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Target with a knitr document.

Source: R/tar_knit.R, R/tar_knit_raw.R
tar_knit.Rd

Shorthand to include knitr document in a targets pipeline.

tar_knit() expects an unevaluated symbol for the name argument, and it supports named ... arguments for knitr::knit() arguments. tar_knit_raw() expects a character string for name and supports an evaluated expression object knit_arguments for knitr::knit() arguments.

Usage

tar_knit(
  name,
  path,
  output_file = NULL,
  working_directory = NULL,
  tidy_eval = targets::tar_option_get("tidy_eval"),
  packages = targets::tar_option_get("packages"),
  library = targets::tar_option_get("library"),
  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"),
  quiet = TRUE,
  ...
)

tar_knit_raw(
  name,
  path,
  output_file = NULL,
  working_directory = NULL,
  packages = targets::tar_option_get("packages"),
  library = targets::tar_option_get("library"),
  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"),
  quiet = TRUE,
  knit_arguments = quote(list())
)

Arguments

name

Name of the target. tar_knit() expects an unevaluated symbol for the name argument, whereas tar_knit_raw() expects a character string for name.

path

Character string, file path to the knitr source file. Must have length 1.

output_file

Character string, file path to the rendered output 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.

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. In addition, as of targets version 1.8.0.9011, a value of NULL is given to upstream dependencies with error = "null" if loading fails.

  • "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:

    1. It is not downstream of the error, and

    2. 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. Possible values:

  • "auto" (default): equivalent to memory = "transient" in almost all cases. But to avoid superfluous reads from disk, memory = "auto" is equivalent to memory = "persistent" for for non-dynamically-branched targets that other targets dynamically branch over. For example: if your pipeline has tar_target(name = y, command = x, pattern = map(x)), then tar_target(name = x, command = f(), memory = "auto") will use persistent memory for x in order to avoid rereading all of x for every branch of y.

  • "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.

  • "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).

For cloud-based file targets (e.g. format = "file" with repository = "aws"), the memory option 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: TRUE to run base::gc() just before the target runs, in whatever R process it is about to run (which could be a parallel worker). FALSE to omit garbage collection. Numeric values get converted to FALSE. The garbage_collection option in tar_option_set() is independent of the argument of the same name in tar_target().

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

Deprecated on 2025-04-08 (targets version 1.10.1.9013). targets has moved to a more efficient scheduling algorithm (https://github.com/ropensci/targets/issues/1458) which cannot support priorities. The priority argument of tar_target() no longer has a reliable effect on execution order.

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 string to control when the current target loads its dependencies into memory before running. (Here, a "dependency" is another target upstream that the current one depends on.) Only relevant when using targets with parallel workers (https://books.ropensci.org/targets/crew.html). Must be one of the following values:

  • "auto" (default): equivalent to retrieval = "worker" in almost all cases. But to avoid unnecessary reads from disk, retrieval = "auto" is equivalent to retrieval = "main" for dynamic branches that branch over non-dynamic targets. For example: if your pipeline has tar_target(x, command = f()), then tar_target(y, command = x, pattern = map(x), retrieval = "auto") will use "main" retrieval in order to avoid rereading all of x for every branch of y.

  • "worker": the worker loads the target's dependencies.

  • "main": the target's dependencies are loaded on the host machine and sent to the worker before the target runs.

  • "none": targets makes no attempt to load its dependencies. With retrieval = "none", loading dependencies is the responsibility of the user. Use with caution.

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".

quiet

Boolean; suppress the progress bar and messages?

...

Named arguments to knitr::knit(). These arguments are unevaluated when supplied to tar_knit(). They are only evaluated when the target actually runs in tar_make(), not when the target is defined.

knit_arguments

Optional language object with a list of named arguments to knitr::knit(). Cannot be an expression object. (Use quote(), not expression().) The reason for quoting is that these arguments may depend on upstream targets whose values are not available at the time the target is defined, and because tar_knit_raw() is the "raw" version of a function, we want to avoid all non-standard evaluation.

Value

A tar_target() object with format = "file". When this target runs, it returns a character vector of file paths. The first file paths are the output files (returned by knitr::knit()) and the knitr source file is last. But unlike knitr::knit(), 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 definition objects" section for background.

Details

tar_knit() is an alternative to tar_target() for knitr reports that depend on other targets. The knitr source should mention dependency targets with tar_load() and tar_read() in the active code chunks (which also allows you to knit the report outside the pipeline if the _targets/ data store already exists). (Do not use tar_load_raw() or tar_read_raw() for this.) Then, tar_knit() defines a special kind of target. It 1. Finds all the tar_load()/tar_read() dependencies in the report 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 report files and the input source file. 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 knitr::knit().

Target definition objects

Most tarchetypes functions are target factories, which means they return target definition objects or lists of target definition objects. target definition 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 definition 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 definition objects.

See also

Other Literate programming targets: tar_quarto(), 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.
targets::tar_script({
  library(tarchetypes)
  # Ordinarily, you should create the report outside
  # tar_script() and avoid temporary files.
  lines <- c(
    "---",
    "title: report",
    "output_format: html_document",
    "---",
    "",
    "```{r}",
    "targets::tar_read(data)",
    "```"
  )
  path <- tempfile()
  writeLines(lines, path)
  list(
    tar_target(data, data.frame(x = seq_len(26), y = letters)),
    tar_knit(name = report, path = path),
    tar_knit_raw(name = "report2", path = path)
  )
})
targets::tar_make()
})
}