tar_quarto: Target with a Quarto project.

In tarchetypes: Archetypes for Targets

Target with a Quarto project.

Description

Shorthand to include a Quarto project in a targets pipeline.

tar_quarto() expects an unevaluated symbol for the name argument and an unevaluated expression for the exectue_params argument. tar_quarto_raw() expects a character string for the name argument and an evaluated expression object for the exectue_params argument.

Usage

tar_quarto(
  name,
  path = ".",
  working_directory = NULL,
  extra_files = character(0),
  execute = TRUE,
  execute_params = list(),
  cache = NULL,
  cache_refresh = FALSE,
  debug = FALSE,
  quiet = TRUE,
  quarto_args = NULL,
  pandoc_args = NULL,
  profile = NULL,
  tidy_eval = targets::tar_option_get("tidy_eval"),
  packages = NULL,
  library = NULL,
  error = targets::tar_option_get("error"),
  memory = targets::tar_option_get("memory"),
  garbage_collection = targets::tar_option_get("garbage_collection"),
  deployment = "main",
  priority = targets::tar_option_get("priority"),
  resources = targets::tar_option_get("resources"),
  retrieval = targets::tar_option_get("retrieval"),
  cue = targets::tar_option_get("cue"),
  description = targets::tar_option_get("description")
)

tar_quarto_raw(
  name,
  path = ".",
  working_directory = NULL,
  extra_files = character(0),
  execute = TRUE,
  execute_params = NULL,
  cache = NULL,
  cache_refresh = FALSE,
  debug = FALSE,
  quiet = TRUE,
  quarto_args = NULL,
  pandoc_args = NULL,
  profile = NULL,
  packages = NULL,
  library = NULL,
  error = targets::tar_option_get("error"),
  memory = targets::tar_option_get("memory"),
  garbage_collection = targets::tar_option_get("garbage_collection"),
  deployment = "main",
  priority = targets::tar_option_get("priority"),
  resources = targets::tar_option_get("resources"),
  retrieval = targets::tar_option_get("retrieval"),
  cue = targets::tar_option_get("cue"),
  description = targets::tar_option_get("description")
)

