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File Organization

Learning Objectives

  • Evaluate folder and file structure of a project.
  • Recognize common problems that occur in file organization.
  • Distinguish between input and output files.
  • Integrate file naming standards into projects.

Activity 01 - Setting up a new project

Using what we have learned so far, we are going to set up a new project in a way that facilitates reproducibility.

Resources:

  • slides
  • good example 1 of a reproducible project in the wild
  • good example 2 of a reproducible project in the wild

Exercise: Imagine you have just been funded for an exciting new project. Working with a partner, create a folder, directory structure and file naming conventions for the project.

Think about these questions as you create your project:

  • What type of study is this?
  • What kind of data are you going to collect?
  • What are the file formats of the raw data?
  • Will the raw data need transformation / modification before analyses?
  • What types of analyses will you do with the data?
  • How will you store and communicate exploratory analyses and results?
  • What software / scripts will you use to do the analyses?
  • How will you make your figures for an eventual paper?
  • Who are your collaborators?