tar_knit {tarchetypes}

Target with a knitr document.

Description

Shorthand to include knitr document in a targets pipeline.

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,
  ...
)

Arguments

name

Symbol, name of the target. A target name must be a valid name for a symbol in R, and it must not start with a dot. Subsequent targets can refer to this name symbolically to induce a dependency relationship: e.g. tar_target(downstream_target, f(upstream_target)) is a target named downstream_target which depends on a target upstream_target and a function f(). In addition, a target's name determines its random number generator seed. In this way, each target runs with a reproducible seed so someone else running the same pipeline should get the same results, and no two targets in the same pipeline share the same seed. (Even dynamic branches have different names and thus different seeds.) You can recover the seed of a completed target with tar_meta(your_target, seed) and run tar_seed_set() on the result to locally recreate the target's initial RNG state.

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.

• "abridge": any currently running targets keep running, but no new targets launch after that. (Visit https://books.ropensci.org/targets/debugging.html to learn how to debug targets using saved workspaces.)

• "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.

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".

quiet

Boolean; suppress the progress bar and messages?

...

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

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().

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 objects" section for background.

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_raw(), tar_quarto(), tar_quarto_raw(), tar_quarto_rep(), tar_quarto_rep_raw(), tar_render(), tar_render_raw(), tar_render_rep(), tar_render_rep_raw()

Examples

if (identical(Sys.getenv("TAR_LONG_EXAMPLES"), "true")) {
targets::tar_dir({ # tar_dir() runs code from a temporary directory.
targets::tar_script({
  # 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(
    targets::tar_target(data, data.frame(x = seq_len(26), y = letters)),
    tarchetypes::tar_knit(report, path)
  )
})
targets::tar_make()
})
}