Cave Fauna of Greece — Analysis

Scripts and outputs for the CFG database, which tracks species occurrences across Greek cave sites.

---

Requirements

• R ≥ 4.6
• System libraries: GDAL, GEOS, PROJ (required by sf)

Restore the exact R package environment:

Rscript -e "renv::restore()"

---

Data

Download the five TSV exports from the CFG database admin panel and place them in data/. File names are auto-detected by pattern — no path changes needed in scripts.

Pattern	Contents
Caves_*.tsv	Cave locations, coordinates, region, protection
Census_*.tsv	Species occurrence records
Species_*.tsv	Taxonomy, classification, conservation status
Census_references_*.tsv	References for census records
Cave_References_*.tsv	References for cave records

---

Running the analysis

All commands run from the repo root. Scripts must be run in order.

# 1. Spatial analysis — run first (produces island areas and richness map)
Rscript scripts/cfg_spatial_analysis.R

# 2. Geology
Rscript scripts/cfg_geology.R

# 3. Thematic questions (any order after steps 1–2)
Rscript scripts/cfg_questions.R
Rscript scripts/cfg_questions_caves.R
Rscript scripts/cfg_questions_islands.R
Rscript scripts/cfg_questions_species.R
Rscript scripts/cfg_questions_temporal.R

# 4. Website figures
Rscript scripts/cfg_website_plots.R

# 5. Composite figures for publication (PNG + TIFF, 300 DPI)
Rscript scripts/cfg_composite_figures.R

Outputs are written to results/ (TSVs), plots/ (individual figures), and figures/ (composite publication figures).

---

Repository layout

scripts/        analysis scripts
data/           TSV exports from CFG database (not tracked)
spatial_data/   shapefiles (not tracked)
results/        computed TSVs
plots/          individual figure PNGs
figures/        composite figures (PNG + TIFF)
website_plots/  figures for the database portal
renv.lock       pinned R package versions