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https://github.com/reconverse/reportfactory
Lightweight infrastructure to handle multiple rmarkdown reports
https://github.com/reconverse/reportfactory
infrastructure knitr r r-package r-packages rmarkdown rmarkdown-document
Last synced: about 2 months ago
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Lightweight infrastructure to handle multiple rmarkdown reports
- Host: GitHub
- URL: https://github.com/reconverse/reportfactory
- Owner: reconverse
- License: other
- Created: 2018-06-13T11:13:28.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2022-12-12T13:38:51.000Z (about 2 years ago)
- Last Synced: 2024-11-17T13:09:39.814Z (about 2 months ago)
- Topics: infrastructure, knitr, r, r-package, r-packages, rmarkdown, rmarkdown-document
- Language: R
- Homepage: https://www.reconverse.org/reportfactory/
- Size: 1.23 MB
- Stars: 83
- Watchers: 6
- Forks: 8
- Open Issues: 9
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- jimsghstars - reconverse/reportfactory - Lightweight infrastructure to handle multiple rmarkdown reports (R)
README
---
output: github_document
---
```{r readmesetup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
[](https://codecov.io/gh/reconverse/reportfactory?branch=master)
[](https://github.com/reconverse/reportfactory/actions)
# Welcome to reportfactory!
**NOTE**
This version of {reportfactory} works in a very different way to the previous
unreleased version. For those already using {reportfactory} in their pipelines
you can obtain the old version using the {remotes} package:
```{r installold, eval = FALSE}
remotes::install_github("reconverse/reportfactory@old_version")
```
You can also download it directly from
https://github.com/reconverse/reportfactory/releases/tag/old_version.
You can install the current version of the package from
[CRAN](https://cran.r-project.org/) with:
```{r, eval=FALSE}
install.packages("reportfactory")
```
The development version can be installed from [GitHub](https://github.com/) with:
```{r, eval=FALSE}
if (!require(remotes)) {
install.packages("remotes")
}
remotes::install_github("reconverse/reportfactory", build_vignettes = TRUE)
```
## reportfactory in a nutshell
{reportfactory} is a R package which facilitates workflows for handling multiple
`.Rmd` reports, compiling one or several reports in one go, and storing outputs
in well-organised, timestamped folders. This is illustrated in the figure below:
There a few key principles it adheres to:
- *Simple*: only focusses on the compilation of reports with minimum overhead
for the user.
- *Non-invasive*: `.Rmd` documents need no alteration to work within the factory.
- *Reproducible*: time-stamped folder structure and customisable subfolders make
viewing the same report over time a breeze; handling of package dependencies
facilitates the deployment of factories on multiple computers.
- *Time-saving*: easy compilation of multiple reports using regular expressions;
book-keeping is handled by the factory and ensures that: i) every report is
compiled in a clean environment and ii) all outputs are stored in a dedicated
folder
## Installing the package
To install the development version of the package, use:
```{r install2, eval = FALSE}
remotes::install_github("reconverse/reportfactory")
```
## Quick start
### Step 1 - Create a new factory
Create and open a new factory. Here, we create the factory with the default settings.
This will create the factory in our current working directory and then move us in to this new factory.
```{r creation}
library(reportfactory)
new_factory("my_factory")
```
```{r, setwd, include=FALSE}
knitr::opts_knit$set(root.dir = file.path(getwd(), "my_factory"))
```
### Step 2 - Add your reports
Here we've already created some with most of the default arguments being set to
TRUE (the default). These default settings include both an example report and
some associated data (`report_sources/example_report.Rmd` and
`data/raw/example_data.csv`). The helper functions below show the state of the
factory.
```{r listing}
list_reports() # list all available report sources
list_deps() # list all of the dependencies of the reports
list_outputs() # currently empty
```
### Step 3 - Compile report(s)
The `compile_reports()` function can be used to compile a report using regular
expressions matched against the full filename of reports within the factory.
This ability to use of regular expressions is useful when you're actively
working on developing your reports but once the factory is setup we recommend
passing full filenames to the function so it is always clear what will be built.
```{r compile}
compile_reports(
reports = "example_report.Rmd"
)
```
Use `list_ouputs()` to view the report outputs.
```{r outputs}
list_outputs()
```
`compile_reports()` can also be used to pass a set of parameters to use with a
parameterised report (here we use a subfolder argument to distinguish the
parameterised reports).
```{r compileparams}
compile_reports(
reports = "example_report.Rmd",
params = list(graph = FALSE),
subfolder = "regional"
)
list_outputs()
```
Note that reports can also be an integer or a logical vector, in which case it
is interpreted as a subset of files output by list_reports(). For instance:
* `compile_reports(reports = c(1, 3))` will compile the first and third
reports listed by list_reports(); and
* `compile_reports(reports = TRUE)` will compile all reports.
### Factory overview
If you want to have an overview of your entire factory then you can use the
`factory_overview()` function:
```{r factoryoverview}
factory_overview()
```
## Contributing guidelines
Contributions are welcome via **pull requests**.
### Code of Conduct
Please note that the reportfactory project is released with a
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.