https://github.com/robitalec/targets-parameterized-bookdown
:hammer_and_wrench: Example repository for rendering a bookdown book, compiling parameterized RMarkdown documents, using the targets package
https://github.com/robitalec/targets-parameterized-bookdown
bookdown bookdown-book r rmarkdown targets
Last synced: 26 days ago
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:hammer_and_wrench: Example repository for rendering a bookdown book, compiling parameterized RMarkdown documents, using the targets package
- Host: GitHub
- URL: https://github.com/robitalec/targets-parameterized-bookdown
- Owner: robitalec
- License: gpl-3.0
- Created: 2021-01-06T21:28:18.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-03-20T04:15:32.000Z (about 4 years ago)
- Last Synced: 2025-02-28T21:49:05.257Z (about 1 month ago)
- Topics: bookdown, bookdown-book, r, rmarkdown, targets
- Language: R
- Homepage:
- Size: 33.2 KB
- Stars: 6
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# targets-parameterized-bookdown
[](https://doi.org/10.5281/zenodo.4624556)
Example repository for rendering a bookdown book, compiling parameterized
Rmarkdown documents, using the [targets](https://github.com/wlandau/targets)
package.
This example extends the
[targets-minimal](https://github.com/wlandau/targets-minimal) example. To mimic
a directory of input files, we split the example data into two chunks.
``` r
library(tidyverse)
data <- read_csv('data/raw_data.csv')
nrows <- 50
data1 <- head(data, n = nrows)
data2 <- tail(data, n = nrows)
write_csv(data1, 'data/split/data1.csv')
write_csv(data2, 'data/split/data2.csv')
```
To setup a target for our input files, we use `tar_files` from
[tarchetypes](https://github.com/wlandau/tarchetypes) (target: paths). Dynamic branching in
subsequent targets is mapped over these files (targets: raw_data, data, hist, fit).
Parameterized RMarkdown documents are generated by mapping over the fitted model
and histograms using a template document (`template/template.Rmd`) (target: report).
Finally, the output documents are merged into a book with bookdown. We use a
custom wrapper function `render_with_deps` to explicitly declare the book's
dependency on the output reports (target: book).
## Notes
* We need to change the extension of the parameterized github_document outputs
(target: report) from `.md` to `.Rmd` because `bookdown` doesn't pick up `.md` files
unless they are explicitly listed with the `rmd_files` argument in `_bookdown.yml`.
See [here](https://github.com/rstudio/bookdown/issues/956).
* The `title` and `output_file` for rendered RMarkdown documents are set in this
example to the name of the branch (target: report). If adapted for your own use, this could
alternatively be set to an id from the data, etc.
* We can't use the `tar_render` function from `tarchetypes` because we need to
call `bookdown::render_book` and not `rmarkdown::render` (target: book).
Therefore, we need to track the `.Rmd` files in separate targets.
* You *may* need to use `pandoc` >= [2.11.2](https://pandoc.org/releases.html#pandoc-2.11.2-2020-11-19) when generating the github_documents (target: report) so ATX style headings are used by default.