fluxtools v0.3.0

Interactive Shiny application for QA/QC for eddy covariance data processing.
Designed to streamline the post‐processing of eddy covariance datasets (e.g., after EddyPro, physical boundary filtering) to detect and remove outliers, and generate reproducible R code for QA/QC public repository submission (i.e., AmeriFlux).

Fluxtools is an independent project and is not affiliated with or endorsed by the AmeriFlux Network. “AmeriFlux” is a registered trademark of Lawrence Berkeley National Laboratory and is used here for identification purposes only.

If you use fluxtools in your workflow, please cite the use of this product.

If you use fluxtools in your workflow, please cite: Key, K. (2025). fluxtools (version 0.3.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.15597159

Table of Contents

• Key Features
  
• Installation
  
• Quickstart
  
• Data Requirements
  
• How It Works
  • Timestamp Parsing & Time Zones
    
  • Interactive QC & Selection
    
  • Outlier Detection
    
  • Code Generation & Copy-All
    
• Download & Reset
  
• Vignette & Docs
  
• Citation
  
• License

Key Features

• Interactive Scatter Plot
  Choose any numeric variable for X (often TIMESTAMP_START) and Y; drag a box or lasso to flag points

• Multi-Year Support
  Upload up to 500 MB of flux‐tower CSV (all years by default, or pick a subset by year)

• Dark/Light Mode
  Toggle UI theme on the fly (switch is in the bottom-right of the side panel)

• ±σ Outlier Highlighting
  Use the slider to mark points beyond N standard deviations from a linear fit; click Select ±σ outliers to add them

• Accumulate & Undo

  • Select data current selection to an accumulated list across variables
  • Clear Selection individual points or clear outliers and selections

• Confirm Removal
  Hit Apply removals to convert flagged Y-values to NA in your data frame and immediately refresh the plot.

• Export Cleaned Data
  Download a .csv with removed points set to NA plus an R-script of all your removal code in one go.

Installation

```r # Install from CRAN install.packages(“fluxtools”)

Install from directly from GitHub

library(devtools) devtools::install_github(“kesondrakey/fluxtools”)

#Load fluxtools and launch the QA/QC application: library(fluxtools)

Add the UTC offset for your flux tower site (e.g., UTC-5 for EST)

run_flux_qaqc(-5)