[help] tracking dependency of manually constructed targets in tar_read

[shirdekel]

Help

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Description

I'm creating automated reports using a report using a template file and knit_expand. However, this involves constructing target names manually to call within tar_read, which means that there's no dependency. Is there a better way of doing this?

report.qmd:

---
title: 'report.qmd source file with parameters'
output_format: html_document
params:
  values: 0
---

assume these lines are in report.qmd.

```{r}
#| label: child
#| results: asis
src <-
  params$values |>
  purrr::pmap(
    function(x, y) {
      knitr::knit_expand(here::here("template.qmd"), x = x, y = y)
    }
  ) |>
  paste(collapse = "\n")
knitr::knit_child(text = src, quiet = TRUE) |>
  cat()
```

template.qmd:

---
title: 'template file'
---
assume these lines are in template.qmd.

```{r}
print(targets::tar_read('test_{{x}}_{{y}}'))
```

_targets.R:

library(targets)
library(tarchetypes)
values <- tibble::tribble(
  ~x, ~y,
  "a1", "b1",
  "a2", "b2"
) |>
  dplyr::mutate(names = paste(x, y, sep = "_"))
list(
  tar_map(
    values = values,
    names = names,
    tar_target(
      test,
      paste(x, y)
    )
  ),
  tar_quarto(
    report,
    path = "report.qmd",
    execute_params = list(
      values = values |>
        dplyr::select(x, y)
    ),
    extra_files = "template.qmd"
  )
)

[wlandau]

This use case is highly custom, and tar_quarto() is not designed for it. I recommend creating your own custom target which declares upstream dependencies, writes the qmd source, and renders it.

tar_target(
 name =  report,
 command = {
    dependency_target
    other_dependency_target
    write_qmd_source_file()
    quarto::quarto_render("qmd_source_file.qmd")
    c("qmd_source_file.qmd", "qmd_source_file.html")
  },
  format = "file"
)

[shirdekel]

And is there an automated way of including targets from a list generated by tar_map (named target_map here)? I tried the below, but the target is constantly invalidated and in tar_visnetwork the dependency is represented by target_map and not connected to the actual targets.

target_map[[2]][tidyselect::eval_select(
          everything(),
          target_map[[2]]
        )]

I also tried recreating the relevant target names and wrapping them in syms(), which didn't work either. Only manually adding in the targets works.

[wlandau]

Is writing the qmd source necessary for the dependency? Would targets not track it by virtue of it being declared in the final character vector?

Only if your use case requires it. If it exists beforehand, you could us it as is.

is there an automated way of including targets from a list generated by tar_map (named target_map here)?
I also tried recreating the relevant target names and wrapping them in syms(), which didn't work either. Only manually adding in the targets works.

Metaprogramming can substitute symbols into expressions, c.f. https://wlandau.github.io/targetopia/contributing.html#metaprogramming and https://books.ropensci.org/targets/static.html#metaprogramming. It can be tricky to get right the first time, and tar_manifest() and tar_glimpse() are good checks.

[shirdekel]

I managed to get a dependency working with tar_target_raw and putting sym("target") in command, but adding more than one gets the error the command of target example_target must have length 1.. tar_eval isn't useful to me here because I don't need to loop. I just want to link a dependency between the quarto target and a number of upstream targets that I refer to within it.

[wlandau]

Maybe something like this?

library(rlang)
library(tarchetypes)
target <- tar_eval(
  tar_target(
    name = report,
    command = {
      dependencies
      run_report()
    }
  ),
  values = list(
    dependencies = as.expression(
      expr(list(!!!syms(c("dependency1", "dependency2"))))
    )
  )
)

target[[1]]$command$expr
#> expression({
#>     list(dependency1, dependency2)
#>     run_report()
#> })

[shirdekel]

Thank you that works!