandoc = rmarkdown::pandoc_options(to = "markdown"),
                                          pre_knit = pre_knit)

pdf_format <- rmarkdown::output_format(knitr = rmarkdown::knitr_options(opts_chunk = list(dev = 'png')),
                                       pandoc = rmarkdown::pandoc_options(to = "latex"))

pre.Rmd

---
knit: (function(inputFile, encoding) {source('_pre_knit.R'); render(inputFile, output_format = custom_format, run_pandoc = FALSE); original = paste0(inputFile,"_tmp.Rmd"); rmarkdown::render(inputFile, encoding = encoding); file.copy(original, inputFile); unlink(original)})
output: 
  pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
enable_caps <- FALSE
emph = function(x){
  if(knitr::is_latex_output()) {
    if(enable_caps) sprintf("\\textsc{%s}", x) else sprintf("\\textbf{%s}", x)
  } else x
}
```

## Intro

This is an R Markdown document `◊emph(with custom formatting)`.  

```{r cars}
summary(cars)
```

## Wait a second

`r enable_caps = TRUE`

In this essay, `◊emph(I will)`