tar_files: Dynamic branching over output or input files.

In wlandau/tarchetypes: Archetypes for Targets

Dynamic branching over output or input files.

Description

Dynamic branching over output or input files. tar_files() expects a unevaluated symbol for the name argument and an unevaluated expression for command, whereas tar_files_raw() expects a character string for the name argument and an evaluated expression object for command. See the examples for a demo.

Usage

tar_files(
  name,
  command,
  tidy_eval = targets::tar_option_get("tidy_eval"),
  packages = targets::tar_option_get("packages"),
  library = targets::tar_option_get("library"),
  format = c("file", "file_fast", "url", "aws_file"),
  repository = targets::tar_option_get("repository"),
  iteration = targets::tar_option_get("iteration"),
  error = targets::tar_option_get("error"),
  memory = targets::tar_option_get("memory"),
  garbage_collection = targets::tar_option_get("garbage_collection"),
  deployment = targets::tar_option_get("deployment"),
  priority = targets::tar_option_get("priority"),
  resources = targets::tar_option_get("resources"),
  storage = targets::tar_option_get("storage"),
  retrieval = targets::tar_option_get("retrieval"),
  cue = targets::tar_option_get("cue"),
  description = targets::tar_option_get("description")
)

tar_files_raw(
  name,
  command,
  packages = targets::tar_option_get("packages"),
  library = targets::tar_option_get("library"),
  format = c("file", "url", "aws_file", "file_fast"),
  repository = targets::tar_option_get("repository"),
  iteration = targets::tar_option_get("iteration"),
  error = targets::tar_option_get("error"),
  memory = targets::tar_option_get("memory"),
  garbage_collection = targets::tar_option_get("garbage_collection"),
  deployment = targets::tar_option_get("deployment"),
  priority = targets::tar_option_get("priority"),
  resources = targets::tar_option_get("resources"),
  storage = targets::tar_option_get("storage"),
  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_files() expects a unevaluated symbol for the name argument and an unevaluated expression for command, whereas tar_files_raw() expects a character string for the name argument and an evaluated expression object for command. See the examples for a demo.
command	R command for the target. tar_files() expects a unevaluated symbol for the name argument and an unevaluated expression for command, whereas tar_files_raw() expects a character string for the name argument and an evaluated expression object for command. See the examples for a demo.
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.
format	Character of length 1. Must be "file", "url", or "aws_file". See the format argument of targets::tar_target() for details.
repository	Character of length 1, remote repository for target storage. Choices: "local": file system of the local machine. "aws": Amazon Web Services (AWS) S3 bucket. Can be configured with a non-AWS S3 bucket using the endpoint argument of tar_resources_aws(), but versioning capabilities may be lost in doing so. See the cloud storage section of https://books.ropensci.org/targets/data.html for details for instructions. "gcp": Google Cloud Platform storage bucket. See the cloud storage section of https://books.ropensci.org/targets/data.html for details for instructions. A character string from tar_repository_cas() for content-addressable storage. Note: if repository is not "local" and format is "file" then the target should create a single output file. That output file is uploaded to the cloud and tracked for changes where it exists in the cloud. The local file is deleted after the target runs.
iteration	Character of length 1, name of the iteration mode of the target. Choices: "vector": branching happens with vctrs::vec_slice() and aggregation happens with vctrs::vec_c(). "list", branching happens with ⁠[[]]⁠ and aggregation happens with list(). "group": dplyr::group_by()-like functionality to branch over subsets of a non-dynamic data frame. For iteration = "group", the target must not by dynamic (the pattern argument of tar_target() must be left NULL). The target's return value must be a data frame with a special tar_group column of consecutive integers from 1 through the number of groups. Each integer designates a group, and a branch is created for each collection of rows in a group. See the tar_group() function to see how you can create the special tar_group column with dplyr::group_by().
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 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: 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. Possible values: "auto": new in targets version 1.8.0.9011, memory = "auto" is equivalent to memory = "transient" for dynamic branching (a non-null pattern argument) and memory = "persistent" for targets that do not use dynamic branching. "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). "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"), 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, FALSE to omit garbage collection. In the case of high-performance computing, gc() runs both locally and on the parallel worker. All this garbage collection is skipped if the actual target is skipped in the pipeline. Non-logical values of garbage_collection are converted to TRUE or FALSE using isTRUE(). In other words, non-logical values are converted FALSE. For example, garbage_collection = 2 is equivalent to garbage_collection = FALSE.
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.
storage	Character string to control when the output of the target is saved to storage. Only relevant when using targets with parallel workers (https://books.ropensci.org/targets/crew.html). Must be one of the following values: "main": the target's return value is sent back to the host machine and saved/uploaded locally. "worker": the worker saves/uploads the value. "none": targets makes no attempt to save the result of the target to storage in the location where targets expects it to be. Saving to storage is the responsibility of the user. Use with caution.
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: "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 target's dependencies. "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. Only applies to the downstream target. The upstream target always runs.
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_files() creates a pair of targets, one upstream and one downstream. The upstream target does some work and returns some file paths, and the downstream target is a pattern that applies format = "file" or format = "url". (URLs are input-only, they must already exist beforehand.) This is the correct way to dynamically iterate over file/url targets. It makes sure any downstream patterns only rerun some of their branches if the files/urls change. For more information, visit https://github.com/ropensci/targets/issues/136 and https://github.com/ropensci/drake/issues/1302.

Value

A list of two targets, one upstream and one downstream. The upstream one does some work and returns some file paths, and the downstream target is a pattern that applies format = "file" or format = "url". 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 Dynamic branching over files: tar_files_input()

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)
  # Do not use temp files in real projects
  # or else your targets will always rerun.
  paths <- unlist(replicate(2, tempfile()))
  file.create(paths)
  list(
    tar_files(name = x, command = paths),
    tar_files_raw(name = "y", command = quote(paths))
  )
})
targets::tar_make()
targets::tar_read(x)
})
}

wlandau/tarchetypes documentation built on Dec. 8, 2024, 4:44 p.m.