Inline R code in YAML

[mbojan]

This is related Q to #452 . Is it generally possible to have inline R code in YAML? It worked in RMarkdown. I can't get it to work using either r 1 + 1 or !expr 1 + 1. Am I missing something? Thanks!

[cderv]

When using the YAML syntax for chunk option using #| inside code blocks, you won't be able to use inline R chunk syntax that knitr supports `r 1 + 1`. The special syntex with !expr needs to be used ans in the example with fig-cap in https://quarto.org/docs/computations/r.html#chunk-options

You'll need last version of Quarto and also it requirees dev version of knitr as we have fixed an issue with this recently.
#547

[mbojan]

Regarding the access of metadata inside the document, this is possible using a feature called shortcodes See https://quarto.org/docs/authoring/shortcodes-and-filters.html#shortcodes for the meta shortcode

@cderv , the shortcodes can only be used to render text and I can't use them in the code chunks, correct?

[cderv]

what do you have in mind ? Having examples helps. Shortcodes are handled by Quarto directly, and not by computations engines, but not sure to see what you are trying to achieve. In case you do not know, there is also parameters features in Quarto: https://quarto.org/docs/computations/parameters.html

[mbojan]

I'm exploring the features you mentioned to check what I can achieve in terms of

What is your usage exactly regarding programming metadata field ? Do you have an example ?

I'm generating HTML reports based on some RDS files and I would like to have titles and some other metadata (e.g. description) containing some info based on the content of these files. I guess can get away with containing these in the first paragraph of the report, but modifying YAML metadata would be much nicer...

... without having to resort to external scripts generating files with metadata or executing Quarto CLI with commandline parameters.

[cderv]

I don't think you will be able to have the same kind of workflow that with rmarkdown where could do some process during knitting that would impact how quarto is working. However, I will be interested to see what workflow you will come up with that would suites you and work with all these.

As we often remind, there is no reason to switch from R Markdown to Quarto if you are happy with the feature there, and especially if you heavily use R for the workflow.

the shortcodes can only be used to render text and I can't use them in the code chunks, correct?

I am still no sure to see clearly how you would like to use shortcodes in code chunk ? Shortcodes should be resolved before computations or after computations in your case ?

[cderv]

To add on other feature that works also within Quarto, you can use var shortcodes within YAML frontmatter when you are using a Quarto project (https://quarto.org/docs/authoring/shortcodes-and-filters.html#var)

This would be

---
title: '{{< var title >}}'
---

and then set the value within _variables.yml files.

[cderv]

@jjallaire with rmarkdown it is possible to use knitr execution to set some YAML field value programatically for Pandoc to read. Example in https://bookdown.org/yihui/rmarkdown-cookbook/dynamic-yaml.html, either using inline R code

---
title: "An analysis of `r nrow(mtcars)` cars"
---

or params

---
title: "`r params$doc_title`"
author: "Smart Analyst"
params:
  doc_title: "The Default Title"
---

With Quarto we can't do exactly the same as R is only use as computation engine but is there any equivalent mechanism to set title using parameters when generating several reports for example ?

Only solution I se and mentioned above is setting metadata using -M when calling quarto render, and can't really be done inside the document.

[jjallaire]

You can also pass --metadata-file on the command line.

[cderv]

Thanks!
I opened an issue about that as I think it is not working as expected, at least on Windows
#613

[mbojan]

It does not work for me on Linux (WSL) either...

[mbojan]

For future generations: from all the discussion above I'm distilling that the metadata in the YAML document header (title, author, date, description etc.)...

1. ... can contain the inline R code `r 1 + 1` but is ignored. YAML fields are not passed through knitr
2. ... can be accessed in the document "body" via shortcodes to render some text (c.f. shortcodes)
3. ... are not visible in code chunks in any form (contrary to metadata object in rmarkdown, c.f. this)
4. ... can't be modified by the code within the qmd file
5. ... can be set externally by using -M, e.g. quarto render file.qmd -M title:"New title". The -M is a pandoc option.
6. ... can be set externally using --metadata-file but that does not seem to work now (c.f. Using --metadata-file to set metadata does not seem to work properly #613). The --metadata-file is a pandoc option.
7. ... can be set externally with the help of project scripts which quarto executes prior rendering documents. This requires using a Quarto project feature.

