Vegetation Ecology Analysis Pipeline

Analysis pipeline for vegetation community data (trees, shrubs, herbs, regeneration) with environmental correlates.

Requirements

• R >= 4.3.0
• renv for dependency management

Quick Start

cd 03_analysis
Rscript run_all.R

Or using Make:

cd 03_analysis
make all

Project Structure

01_data/          # READ-ONLY input data
02_manuscripts/   # Manuscript drafts (not overwritten by pipeline)
03_analysis/      # All generated artifacts

Pipeline Stages

Script	Description
01_setup.R	Environment setup, package loading, path configuration
02_data_inspect_qc_harmonize.R	Data inspection, QC, harmonization
03_build_matrices.R	Build community matrices
04_nmds_envfit.R	NMDS ordination with environmental fitting
05_permanova_dispersion.R	PERMANOVA and dispersion tests
06_cca_vif_permutation.R	CCA with VIF and permutation tests
07_indicator_species.R	Indicator species analysis
08_diversity_regeneration_metrics.R	Diversity and regeneration metrics
09_ml_regeneration_rf_xgb.R	ML models (Random Forest, XGBoost)
10_publication_figures_and_tables.R	Publication-ready outputs

Expected Outputs

• 03_outputs/: Processed data, tables, figures
• 04_results/: Ordinations, statistical tests, indicator species, ML results
• 06_reports/: HTML and PDF reports

Reproducibility

• renv.lock captures exact package versions
• sessionInfo.txt records R session details
• RUN_METADATA.json logs each pipeline run

Data Availability

The data supporting the findings of this study are available in the Supporting Information (Appendices S1–S10). Processed community matrices, environmental predictors, and statistical outputs are archived in the project repository accompanying this submission. A public repository with a DOI will be provided upon manuscript acceptance to ensure reproducibility and transparency: https://github.com/wangdiues/Vegetation_Ecology