knitr_in: Declare 'knitr'/'rmarkdown' source files as dependencies....

In wlandau-lilly/drake: A Pipeline Toolkit for Reproducible Computation at Scale

Declare knitr/rmarkdown source files as dependencies.

Description

knitr_in() marks individual knitr/R Markdown reports as dependencies. In drake, these reports are pieces of the pipeline. R Markdown is a great tool for displaying precomputed results, but not for running a large workflow from end to end. These reports should do as little computation as possible.

Usage

knitr_in(...)

Arguments

...	Character strings. File paths of knitr/rmarkdown source files supplied to a command in your workflow plan data frame.

Details

Unlike file_in() and file_out(), knitr_in() does not work with entire directories.

Value

A character vector of declared input file paths.

Keywords

drake_plan() understands special keyword functions for your commands. With the exception of target(), each one is a proper function with its own help file.

• target(): give the target more than just a command. Using target(), you can apply a transformation (examples: ⁠https://books.ropensci.org/drake/plans.html#large-plans⁠), # nolint supply a trigger (⁠https://books.ropensci.org/drake/triggers.html⁠), # nolint or set any number of custom columns.

• file_in(): declare an input file dependency.

• file_out(): declare an output file to be produced when the target is built.

• knitr_in(): declare a knitr file dependency such as an R Markdown (⁠*.Rmd⁠) or R LaTeX (⁠*.Rnw⁠) file.

• ignore(): force drake to entirely ignore a piece of code: do not track it for changes and do not analyze it for dependencies.

• no_deps(): tell drake to not track the dependencies of a piece of code. drake still tracks the code itself for changes.

• id_chr(): Get the name of the current target.

• drake_envir(): get the environment where drake builds targets. Intended for advanced custom memory management.

See Also

file_in(), file_out(), ignore(), no_deps()

Examples

## Not run: 
isolate_example("contain side effects", {
if (requireNamespace("knitr", quietly = TRUE)) {
# `knitr_in()` is like `file_in()`
# except that it analyzes active code chunks in your `knitr`
# source file and detects non-file dependencies.
# That way, updates to the right dependencies trigger rebuilds
# in your report.
# The mtcars example (`drake_example("mtcars")`)
# already has a demonstration

load_mtcars_example()
make(my_plan)

# Now how did drake magically know that
# `small`, `large`, and `coef_regression2_small` were
# dependencies of the output file `report.md`?
# because the command in the workflow plan had
# `knitr_in("report.Rmd")` in it, so drake knew
# to analyze the active code chunks. There, it spotted
# where `small`, `large`, and `coef_regression2_small`
# were read from the cache using calls to `loadd()` and `readd()`.
}
})

## End(Not run)

wlandau-lilly/drake documentation built on Dec. 3, 2024, 11:09 p.m.