coogunkoya-lgtm/Ota-Pipeline---Geochemical-Modelling-and-Ecologycal-Risk

GEOCHEMICAL MODELLING AND ECOLOGICAL RISK OF HEAVY METALS IN INDUSTRIAL AGRICULTURAL SOILS: A PYTHON-DRIVEN APPROACH FROM SOUTHWESTERN NIGERIA # Ota Heavy Metals Python Pipeline A six-module Python pipeline for geochemical contamination indexing and human health risk assessment of heavy metals in agricultural soils, developed for: > Ogunkoya, C. O. "Geochemical Modelling and Ecological Risk of Heavy > Metals in Industrial Agricultural Soils: A Python-Driven Approach from > Southwestern Nigeria." (manuscript under revision, African Scientific > Reports / target journal) ## What this pipeline does Given a single CSV of raw soil metal concentrations (Cu, Pb, Zn, Cd, Hg), this pipeline computes: 1. **Module 1 (`module1_ingestion.py`)** — data validation and detection-limit flagging 2. **Module 2 (`module2_compliance.py`)** — WHO/FAO permissible limit screening 3. **Module 3 (`module3_cf.py`)** — Contamination Factor (CF) 4. **Module 4 (`module4_ecological_risk.py`)** — Hakanson (1980) ecological risk factor (Er) and Risk Index (RI) 5. **Module 5 (`module5_statistics.py`)** — Pearson/Spearman correlation and Shapiro-Wilk normality testing, with Bonferroni multiple-comparison correction 6. **Module 6 (`module6_hhra.py`)** — US EPA RAGS human health risk assessment (CDI, HQ, HI) for adult and child receptors ## Important scope note This pipeline does **not** compute oral carcinogenic risk (CR) for Cd or Pb. The US EPA IRIS database does not provide a validated oral slope factor (CSF) for either metal via the soil ingestion pathway: IRIS provides only an inhalation unit risk for cadmium, and withdrew its quantitative oral slope factor for lead in favour of the IEUBK blood-lead model. Risk characterisation in this pipeline relies exclusively on the non-carcinogenic Hazard Quotient (HQ) / Hazard Index (HI) framework and regulatory exceedance of WHO/FAO soil quality limits. ## Quick start ```bash pip install pandas numpy scipy pytest python run_pipeline.py data/soil_concentrations.csv ``` This writes six CSV files to `outputs/`, one per module, and prints a consolidated console report. ## Running the tests …