Arguments

name	Name of the target. tar_quarto() expects an unevaluated symbol for the name argument, and tar_quarto_raw() expects a character string for name.
path	Character string, path to the Quarto source file.
working_directory	Optional character string, path to the working directory to temporarily set when running the report. The default is NULL, which runs the report from the current working directory at the time the pipeline is run. This default is recommended in the vast majority of cases. To use anything other than NULL, you must manually set the value of the store argument relative to the working directory in all calls to tar_read() and tar_load() in the report. Otherwise, these functions will not know where to find the data.
extra_files	Character vector of extra files and directories to track for changes. The target will be invalidated (rerun on the next tar_make()) if the contents of these files changes. No need to include anything already in the output of tar_quarto_files(), the list of file dependencies automatically detected through quarto::quarto_inspect().
execute	Whether to execute embedded code chunks.
execute_params	Named collection of parameters for parameterized Quarto documents. These parameters override the custom custom elements of the params list in the YAML front-matter of the Quarto source files. tar_quarto() expects an unevaluated expression for the exectue_params argument, whereas tar_quarto_raw() expects an evaluated expression object.
cache	Cache execution output (uses knitr cache and jupyter-cache respectively for Rmd and Jupyter input files).
cache_refresh	Force refresh of execution cache.
debug	Leave intermediate files in place after render.
quiet	Suppress warning and other messages.
quarto_args	Character vector of other quarto CLI arguments to append to the Quarto command executed by this function. This is mainly intended for advanced usage and useful for CLI arguments which are not yet mirrored in a dedicated parameter of this R function. See ⁠quarto render --help⁠ for options.
pandoc_args	Additional command line arguments to pass on to Pandoc.
profile	Quarto project profile(s) to use. Either a character vector of profile names or NULL to use the default profile.
tidy_eval	Logical, whether to enable tidy evaluation when interpreting command and pattern. If TRUE, you can use the "bang-bang" operator ⁠!!⁠ to programmatically insert the values of global objects.
packages	Character vector of packages to load right before the target runs or the output data is reloaded for downstream targets. Use tar_option_set() to set packages globally for all subsequent targets you define.
library	Character vector of library paths to try when loading packages.
error	Character of length 1, what to do if the target stops and throws an error. Options: "stop": the whole pipeline stops and throws an error. "continue": the whole pipeline keeps going. "null": The errored target continues and returns NULL. The data hash is deliberately wrong so the target is not up to date for the next run of the pipeline. "abridge": any currently running targets keep running, but no new targets launch after that. "trim": all currently running targets stay running. A queued target is allowed to start if: It is not downstream of the error, and It is not a sibling branch from the same tar_target() call (if the error happened in a dynamic branch). The idea is to avoid starting any new work that the immediate error impacts. error = "trim" is just like error = "abridge", but it allows potentially healthy regions of the dependency graph to begin running. (Visit https://books.ropensci.org/targets/debugging.html to learn how to debug targets using saved workspaces.)
memory	Character of length 1, memory strategy. If "persistent", the target stays in memory until the end of the pipeline (unless storage is "worker", in which case targets unloads the value from memory right after storing it in order to avoid sending copious data over a network). If "transient", the target gets unloaded after every new target completes. Either way, the target gets automatically loaded into memory whenever another target needs the value. For cloud-based dynamic files (e.g. format = "file" with repository = "aws"), this memory strategy applies to the temporary local copy of the file: "persistent" means it remains until the end of the pipeline and is then deleted, and "transient" means it gets deleted as soon as possible. The former conserves bandwidth, and the latter conserves local storage.
garbage_collection	Logical, whether to run base::gc() just before the target runs.
deployment	Character of length 1. If deployment is "main", then the target will run on the central controlling R process. Otherwise, if deployment is "worker" and you set up the pipeline with distributed/parallel computing, then the target runs on a parallel worker. For more on distributed/parallel computing in targets, please visit https://books.ropensci.org/targets/crew.html.
priority	Numeric of length 1 between 0 and 1. Controls which targets get deployed first when multiple competing targets are ready simultaneously. Targets with priorities closer to 1 get dispatched earlier (and polled earlier in tar_make_future()).
resources	Object returned by tar_resources() with optional settings for high-performance computing functionality, alternative data storage formats, and other optional capabilities of targets. See tar_resources() for details.
retrieval	Character of length 1, only relevant to tar_make_clustermq() and tar_make_future(). Must be one of the following values: "main": the target's dependencies are loaded on the host machine and sent to the worker before the target runs. "worker": the worker loads the targets dependencies. "none": the dependencies are not loaded at all. This choice is almost never recommended. It is only for niche situations, e.g. the data needs to be loaded explicitly from another language.
cue	An optional object from tar_cue() to customize the rules that decide whether the target is up to date.
description	Character of length 1, a custom free-form human-readable text description of the target. Descriptions appear as target labels in functions like tar_manifest() and tar_visnetwork(), and they let you select subsets of targets for the names argument of functions like tar_make(). For example, tar_manifest(names = tar_described_as(starts_with("survival model"))) lists all the targets whose descriptions start with the character string "survival model".

Details

tar_quarto() is an alternative to tar_target() for Quarto projects and standalone Quarto source documents that depend on upstream targets. The Quarto R source documents (⁠*.qmd⁠ and ⁠*.Rmd⁠ files) should mention dependency targets with tar_load() and tar_read() in the active R code chunks (which also allows you to render the project outside the pipeline if the ⁠_targets/⁠ data store already exists). (Do not use tar_load_raw() or tar_read_raw() for this.) Then, tar_quarto() defines a special kind of target. It 1. Finds all the tar_load()/tar_read() dependencies in the R source reports and inserts them into the target's command. This enforces the proper dependency relationships. (Do not use tar_load_raw() or tar_read_raw() for this.) 2. Sets format = "file" (see tar_target()) so targets watches the files at the returned paths and reruns the report if those files change. 3. Configures the target's command to return both the output rendered files and the input dependency files (such as Quarto source documents). All these file paths are relative paths so the project stays portable. 4. Forces the report to run in the user's current working directory instead of the working directory of the report. 5. Sets convenient default options such as deployment = "main" in the target and quiet = TRUE in quarto::quarto_render().

