Correlation Analysis: Alpha Diversity vs Soil Features Using Rarefied SABR 2023 Data

[jibarozzo]

Objective

Test correlations between alpha diversity metrics and environmental features (nitrate_ppm, ammonia_ppm, n_available, gnha, gwc_g_g) using the multi-iteration rarefied data frame mtr_rrfy_df.

Data Sources

• Input: data/output/processed/sabr_2023_mtr_rrfy_df.rda (multi-iteration rarefied data frame with diversity indices and metadata)
• Metadata: data/output/processed/sabr_2023_metadata_clean.rda (for sample info/covariates)
• Analysis directory for outputs: analysis/
• Plots directory: outputs/plots/

Checklist

• Verify and QC environmental features: nitrate_ppm, ammonia_ppm, n_available, gnha, gwc_g_g
• Explore autocorrelations between features
• Explore univariate correlations (Spearman) between alpha metrics (observed, Shannon, Simpson, inv_simpson) and each feature
• Visualize scatterplots for each alpha-feature pair with rho and p-value annotations
• Adjust for covariates (plant, plot, location, date) in models if indicated by exploratory results
• Fit linear/mixed models if feasible: alpha ~ feature (+ covariates)
• Report FDR-adjusted p-values across all tests
• Summarize results in tables and figures, export to analysis/ and outputs/plots/
• Document script steps and output file paths for reproducibility

Acceptance Criteria

• Results are reproducible from the rarefied data frame
• At least one significant (FDR q < 0.1) association OR a clear null result with power discussion
• All code and outputs are saved to designated directories

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Reference: Issue created to operationalize post-PR #8 workflow for SABR 2023 alpha diversity analysis.

[jibarozzo]

Partially addressed by #10