Batching is important for optimizing the efficiency
of heavily dynamically-branched workflows:
https://books.ropensci.org/targets/dynamic.html#batching.
tar_rep_raw()
is just like tar_rep()
except the
name is a character string and the command is a
language object.
Usage
tar_rep_raw(
name,
command,
batches = 1,
reps = 1,
rep_workers = 1,
tidy_eval = targets::tar_option_get("tidy_eval"),
packages = targets::tar_option_get("packages"),
library = targets::tar_option_get("library"),
format = targets::tar_option_get("format"),
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
Character of length 1, 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 nameddownstream_target
which depends on a targetupstream_target
and a functionf()
. 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 withtar_meta(your_target, seed)
and runtar_seed_set()
on the result to locally recreate the target's initial RNG state.- command
Expression object with code to run multiple times. Must return a list or data frame when evaluated.
- batches
Number of batches. This is also the number of dynamic branches created during
tar_make()
.- reps
Number of replications in each batch. The total number of replications is
batches * reps
.- rep_workers
Positive integer of length 1, number of local R processes to use to run reps within batches in parallel. If 1, then reps are run sequentially within each batch. If greater than 1, then reps within batch are run in parallel using a PSOCK cluster.
- tidy_eval
Whether to invoke tidy evaluation (e.g. the
!!
operator fromrlang
) as soon as the target is defined (beforetar_make()
). Applies to thecommand
argument.- 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
Optional storage format for the target's return value. With the exception of
format = "file"
, each target gets a file in_targets/objects
, and each format is a different way to save and load this file. See the "Storage formats" section for a detailed list of possible data storage formats.- 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 theendpoint
argument oftar_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.
Note: if
repository
is not"local"
andformat
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 withvctrs::vec_slice()
and aggregation happens withvctrs::vec_c()
."list"
, branching happens with[[]]
and aggregation happens withlist()
."group"
:dplyr::group_by()
-like functionality to branch over subsets of a non-dynamic data frame. Foriteration = "group"
, the target must not by dynamic (thepattern
argument oftar_target()
must be leftNULL
). The target's return value must be a data frame with a specialtar_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 thetar_group()
function to see how you can create the specialtar_group
column withdplyr::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."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 returnsNULL
. 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 (unlessstorage
is"worker"
, in which casetargets
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"
withrepository = "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, ifdeployment
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 intargets
, 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 oftargets
. Seetar_resources()
for details.- storage
Character of length 1, only relevant to
tar_make_clustermq()
andtar_make_future()
. 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"
: almost never recommended. It is only for niche situations, e.g. the data needs to be loaded explicitly from another language. If you do use it, then the return value of the target is totally ignored when the target ends, but each downstream target still attempts to load the data file (except whenretrieval = "none"
).If you select
storage = "none"
, then the return value of the target's command is ignored, and the data is not saved automatically. As with dynamic files (format = "file"
) it is the responsibility of the user to write to the data store from inside the target.The distinguishing feature of
storage = "none"
(as opposed toformat = "file"
) is that in the general case, downstream targets will automatically try to load the data from the data store as a dependency. As a corollary,storage = "none"
is completely unnecessary ifformat
is"file"
.
- retrieval
Character of length 1, only relevant to
tar_make_clustermq()
andtar_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()
andtar_visnetwork()
, and they let you select subsets of targets for thenames
argument of functions liketar_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"
.
Value
A list of two target objects, 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"
.
See the "Target objects" section for background.
Details
tar_rep_raw()
creates two targets:
an upstream local stem
with an integer vector of batch ids, and a downstream pattern
that maps over the batch ids. (Thus, each batch is a branch.)
Each batch/branch replicates the command a certain number of times.
Both batches and reps within each batch
are aggregated according to the method you specify
in the iteration
argument. If "list"
, reps and batches
are aggregated with list()
. If "vector"
,
then vctrs::vec_c()
. If "group"
, then vctrs::vec_rbind()
.
Replicate-specific seeds
In ordinary pipelines, each target has its own unique deterministic
pseudo-random number generator seed derived from its target name.
In batched replicate, however, each batch is a target with multiple
replicate within that batch. That is why tar_rep()
and friends give each replicate its own unique seed.
Each replicate-specific seed is created
based on the dynamic parent target name,
tar_option_get("seed")
(for targets
version 0.13.5.9000 and above),
batch index, and rep-within-batch index.
The seed is set just before the replicate runs.
Replicate-specific seeds are invariant to batching structure.
In other words,
tar_rep(name = x, command = rnorm(1), batches = 100, reps = 1, ...)
produces the same numerical output as
tar_rep(name = x, command = rnorm(1), batches = 10, reps = 10, ...)
(but with different batch names).
Other target factories with this seed scheme are tar_rep2()
,
tar_map_rep()
, tar_map2_count()
, tar_map2_size()
,
and tar_render_rep()
.
For the tar_map2_*()
functions,
it is possible to manually supply your own seeds
through the command1
argument and then invoke them in your
custom code for command2
(set.seed()
, withr::with_seed
,
or withr::local_seed()
). For tar_render_rep()
,
custom seeds can be supplied to the params
argument
and then invoked in the individual R Markdown reports.
Likewise with tar_quarto_rep()
and the execute_params
argument.
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 branching:
tar_combine()
,
tar_combine_raw()
,
tar_map()
,
tar_map2()
,
tar_map2_count()
,
tar_map2_count_raw()
,
tar_map2_raw()
,
tar_map2_size()
,
tar_map2_size_raw()
,
tar_map_rep()
,
tar_map_rep_raw()
,
tar_rep()
,
tar_rep2()
,
tar_rep2_raw()
,
tar_rep_map()
,
tar_rep_map_raw()
Examples
if (identical(Sys.getenv("TAR_LONG_EXAMPLES"), "true")) {
targets::tar_dir({ # tar_dir() runs code from a temporary directory.
targets::tar_script({
list(
tarchetypes::tar_rep_raw(
"x",
expression(data.frame(x = sample.int(1e4, 2))),
batches = 2,
reps = 3
)
)
})
targets::tar_make(callr_function = NULL)
targets::tar_read(x)
})
}