Processing of the carbon gas chamber flux, with automatic window detection and manual improvement.

This repository contains a complete processing pipeline for chamber-based carbon flux measurements. This includes automatic and manual window selection, visualisation, and flux computation for CO₂ and CH₄. The code handles the pre-processing and quality control of gas concentration slopes, converting them to fluxes with environmental covariates.

Key components:

1. Raw data splitting (01_raw_data_split.R): Prepares and organizes raw chamber measurement files.
2. Automatic window detection (02_auto_window_detection.R): Identifies candidate flux windows by maximizing linearity (R²) of gas trends.
3. Manual window QC app (03_manual_chamber_window_qc_app.R): Shiny application for visual inspection and adjustment of selected windows, showing mixing ratios, slope diagnostics, air temperature (AT), PAR, etc. Edits are auto-saved on navigation.
4. Flux post-processing (04_ChamberFlux_Postprocessing.R): Computes slopes, derives fluxes using ideal gas assumptions, attaches environmental metrics, and classifies CO₂ flux as ER/NEE.