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RE-rosgen

Research activity applying reproducibility principles to a GIS-based implementation of Rosgen Stream Classification.

Templates for Reproducible and Replicable Research

A template repository that contains a folder structure, template documents, and best practice suggestions for conducting reproducible geographic research. The folder structure presented here can be used to

  1. pre-register, document, and share original research, or
  2. document, organize, and share a reproduction and/or replication of original research.

An overview of the folder structure of this repository is provided below. The README.md and index.csv files contained in each folder provide details about the structure of that folder and suggestions on its use. The docs/report/ folder contains templates to facilitate 1) the pre-registration of original research, and 2) report the complete details of attempted reproductions and replications of original research.

Repository Overview

Reproduction of <Study Name>
|- docs/           # study documentation
|  +- instruction/ # materials for teaching
|  +- manuscript/  # manuscript components
|  +- presentation/# materials for teaching
|  +- report/      # preanalysis plan, reproduction/replication report
|
|- data/           # raw data, which are not changed once created
|  +- raw/         # raw data, will not be altered
|  	  +- private/  # for private/confidential data or data too large to version control
|  	  +- private/  # for public data to be version controlled
|  +- derived/     # derived data, will not be altered once created
|  	  +- private/  # for private/confidential data or data too large to version control
|  	  +- private/  # for public data to be version controlled
|  +- scratch/     # temporary files that can be safely deleted or lost; no version control
|  +- metadata/    # documentation of metadata
|
|- procedure/      # methods documentation
|  +- code/        # any programmatic code, clearly named and commented
|  +- environment/ # documentation of the hardware and software environment
|  +- protocols/   # any non-computational protocols
|
|- results         # all output from workflows and analyses
|  +- figures/     # graphs, likely designated for manuscript
|  +- maps/        # maps, likely designated for manuscript  
|  +- other/       # diagrams, images, and other non-graph graphics
|
|- readme.md       # the top level description of content
|- study.Rmd       # executable Rmarkdown , if applicable
|- Makefile        # executable Makefile, if applicable
|- study.Rproj     # RStudio project, if applicable
|- .gitignore      # Git Ignore instructions to ignore systems files, private data, and scratch data

Reproducible Research Practices

Every research project is different. This repository is designed to serve as a flexible guide capable of structuring work completed throughout the lifecycle of different types of research project. No matter the project type, a few key suggested practices when using this repository include:

  • Keeping original, raw data in the data/raw folder. Do not alter that file during data analysis.
  • Keeping data derived from the raw data (e.g. subsets) separate from the raw data in the data/derived folder.
  • Keeping Exploratory/experimental outputs in the data/Scratch folder. Files in this folder should be able to be deleted without negatively impacting the project.
  • Limiting manual changes to data. Conduct as much data processing and analysis as possible with code.
  • Keeping code in simple text files that are human readable.
  • Explicitly tying procedural documents or code together so it is clear how things work together
  • Creating a top-level Makefile or Rmarkdown file that documents computational work in executable form.
  • Providing a executable electronic research compendia that shares the entire computational environment
  • Keeping a README in each folder, describing the purpose of the directory and its contents.
  • Maintaining a formal metadata descriptor at the root of the package that describes all the important input and output data files.

References

The structure of this repository closely follows the excellent rr-init repository, which in turn follows Nobel (2009). We have also incorporated structural ideas from Gandrud (2015) and Camerer et al. (2016, 2018). Reference information related to the Pre-registration Template and Replication Report Template is included in the /docs folder.