EcoFlux Lab
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  1. 4. Quick Start Tutorial - Recommended for First-Time Users
  • Pipeline Documentation
  • 1. Motivation: The Importance of Flux Data Standardization and Reproducibility
    • 1.1   Note: High Frequency Data Processing
  • 2. Software Installation
    • 2.1   Install Software: Git (optional)
    • 2.2   Download Biomet.net Library
    • 2.3   Install Software: Matlab
    • 2.4   Configure Matlab for Biomet.net
    • 2.5   Install Software: R/RStudio
    • 2.6   Install Software: Python (optional)
  • 3. Data Cleaning Principles
  • 4. Quick Start Tutorial - Recommended for First-Time Users
    • 4.1   Quick Start Tutorial: Project Directory Structure and Matlab Configuration
    • 4.2   Quick Start Tutorial: Create Database from Raw Data and Visualize Contents
    • 4.3   Quick Start Tutorial: Create your First Stage INI File for Data Cleaning
    • 4.4   Quick Start Tutorial: Create Your Second Stage INI File for Data Cleaning
    • 4.5   Quick Start Tutorial: Third Stage Cleaning and Converting to Ameriflux Output
  • 5. Full Documentation: Features, Details, and Other Useful Information for Advanced Users
    • 5.1   Full Documentation: Project Directory Structure and Matlab Configuration
    • 5.2   Full Documentation: Create Database from Raw Data and Inspect Contents
    • 5.3   Full Documentation: First Stage INI files
    • 5.4   Full Documentation: Second Stage INI Files
    • 5.5   Full Documentation: Third Stage Cleaning and Converting to Ameriflux Output
  • 6. Data Visualization
    • 6.1   Matlab plotApp
    • 6.2   R-Shiny App
    • 6.3   Other Biomet.net Plotting Tools
  • 7. Troubleshooting and FAQ
    • 7.1   Recommended Software Versions
    • 7.2   Recently Added Features

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  • 4.   Quick Start Tutorial - Recommended for First-Time Users

4.   Quick Start Tutorial - Recommended for First-Time Users

If you are a first-time user of this data-cleaning pipeline, we recommend that you follow this “quick-start” tutorial (all of section 4). We provide sample data and template files along with instructions for creating your first and second stage INI files, editing the relevant third stage configuration files, and outputting your clean data in the correct format for submission to Ameriflux.