jaeyk / makereproducible

R package for making a project computationally reproducible before sharing it

makereproducible

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

Author: Jae Yeon Kim

File an issue if you have problems, questions or suggestions.

Installation

## 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 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(). 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 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)

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

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

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 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. (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