Targets to render a parameterized Quarto document with multiple sets of parameters.
Usage
tar_quarto_rep(
name,
path,
execute_params = data.frame(),
batches = NULL,
extra_files = character(0),
execute = TRUE,
cache = NULL,
cache_refresh = FALSE,
debug = FALSE,
quiet = TRUE,
pandoc_args = NULL,
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"),
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"),
retrieval = targets::tar_option_get("retrieval"),
cue = targets::tar_option_get("cue")
)
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 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 runset.seed()
on the result to locally recreate the target's initial RNG state.- path
Character string, file path to the Quarto source file. Must have length 1.
- execute_params
Code to generate a data frame or
tibble
with one row per rendered report and one column per Quarto parameter. You may also include anoutput_file
column to specify the path of each rendered report. If included, theoutput_file
column must be a character vector with one and only one output file for each row of parameters. If anoutput_file
column is not included, then the output files are automatically determined using the parameters, and the default file format is determined by the YAML front-matter of the Quarto source document. Only the first file format is used, the others are not generated. Quarto parameters must not be namedtar_group
oroutput_file
. Thisexecute_params
argument is converted into the command for a target that supplies the Quarto parameters.- batches
Number of batches. This is also the number of dynamic branches created during
tar_make()
.- extra_files
Character vector of extra files that
targets
should track for changes. If the content of one of these files changes, then the report will rerun over all the parameters on the nexttar_make()
. These files are extra files, and they do not include the Quarto source document or rendered output document, which are already tracked for changes. Examples include bibliographies, style sheets, and supporting image files.- execute
Whether to execute embedded code chunks.
- 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.
- pandoc_args
Additional command line options to pass to pandoc.
- 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 workers created with
future::plan(future.callr::callr, workers = rep_workers)
and invoked withfurrr::future_map()
.- tidy_eval
Logical of length 1, whether to use tidy evaluation to resolve
execute_params
. Similar to thetidy_eval
argument oftargets::tar_target()
.- packages
Character vector of packages to load right before the target builds 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.- iteration
Character of length 1, name of the iteration mode of the target. Choices:
"vector"
: branching happens withvectors::vec_slice()
and aggregation happens withvctrs::vec_c()
."list"
, branching happens with[[]]
and aggregation happens withlist()
. In the case of list iteration,tar_read(your_target)
will return a list of lists, where the outer list has one element per batch and each inner list has one element per rep within batch. To un-batch this nested list, calltar_read(your_target, recursive = FALSE)
."group"
:dplyr::group_by()
-like functionality to branch over subsets of a data frame. 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, only relevant to
tar_make_clustermq()
andtar_make_future()
. If"worker"
, the target builds on a parallel worker. If"main"
, the target builds on the host machine / process managing the pipeline.- 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 built 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.- 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 builds."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.
Value
A list of target objects to render the Quarto
reports. Changes to the parameters, source file, dependencies, etc.
will cause the appropriate targets to rerun during tar_make()
.
See the "Target objects" section for background.
Details
tar_quarto_rep()
is an alternative to tar_target()
for
a parameterized Quarto document that depends on other targets.
Parameters must be given as a data frame with one row per
rendered report and one column per parameter. An optional
output_file
column may be included to set the output file path
of each rendered report. (See the execute_params
argument for details.)
The Quarto source should mention other dependency targets
tar_load()
and tar_read()
in the active code chunks
(which also allows you to render the report
outside the pipeline if the _targets/
data store already exists
and appropriate defaults are specified for the parameters).
(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 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 the output
report files: the rendered document, the source file,
and file paths mentioned in files
. 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()
.
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.
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.
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.
See also
Other Literate programming targets:
tar_knit_raw()
,
tar_knit()
,
tar_quarto_raw()
,
tar_quarto_rep_raw()
,
tar_quarto()
,
tar_render_raw()
,
tar_render_rep_raw()
,
tar_render_rep()
,
tar_render()
Examples
if (identical(Sys.getenv("TAR_LONG_EXAMPLES"), "true")) {
targets::tar_dir({ # tar_dir() runs code from a temporary directory.
# Parameterized Quarto:
lines <- c(
"---",
"title: 'report.qmd file'",
"output_format: html_document",
"params:",
" par: \"default value\"",
"---",
"Assume these lines are in a file called report.qmd.",
"```{r}",
"print(params$par)",
"```"
)
writeLines(lines, "report.qmd") # In tar_dir(), not the user's file space.
# The following pipeline will run the report for each row of params.
targets::tar_script({
library(tarchetypes)
list(
tar_quarto_rep(
report,
path = "report.qmd",
execute_params = tibble::tibble(par = c(1, 2))
)
)
}, ask = FALSE)
# Then, run the targets pipeline as usual.
})
}