Data Cleaning Pipeline Documentation and Instructions

Compiled by: Rosie Howard, 2024
Edits and contributions: Zoran Nesic, Sara Knox, June Skeeter, Paul Moore, and other EcoFlux Lab members and affiliates.

Revisions:
- October 2024: these are the “quick-start” instructions for new users of the data-cleaning pipeline. The full documentation will be made available at a later date.

Useful links

• Link to Overview of Data Cleaning Pipeline slides presented during FLUXNET-CH4 V2.0 Workshop (on Day 1: Afternoon, and Day 2: Morning and Afternoon).
• Link to YouTube playlist of ALL presentations from FLUXNET-CH4 V2.0 Workshop.

Documentation outline

1. Motivation: The Importance of Flux Data Standardization and Reproducibility
    1.1  Note on EddyPro Processing of High Frequency Data
   

2. Software Installation
    2.1  Install Software: Git, and Create Github account (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: Project Directory Structure

5. Quick Start: Create Database
    5.1  Quick Start: Create Database and Visualize
   

6. Quick Start: Create INI Files for Data Cleaning
    6.1  Quick Start: First Stage INI File
    6.2  Quick Start: Second Stage INI File
    6.3  Quick Start: Third Stage and Ameriflux Output
   

7. Data Visualization
    7.1  Matlab plotApp
    7.2  R-Shiny App
   

8. Troubleshooting and FAQ
    8.1  Recommended Software Versions