Rendering a parametrised Quarto report for multiple input parameters overwrites output figures

[milanmlft]

Taking the following example Quarto file:

# life_expectancy_report.qmd
---
title: "Life Expectancy Report for `r params$country`"
format: html
params:
  country: "Afghanistan"
---

```{r}
library(tidyverse)
library(gapminder)
```

```{r}
#| label: life-expectancy-data
life_expectancy <-
  gapminder |>
  filter(country == params$country)
```

## Life Expectancy in `r params$country`

```{r}
#| label: life-expectancy-plot
ggplot(life_expectancy, aes(year, lifeExp)) +
  geom_line() +
  theme_minimal()
```

When we generate this report for different countries with the following script:

library(quarto)
countries <- c("Afghanistan", "Belgium", "India", "United Kingdom")

for (country in countries) {
  quarto_render(
    input = "life_expectancy_report.qmd",
    output_file = paste0("life_expectancy_", country, ".html"),
    execute_params = list(country = country)
  )
}

We get a different report for each country, but they will all show the exact same plot (namely the one for the last country).

I suspect this is because Quarto will overwrite life_expectancy_report_files/figure-html/life-expectancy-plot-1.png for each input parameter and thus the final HTML files will all show the same plot.

This behaviour is different from rmarkdown::render(), which would correctly show the specific plot in each report.

[llrs-roche]

There are two possible approaches:

1. copy the input file each time and rename it on the desired rendering location: file.copy
2. Make the html self-contained so it doesn't depend on external files.

[cderv]

Some thought. This is possibly a problem at quarto level and maybe linked to this

• Rendering a document in subfolder with -o flag leads to libs not found quarto-cli#5765

This behaviour is different from rmarkdown::render(), which would correctly show the specific plot in each report.

I need to look into that also to find the difference in case this is something else.

[cderv]

So in R markdown the figure folder is computed with the output filename

files_dir_slash <- file.path(output_dir, knitr_files_dir(basename(output_file)))
# ...
knitr::opts_chunk$set(fig.path = paste0(
  pandoc_path_arg(files_dir_slash, backslash = FALSE),
  "/figure-", base_pandoc_to, "/"
))

By default, output file name is derived from input one, unless rmarkdown::render(output_file=) is used.

In Quarto this is different because rmarkdown::render() is not passed any output file... So it will use the default behavior so input name. quarto_render(output_file=) is passing output file name to Quarto which is different than rmarkdown output, as in Quarto rmarkdown output is an intermediary.

This is ultimately Quarto CLI issue here... 🤔
https://github.com/quarto-dev/quarto-cli/blob/bf038503cd0290ef040288e763174497f5bd7d0b/src/command/render/render-files.ts#L151-L152

// compute filesDir
const filesDir = inputFilesDir(context.target.source);

Only the input file is taken into account by Quarto

[cderv]

So currently for param rendering, the workflow needs to take input into account

countries <- c("Afghanistan", "Belgium", "India", "United Kingdom")
for (country in countries) {
  input <- sprintf("life_expectancy_report-%s.qmd", gsub("\\s", "-", country))
  fs::file_copy("life_expectancy_report.qmd", input)
  quarto_render(
    input = input,
    output_file = paste0("life_expectancy_", country, ".html"),
    execute_params = list(country = country)
  )
  fs::file_delete(input)
}
```

[milanmlft]

So currently for param rendering, the workflow needs to take input into account

countries <- c("Afghanistan", "Belgium", "India", "United Kingdom")
for (country in countries) {
input <- sprintf("life_expectancy_report-%s.qmd", gsub("\s", "-", country))
fs::file_copy("life_expectancy_report.qmd", input)
quarto_render(
input = input,
output_file = paste0("life_expectancy_", country, ".html"),
execute_params = list(country = country)
)
fs::file_delete(input)
}

Sure, this works. But it would be nice if Quarto supported this without the hacky workaround, so that it can properly replace RMarkdown's behaviour.

[cderv]

Yes I understand.

Unfortunately, this is a bit of a tricky interaction between

• Quarto own file handling logic
• Parameter support that is knitr feature directly (as Quarto does only passthrough right now)

When there is a better execution planner logic in Quarto, this will be easier to add such feature.

This type of use case is for me in the category of "Workflow with Quarto". And this is always where tools needs to decide to:

• internalize file handling logic and such workflow with configuration
• leave the user to use its own workflow tools to handle multiple rendering

I wonder if in this case, such logic could leave in this quarto R package as a wrapper function that does the above

A simplify generic version would be to use hash based on output_file name to be sure input name is different

quarto_render_variant <- function(input, output_file, ...) {
  unique_input <- sprintf("%s-%s.%s", xfun::sans_ext(input), rlang::hash(output_file), xfun::file_ext(input))
  on.exit({
    if (file.exists(unique_input)) {
      file.remove(unique_input)
    }}, add = TRUE)
  quarto_render(unique_input, output_file = output_file, ...)
}

Not ideal but would help.

Anyhow, this is to be fixed in Quarto CLI ultimately. I'll look into it.