https://github.com/tiernanmartin/drakepkg
Demonstrate A Drake Workflow Package
https://github.com/tiernanmartin/drakepkg
Last synced: 3 months ago
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Demonstrate A Drake Workflow Package
- Host: GitHub
- URL: https://github.com/tiernanmartin/drakepkg
- Owner: tiernanmartin
- License: other
- Created: 2018-07-25T17:29:56.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-03-06T19:52:09.000Z (almost 5 years ago)
- Last Synced: 2024-08-06T03:03:57.681Z (7 months ago)
- Language: R
- Size: 2.27 MB
- Stars: 29
- Watchers: 2
- Forks: 5
- Open Issues: 5
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
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README
---
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
[](http://www.repostatus.org/#wip)
# drakepkg
**Cascadia R Conference 2019 Update:** the slides from Tiernan Martin's talk can be downloaded here: [drakepkg-slides-cascadiarconf2019.pdf](https://github.com/tiernanmartin/drakepkg/raw/master/drakepkg-slides-cascadiarconf2019.pdf)
The goal of [`drakepkg`](https://github.com/tiernanmartin/drakepkg) is to demonstrate how a [`drake`](https://ropensci.github.io/drake/) workflow can be organized as an R package.
Why do this? Because the package system in R provides a widely-adopted method of structuring, documenting, testing, and sharing R code. While most R packages are general purpose, this approach applies the same framework to a specific workflow (or set of workflows). It increases the reproducibility of a complex workflow without requiring users to recreate the workflow's environment with a container image (although that approach is compatible with [`drakepkg`](https://github.com/tiernanmartin/drakepkg) - see [januz/drakepkg](https://github.com/januz/drakepkg)).
The [`drakepkg`](https://github.com/tiernanmartin/drakepkg) package is experimental in nature and currently requires some inconvenient steps (see the [drake manual - 7.1.4 Workflows as R packages](https://ropenscilabs.github.io/drake-manual/best-practices.html#workflows-as-r-packages)); please use caution when applying this approach to your own work.
## Installation
You can install the released version of [`drakepkg`](https://github.com/tiernanmartin/drakepkg) from its Github [repository](https://github.com/tiernanmartin/drakepkg) with:
``` {r install, eval=FALSE}
devtools::install_packages("tiernanmartin/drakepkg")
```
## Usage
The following table shows how each feature of a [`drake`](https://ropensci.github.io/drake/) workflow is made accessible within an R package:
| `drake` | R Package |
|:------------------------- |:---------------------------------------------------------- |
| plans, commands | functions (`R/*.R`) |
| targets | stored in the cache (`.drake/`) |
| input files, output files | internal data (`inst/intdata/*`), external data (`inst/extdata/*`), images and documents (`inst/documents/*`) |
The package comes with two example [`drake`](https://ropensci.github.io/drake/) plans, both of which are loosely based on the `main` example included in the [`drake`](https://ropensci.github.io/drake/) package:
1. An introductory plan: `drakepkg::get_example_plan_simple()`
2. A plan that involves downloading external data: `drakepkg::get_example_plan_external()`
The first plan looks like this:
```{r library, echo = FALSE, message=FALSE, warning=FALSE}
library(drakepkg)
```
```{r simple-plan}
get_example_plan_simple()
```
Several commands used in the plan (e.g,`create_plot()`, `write_report_simple()`) are included as part of the [`drakepkg`](https://github.com/tiernanmartin/drakepkg) R package and so is the plan itself; the documentation for each of these functions can be accessed using R's `help()` function (for example, `help(get_example_plan_simple)`).
Once you have installed and loaded [`drakepkg`](https://github.com/tiernanmartin/drakepkg), you can reproduce the introductory plan's workflow by performing the following steps:
1. Copy the package's directories and source code files into your working directory with the `copy_drakepkg_files()` function
2. View the plan (`get_example_plan_simple()`) and then make it (`make(get_example_plan_simple())`)
3. Access the plan's targets using `drake` functions like `readd()` or `loadd()`
4. View the html documents created by the workflow in the `documents/` directory
```{r step1, eval=FALSE}
# Step 1: copy the source code files into the working directory
copy_drakepkg_files()
```
```{r step2A}
# Step 2A: view the example plan
get_example_plan_simple()
```
```{r step2B}
# Step 2B: make the example plan
make(get_example_plan_simple())
```
```{r step3}
# Step 3: examine the plan's targets
readd(fit)
readd(hist)
```
This example and others are available in the package vignette (`vignette('drakepkg')`).