Value

A target object with format = "file". When this target runs, it returns a character vector of file paths: the rendered documents, the Quarto source files, and other input and output files. The output files are determined by the YAML front-matter of standalone Quarto documents and ⁠_quarto.yml⁠ in Quarto projects, and you can see these files with tar_quarto_files() (powered by quarto::quarto_inspect()). All returned paths are relative paths to ensure portability (so that the project can be moved from one file system to another without invalidating the target). See the "Target objects" section for background.

Quarto troubleshooting

If you encounter difficult errors, please read https://github.com/quarto-dev/quarto-r/issues/16. In addition, please try to reproduce the error using quarto::quarto_render("your_report.qmd", execute_dir = getwd()) without using targets at all. Isolating errors this way makes them much easier to solve.

Literate programming limitations

Literate programming files are messy and variable, so functions like tar_render() have limitations: * Child documents are not tracked for changes. * Upstream target dependencies are not detected if tar_read() and/or tar_load() are called from a user-defined function. In addition, single target names must be mentioned and they must be symbols. tar_load("x") and tar_load(contains("x")) may not detect target x. * Special/optional input/output files may not be detected in all cases. * tar_render() and friends are for local files only. They do not integrate with the cloud storage capabilities of targets.

Target objects

Most tarchetypes functions are target factories, which means they return target objects or lists of target objects. Target objects represent skippable steps of the analysis pipeline as described at https://books.ropensci.org/targets/. Please read the walkthrough at https://books.ropensci.org/targets/walkthrough.html to understand the role of target objects in analysis pipelines.

For developers, https://wlandau.github.io/targetopia/contributing.html#target-factories explains target factories (functions like this one which generate targets) and the design specification at https://books.ropensci.org/targets-design/ details the structure and composition of target objects.

See Also

Other Literate programming targets: tar_knit(), tar_quarto_rep(), tar_render(), tar_render_rep()

Examples

if (identical(Sys.getenv("TAR_LONG_EXAMPLES"), "true")) {
targets::tar_dir({  # tar_dir() runs code from a temporary directory.
# Unparameterized Quarto document:
lines <- c(
  "---",
  "title: report.qmd source file",
  "output_format: html",
  "---",
  "Assume these lines are in report.qmd.",
  "```{r}",
  "targets::tar_read(data)",
  "```"
)
writeLines(lines, "report.qmd")
# Include the report in a pipeline as follows.
targets::tar_script({
  library(tarchetypes)
  list(
    tar_target(data, data.frame(x = seq_len(26), y = letters)),
    tar_quarto(name = report, path = "report.qmd")
  )
}, ask = FALSE)
# Then, run the pipeline as usual.

# Parameterized Quarto:
lines <- c(
  "---",
  "title: 'report.qmd source file with parameters'",
  "output_format: html_document",
  "params:",
  "  your_param: \"default value\"",
  "---",
  "Assume these lines are in report.qmd.",
  "```{r}",
  "print(params$your_param)",
  "```"
)
writeLines(lines, "report.qmd")
# Include the report in the pipeline as follows.
unlink("_targets.R") # In tar_dir(), not the user's file space.
targets::tar_script({
  library(tarchetypes)
  list(
    tar_target(data, data.frame(x = seq_len(26), y = letters)),
    tar_quarto(
      name = report,
      path = "report.qmd",
      execute_params = list(your_param = data)
    ),
    tar_quarto_raw(
      name = "report2",
      path = "report.qmd",
      execute_params = quote(list(your_param = data))
    )
  )
}, ask = FALSE)
})
# Then, run the pipeline as usual.
}

tarchetypes documentation built on Sept. 30, 2024, 9:18 a.m.