Impact of Cover Crops on Nitrous Oxide Emissions in Sorghum Systems

This repository contains data and analysis scripts for a study investigating the impact of cover crops on nitrous oxide (N₂O) emissions in sorghum systems. The study compares N₂O fluxes from sorghum and sorghum intercropped with rye, as well as other treatments including corn and soy.

📊 Reproducible Research Companion

New! We've created a comprehensive Reproducible Research Companion document that consolidates all analysis code for the manuscript "Integrating Winter Cover Crops With Biomass Sorghum Can Reduce Nitrogen Losses".

This document includes:

• ✅ Complete code for all 5 figures and 2 tables in the manuscript
• ✅ Scientific context for each analysis
• ✅ Clean, publication-ready code with exploratory analysis removed
• ✅ Consistent styling and transparent methodology
• ✅ Self-contained HTML output suitable for sharing

Viewing the Companion

Visit the GitHub Pages site to view the rendered document, or open Reproducible_Research_Companion.qmd locally to see the source code.

Rendering Locally

To render the document yourself:

# Install Quarto if needed: https://quarto.org/docs/get-started/
quarto render Reproducible_Research_Companion.qmd

Note: Figure 5 (Biomass Yields) requires sorghum biomass data files that are stored externally. The code is provided with eval: false to show the complete workflow. Users with access to these files can update the paths and enable execution.

Data: data/clean_leaching.csv

This file contains cleaned, plot‑level tile drainage data used for the nitrate leaching analyses (Figure 3 and related tables). Each row represents a date × plot observation with flow, concentration, and derived nitrogen loss fields.

Key columns (units):

• date: Sampling date (YYYY‑MM‑DD).
• year: Year extracted from date.
• plot: Plot identifier (string; leading zeros preserved in some plots).
• treatment: Treatment label (e.g., Sorghum, Sorghum + Rye, Corn, Soy).
• flow_gallons: Drain flow volume (gallons).
• flow_l: Drain flow volume (liters).
• nitrate_mg_ml: Nitrate concentration; stored as mg/L (naming legacy).
• ammonia_mg_l: Ammonium concentration (mg/L).
• nitrate_loss_mg: Nitrate‑N mass loss (mg).
• ammonia_loss_mg: Ammonium‑N mass loss (mg).
• total_n_loss_mg: Total inorganic N loss (mg) = nitrate + ammonium.
• cumulative_flow_l: Cumulative flow by plot and year (liters).
• cumulative_n_loss_mg: Cumulative total N loss by plot and year (mg).
• sample_y_n, approx_nitrate_mg_l, approx_ammonia_mg_l: Sampling flags and imputed concentration fields used during cleaning.

Leaching loss calculation used in the manuscript:

1. Per‑day N loss (kg N ha⁻¹ d⁻¹): daily_n_loss_kgha = (total_n_loss_mg / 1e6) / plot_area_ha
2. Annual cumulative leaching per plot (kg N ha⁻¹): annual_cumulative_leaching = (max(cumulative_n_loss_mg) / 1e6) / plot_area_ha

Where plot_area_ft2 = 120 * 160 and plot_area_ha = plot_area_ft2 / 107639.1041671.

These are the values used for annual treatment comparisons, statistical tests, and the leaching panels in the manuscript.