Giter VIP home page Giter VIP logo

bio-mate's Introduction

Readme

Where do I start?

You can load this project in RStudio by opening the file called 'NPQ_correction.Rproj'.

Project structure

File Description Usage
README.md Description of project Human editable
NPQ_correction.Rproj Project file Loads project
LICENSE User permissions Read only
.worcs WORCS metadata YAML Read only
preregistration.rmd Preregistered hypotheses Human editable
prepare_data.R Script to process raw data Human editable

Reproducibility

This project uses the Workflow for Open Reproducible Code in Science (WORCS) to ensure transparency and reproducibility. The workflow is designed to meet the principles of Open Science throughout a research project.

  • To learn how WORCS helps researchers meet the TOP-guidelines and FAIR principles, read the preprint at https://osf.io/zcvbs/
  • To get started with worcs, see the setup vignette
  • For detailed information about the steps of the WORCS workflow, see the workflow vignette
  • For a brief overview of the steps of the WORCS workflow, see below.

WORCS: Steps to follow for a project

Phase 1: Study design

  1. Create a (Public or Private) remote repository on a 'Git' hosting service
  2. When using R, initialize a new RStudio project using the WORCS template. Otherwise, clone the remote repository to your local project folder.
  3. Add a README.md file, explaining how users should interact with the project, and a LICENSE to explain users' rights and limit your liability. The worcs project template does this automatically.
  4. Optional: Preregister your analysis by committing a plain-text preregistration and tagging the commit as "preregistration".
  5. Optional: Upload the preregistration to a dedicated preregistration server
  6. Optional: Add study Materials to the repository

Phase 2: Writing and analysis

  1. Create an executable script documenting the code required to load the raw data into a tabular format, and de-identify human subjects if applicable
  2. Save the data into a plain-text tabular format like .csv. When using open data, commit this file to 'Git'. When using closed data, commit a checksum of the file, and a synthetic copy of the data.
  3. Write the manuscript using a dynamic document generation format, with code chunks to perform the analyses.
  4. Commit every small change to the 'Git' repository
  5. Cite essential references with @, and non-essential references with @@

Phase 3: Submission and publication

  1. Use dependency management to make the computational environment fully reproducible
  2. Optional: Add a WORCS-badge to your project's README file
  3. Make a Private 'Git' remote repository Public
  4. Optional: Create a project page on the Open Science Framework
  5. Connect your 'OSF' project page to the 'Git' remote repository
  6. Add an open science statement to the Abstract or Author notes, which links to the 'Git' remote repository or 'OSF' page
  7. Render the dynamic document to PDF
  8. Optional: Publish the PDF as a preprint, and add it to the OSF project
  9. Submit the paper, and tag the release of the submitted paper, as in Step 3.

Notes for cautious researchers

Some researchers might want to share their work only once the paper is accepted for publication. In this case, we recommend creating a "Private" repository in Step 1, and completing Steps 13-18 upon acceptance.

bio-mate's People

Contributors

kimbaldry avatar

Watchers

Michael Sumner avatar Rob Johnson avatar  avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.