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README.rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
original_files <- dir()
```
<!-- # ijtiff <img src="man/figures/logo.png" height="140" align="right"> -->
<!-- Code status -->
[](https://travis-ci.org/ROpenSci/Rclean)
[](https://codecov.io/github/ROpenSci/Rclean?branch=master)
<!-- R status -->
[](https://cran.r-project.org/package=Rclean)
[](http://www.rdocumentation.org/packages/Rclean)
<!-- Dev status -->
[](http://www.repostatus.org/#active)
[](https://www.tidyverse.org/lifecycle/#maturing)
<!-- Package Review -->
[](https://github.com/ropensci/software-review/issues/327)
[](http://joss.theoj.org/papers/334d80d5508056dc6e7e17c6fd3ed5a6)
<!-- Archiving -->
[](https://zenodo.org/badge/latestdoi/102645585)
Quick Start Guide
=================
- [Rclean](https://github.com/MKLau/Rclean) was created to help
scientists more *easily* write “cleaner” code.
- Written with research scientists that are results oriented in mind,
the package’s primary function provides a simple way to isolate
the minimal code you need to produce a specific result, such as a
statistical table or a figure. By focusing on specific results
(aka. variables), large and/or complicated analytical scripts can
be paired down to the essentials and easily re-factored to be more
robust and easily shared.
- Below, you'll find a brief introduction to get you started using the
package. For more details, see `vignette("Rclean")`.
Install
=======
You can install the most up to date version easily with
[devtools](https://github.com/hadley/devtools):
```{r eval = FALSE}
install.packages("devtools")
devtools::install_github("MKLau/Rclean")
```
You will also likely need to install the
[RGraphViz](bioconductor.org/packages/release/bioc/html/Rgraphviz.html):
```{R install_rgraphviz, eval = FALSE}
install.packages("BiocManager")
BiocManager::install("Rgraphviz")
```
Once installed, per usual R practice just load the *Rclean* package
with:
```{r eval = TRUE}
library(Rclean)
```
Usage
=====
```{r eval = TRUE, echo = FALSE, results = "hide"}
library(CodeDepends)
script <- system.file(
"example",
"simple_script.R",
package = "Rclean")
```
*Rclean* usage is simple. Have a script with code you want to clean
saved to disk. Then, just run the `clean` function with the path to
the script as the input. Here, we can use an example script that is
included with the package:
```{r eval = FALSE}
script <- system.file("example", "simple_script.R", package = "Rclean")
```
Here's a quick look at the code:
```{r eval = TRUE}
readLines(script)
```
You can get a list of the variables found in an object with
`get_vars`.
```{r eval = TRUE}
get_vars(script)
```
Sometimes for more complicated scripts, it can be helpful to see a
network graph showing the interdependencies of
variables. `code_graph` will produce a network diagram showing which
lines of code produce or use which variables:
```{r eval = TRUE, out.width = "75%", dpi = 300}
code_graph(script)
```
Now, we can pick the result we want to focus on for cleaning:
```{r eval = TRUE}
clean(script, "tab.15")
```
We can also select several variables at the same time:
```{r eval = TRUE}
my.vars <- c("tab.12", "tab.15")
clean(script, my.vars)
```
While just taking a look at the simplified code can be very helpful,
you can also save the code for later use or sharing (e.g. creating a
reproducible example for getting help) with `keep`:
```{r eval = FALSE}
my.code <- clean(script, my.vars)
keep(my.code, file = "results_tables.R")
```
If you would like to copy your code to your clipboard, you can do that
by not specifying a file path. You can now paste the simplified as needed.
```{r eval = FALSE}
keep(my.code)
```
Contributing
============
This is an open-source project. If you would like to contribute to the
project, please check out [CONTRIBUTING.md](CONTRIBUTING.md).
Please note that the 'Rclean' project is released with a
[Contributor Code of Conduct](CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.
