Dynamically set R markdown title, output filename, and global variables

Question

I have to run markdown reports for 2 subjects (math and reading) on a regular basis. I currently have to set the subject variable in the title of the markdown, in the output filename (.html file), and again within the R code chunks for data processing. I would like to set this variable one time and have the title, output file, and analyses all adjust. Is there a way to do this?

I know the title can be made dynamic through the params YAML header but that doesn't help with the output filename or within the R code chunks.

See a portion of my current code below. Notice the reading variable is specified 3 times (title, output file name, and within the R code chunk under "Presets". I would like to specify "reading" one time (preferably at the top of the script).

---
title: Reading Investigation"
author: "xxx"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    code_folding: hide
    depth: 3
    fig_height: 10
    fig_width: 12
    highlight: tango
    number_sections: no
    theme: cerulean
    toc: yes
    toc_float: yes
    
knit: (function(inputFile, encoding) 
{ rmarkdown::render(inputFile, encoding = encoding, 
output_file = paste0('folder/reading_output_', Sys.Date(), '.html') )}) 
---

```{r, message=FALSE, echo=FALSE, warning=FALSE, results='hide', comment="", fig.height=10, fig.width=12}

# Libraries ------------------------------------------------------------------

library(RODBC)
library(tidyverse)
library(ggplot2)
library(kableExtra)

# Set up ------------------------------------------------------------------
options(scipen=999)

#### Presets
subject = "reading" # "math", "reading"
```

shafee · Answer 1 · 2022-08-19T00:50:11.540

To set the output file name dynamically, we have to rely on params and params can be used to set document title dynamically and define variable in r-code chunk too.

Using Helper Render function

dynamic_metadata.Rmd

---
author: "xxx"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    code_folding: hide
    depth: 3
    fig_height: 10
    fig_width: 12
    highlight: tango
    number_sections: no
    theme: cerulean
    toc: yes
    toc_float: yes
params: 
    set_title: "reading"
title: "`r paste(tools::toTitleCase(params$set_title), 'Investigation')`"
---

```{r}

#### Presets
subject = params$set_title # "math", "reading"

subject
```

Then we have to define this function in r-console or in a separate R file (i.e. R script) and then call it from r-console or from that R file with sub as either reading or math.

render_subject <- function(sub) {
  rmarkdown::render(
    input = "dynamic_metadata.Rmd",
    params = list(set_title = sub),
    output_file = paste0('folder/', sub, '_output_', Sys.Date(), '.html')
  )
}


render_subject("reading")
render_subject("math")

The rendered output files look like this,

And the filenames in the folder directory,

+---folder
|       math_output_2022-08-18.html
|       reading_output_2022-08-18.html

Using Custom function in knit

Another way of doing this could be based on this answer on dynamically naming output file,

---
author: "xxx"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
  html_document:
    code_folding: hide
    depth: 3
    fig_height: 10
    fig_width: 12
    highlight: tango
    number_sections: no
    theme: cerulean
    toc: yes
    toc_float: yes
params: 
    set_title: "math" # reading

title: "`r paste(tools::toTitleCase(params$set_title), 'Investigation')`"
knit: >
  (function(input_file, encoding) {
    # Render, keeping intermediate files for extracting front matter
    md_dir <- tempdir()
    output_file_temp <- rmarkdown::render(
      input = input_file,
      output_file = tempfile(),
      intermediates_dir = md_dir,
      clean = FALSE
    )
    
    # Get the rendered front matter from the intermediate Markdown file
    md_file <- fs::path_ext_set(fs::path_file(input_file), ".knit.md")
    metadata <- rmarkdown::yaml_front_matter(fs::path(md_dir, md_file))
    
    # Extract the subject name from title of rendered file
    output_name <- with(metadata, {
      sub = sub(" .*$", "", tolower(title))
      paste0(fs::path_home_r(), '/folders/', sub, '_output_', Sys.Date(), '.html')
    })

    # Add the file extension and move to R's definition of the home directory
    output_ext <- fs::path_ext(output_file_temp)
    output_file <- fs::path_ext_set(output_name, output_ext)
    fs::file_move(output_file_temp, output_file)

    message("Output moved to: ", output_file)
  })
---

```{r}

#### Presets
subject = params$set_title # "math", "reading"

subject
```

The rendered output files look like the 1st option. One thing to note is that we would need the {fs} package installed before we proceed with this second approach.

This looks like the title and code chunks can be dealt with purely with the YAML, but to also get the output file name requires a helper function to set a parameter in `rmarkdown::render`. I am still interested if there is a way to do it all without a helper render function. — Brian Diggs, Aug 18 '22 at 23:12
@BrianDiggs, see the updated answer. The second method also relies on `params` but without using a helper render function. And AFAIK, though it's possible to set the title dynamically using a global variable, its not possible to define the output file name with that global variable. So ultimately we have to rely on the params — shafee, Aug 19 '22 at 04:35

Dynamically set R markdown title, output filename, and global variables

1 Answers1

Using Helper Render function

Using Custom function in knit