Parameterized R Markdown with dynamic branching.
Targets to render a parameterized R Markdown report with multiple sets of parameters.
tar_render_rep(
name,
path,
params = data.frame(),
batches = NULL,
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"),
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"),
quiet = TRUE,
...
)name |
Symbol, name of the target. Subsequent targets
can refer to this name symbolically to induce a dependency relationship:
e.g. |
path |
Character string, file path to the R Markdown source file. Must have length 1. |
params |
Code to generate a data frame or |
batches |
Number of batches to group the R Markdown files. For a large number of reports, increase the number of batches to decrease target-level overhead. Defaults to the number of reports to render (1 report per batch). |
packages |
Character vector of packages to load right before
the target builds. Use |
library |
Character vector of library paths to try
when loading |
format |
Optional storage format for the target's return value.
With the exception of
|
iteration |
Character of length 1, name of the iteration mode of the target. Choices:
|
error |
Character of length 1, what to do if the target
runs into an error. If |
deployment |
Character of length 1, only relevant to
|
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 |
resources |
A named list of computing resources. Uses:
|
retrieval |
Character of length 1, only relevant to
|
cue |
An optional object from |
quiet |
An option to suppress printing of the pandoc command line. |
... |
Other named arguments to |
tar_render_rep() is an alternative to tar_target() for
parameterized R Markdown reports that depend 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.
The R Markdown 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_render() 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 then the *_files/ directory if it exists. 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 rmarkdown::render().
A list of target objects to render the R Markdown
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.
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.
Other Literate programming targets:
tar_knit_raw(),
tar_knit(),
tar_render_raw(),
tar_render_rep_raw(),
tar_render()
if (identical(Sys.getenv("TAR_LONG_EXAMPLES"), "true")) {
targets::tar_dir({ # tar_dir() runs code from a temporary directory.
# Parameterized R Markdown:
lines <- c(
"---",
"title: 'report.Rmd file'",
"output_format: html_document",
"params:",
" par: \"default value\"",
"---",
"Assume these lines are in a file called report.Rmd.",
"```{r}",
"print(params$par)",
"```"
)
# The following pipeline will run the report for each row of params.
targets::tar_script({
library(tarchetypes)
list(
tar_render_rep(
report,
"report.Rmd",
params = tibble::tibble(par = c(1, 2))
)
)
}, ask = FALSE)
# Then, run the targets pipeline as usual.
})
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.