| tags: [ open science computational reproducibility data science containerisation informatics ] categories: [planning ]

Ropensci

Problem

Replication effort:

There are many sources of error (as to why claim is not supported, or approximate result[significance in same direction, effect size]):

  • actual data is not reflected in code files
  • Can’t match the environment: Missing packages
  • etc, etc, etc

One model of addressing these issues is using Docker:

Docker goes some way to solving this…. BUT: It’s really hard to get docker up and running - you need specialised knowledge of how to get your code and data etc. into docker, and it’s really hard to implement it. Also people don’t know about it so people are using this other model:

Dryad + code + etc. downloading separately….

Proposed solution

The fundamental objective is to create some sort of a tioe-capsule:

The output: Some version of a “docker-like” system where you can:

  1. match the environment such that you can at least get the code to run
  2. run the code, in a make-like manner

The Process

Let’s make going from code, data, packages and instructions to -> docker EASY!! Time capsule your R project.

Analogy: Blogdown for Hugo.

Features of the output <dockerfile>: painless for independent analysts to 1. obtain, 2. re-run. Defining “re-run”: starting step, black box – just output, next steps: the environment is accessible to the independent analyst so they check for implementation validity of the code, check for intermediate outputs, etc. etc.

Consumer perspective, grey box edition:

Expected Outputs

  1. R package - set of commands akin to blogdown for hugo in Rstudio. The user can timecapsule their R project.
  2. Shiny App - This package will be loaded so that the functions are available for implementation in a shinhy app, where the user can simply upload their data + code + etc etc and then hit “TImecapsule my R project”, and the app using the package creates a <docker file>, that the user can then download.