https://github.com/jaeyk/makereproducible

R package for making a project computationally reproducible before sharing it
https://github.com/jaeyk/makereproducible

here r reproducibility transparency

Last synced: about 1 month ago
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R package for making a project computationally reproducible before sharing it

• Host: GitHub
• URL: https://github.com/jaeyk/makereproducible
• Owner: jaeyk
• License: mit
• Created: 2020-06-05T20:03:26.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-10-10T23:25:45.000Z (about 4 years ago)
• Last Synced: 2024-08-04T00:11:33.122Z (5 months ago)
• Topics: here, r, reproducibility, transparency
• Language: R
• Homepage: https://jaeyk.github.io/makereproducible/
• Size: 67.4 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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• awesome-dlab - makereproducible

README

        

# makereproducible

An R Package for Making a Project Computationally Reproducible Before Sharing it

Author: [Jae Yeon Kim](https://jaeyk.github.io/)

File an [issue](https://github.com/jaeyk/makereproducible/issues) if you have problems, questions or suggestions.

## Installation

```r

## Install the current development version from GitHub

devtools::install_github("jaeyk/makereproducible",

        dependencies = TRUE)

library(makereproducible)

```

## Usage

### `make_here`

[Creating self-contained projects is great](https://swcarpentry.github.io/r-novice-gapminder/02-project-intro/) to increase research reproducibility and make your life easier. To make a project self-contained, one of the things you need to do is [**STOP** using `setwd()` and **START** using alternatives like `here()`](https://github.com/jennybc/here_here). The problem is people, including, and especially me, are lazy. We know the best practice, but we don't follow it.

The `make_here()` function nudges you to make your project self-contained before sharing it with other people. It does this by saving typing time to turn [the relative or absolute path](https://r4ds.had.co.nz/workflow-projects.html) in your R code into the arguments in the `here()` function.

To learn how to use it, see the examples below.

1. Not self-contained because this absolute path only works in my laptop! (**BAD**)

```r

read_csv("/home/jae/validating-two-linked-fates/raw_data/sub-data.txt")

```

2. Voila! Now, the project is self-contained. (**GOOD**)

```r

read_csv(make_here("/home/jae/validating-two-linked-fates/raw_data/sub-data.txt"))

```

## Instructions

**Only two conditions** are needed to make the `make_here()` function work.

- I assume that you created a main directory for your project (e.g., `foo`) and divided different types of files into different subdirectories (`data`, `R`, etc.).

- I assume that you did [one of the followings](https://github.com/jennybc/here_here#the-fine-print) required by `here` package:

  - Had a checkout from a version control system like Git. (e.g., You have a subdirectory named `.git`.)

  - [Made your project an RStudio project.](https://r4ds.had.co.nz/workflow-projects.html) (**strongly recommended**)

  - Put an empty file named `.here` in the main project directory (**minimal effort**).

- `here::dr_here()` helps to check whether these two conditions were met. If setup correclty, you should be able to see something like the following: `here() starts at [your main project directory], because it [satisfies one of the conditions listed above].`

## How to cite

If you would like to cite, please do something like the following:

```

Jae Yeon Kim. (2020). makereproducible. R package version 0.1.0. Retrieved from https://github.com/jaeyk/makereproducible

```