Is the above a fair summary @cderv @jjallaire ?

[jjallaire]

This summary does seem correct but some of these limitations will soon be lifted by fixes we have in flight (cc @dragonstyle )

[RoelVerbelen]

Has there been any more recent development to enable using parameters in the YAML header?

Based on this discussion and this related stack overflow question I tried the following to no avail (using quarto 1.4.549):

---
title: "`{python} my_parameter` {{< meta my_parameter >}} {{< meta params.my_parameter >}}"
jupyter:
  kernel: python3
---

```{python}
#| include: false
#| tags: [parameters]

my_parameter = 'test'
```

`{python} my_parameter`

{{< meta my_parameter >}} 

{{< meta params.my_parameter >}}

[cderv]

YAML fields can't have inline code like that - it is parsed before execution happens, so it does not work. Also setting parameter for use with Jupyter is not something you can access in meta shortcode. Where did you see this usage ? This won't work either.

Can you detail exactly your use case ? or Is the question generic ?

Depending on what you want to do, there could be different solutions. But the title YAML field is quite specific as it must be known early for the processing of Quarto project. Having a real use case could help us show example

[RoelVerbelen]

Hi @cderv, thanks for your reply.

The use of meta shortcode in the YAML was claimed to work in this answer on stackoverflow of the same question (in R context).

In terms of my use cases: for data science projects, I set up exploratory data analysis reports which get run under various settings (e.g. changing the outcome variable, the data set (version) used, the filter settings) and like to see that reflected in the (sub)title of the report for immediate reference. Likewise, I build many different models and use the same reporting template for model evaluation. Elaborating on the latter with some code, using R and R markdown, I would run for example:

rmarkdown::render(
  here("code", "freq-model-evaluation.Rmd"),
  output_file = glue(here("output", "html", "freq-model-evaluation-{model}-{version}.html")),
  params = list(
    actual = "claim_number",
    modelled = "modelled_freq",
    exposure = "exposure",
    model = "gbm",
    version = 1
  ),
  envir = new.env()
)

And the YAML header in my .Rmd would contain:

---
title: "Frequency modelling" 
subtitle: "`r paste('Model evaluation for', params$model, 'version', params$version)`"
---

I'm now trying to set up a similar workflow in Python and Quarto.

Based on the quarto.render() code here, I've set up a generic Python function to render a quarto report in an interactive terminal (as is convenient for interactive data science projects and for looping over various parameter settings easily within Python). Moving the title setting to this function (using the -M title:"New title" method) would technically work but not be an elegant solution as it decouples the title set in the YAML of the file itself and moves it to the generic Python quarto rendering function.

[cderv]

The use of meta shortcode in the YAML

Meta shortcode in YAML should work. Inline R code should not. So you could fill subtitle using shortcode (meta or env, or var for project with variables yml file). It should work with title to I believe.

Did you try meta shortcode or other already ?

---
title: "{{< meta my_title >}}"
format: html
---

Content

then

quarto preview test.qmd --metadata my_title="filled"

This is working for me

[mcanouil]

Better than using inline in YAML, I suggest to produce YAML:

---
title: "Frequency modelling" 
format: html
params:
  version: 1
  model: "the best"
engine: knitr
---

```{r}
#| output: asis
cat(
  "---",
  sprintf(
    "subtitle: Model evaluation for %s version %s\n",
    params[["model"]],
    params[["version"]]
  ),
  "---",
  sep = "\n"
)
```

You can also use --metadata-file my-meta.yml, see https://github.com/mcanouil/generate-quarto-invoices as a demo.

The variable shortcode is also one way to make it work:

But be careful of where you are using shortcode as it might not work well for anchor links (#8546).