gpaasi/childhood-blackwater-fever-scoping-review

A comprehensive scoping review of blackwater fever among children in sub-Saharan Africa, including data extraction, PRISMA-ScR workflows, analysis scripts, and visualizations for transparent, reproducible research # blackwater fever scoping review --- ## table of contents 1. overview 2. repository structure 3. data description 4. installation & environment setup 5. workflow 1: data management & table preparation 6. workflow 2: prisma flow diagram 7. running the pipeline 8. how to cite 9. license 10. zenodo deposition 11. contact information --- ## overview this repository contains all materials, data and reproducible workflows to conduct and report a scoping review on blackwater fever among children in sub–saharan africa. it includes raw and processed data, analysis scripts, figures, supplementary files, and detailed documentation to ensure transparency and ease of peer review. **key objectives:** - map prevalence and incidence of blackwater fever in children across sub–saharan africa - characterize clinical features and diagnostic approaches - identify genetic, treatment-related and environmental risk factors - highlight knowledge gaps and propose future research priorities --- ## repository structure ```txt bwf-scoping-review/ ├── README.md ← this file (project overview & instructions) ├── LICENSE.md ← cc by 4.0 license text ├── CITATION.cff ← citation metadata for github/zenodo ├── zenodo.json ← metadata for zenodo deposition ├── data/ │ ├── raw/ │ │ ├── search_strategy_final.doc ← final search syntax across databases │ │ ├── screening_log.csv ← records screened at each stage │ │ └── included_studies_raw.xlsx ← initial table of included studies │ └── processed/ │ ├── included_studies_clean.csv ← cleaned and annotated study table │ └── screening_counts.yaml ← counts for prisma flow diagram ├── scripts/ │ ├── parse_included_studies.R ← cleans raw table to csv │ └── generate_prisma_flow.R ← creates prisma-scr flow diagram ├── figures/ │ ├── f …