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/ │ │ ├── searchstrategyfinal.doc ← final search syntax across databases │ │ ├── screeninglog.csv ← records screened at each stage │ │ └── includedstudiesraw.xlsx ← initial table of included studies │ └── processed/ │ ├── includedstudiesclean.csv ← cleaned and annotated study table │ └── screeningcounts.yaml ← counts for prisma flow diagram ├── scripts/ │ ├── parseincludedstudies.R ← cleans raw table to csv │ └── generateprismaflow.R ← creates prisma-scr flow diagram ├── figures/ │ ├── figure1prismaflow.png ← prisma-scr flow diagram │ ├── figure2geographicdistribution.png ← map of study locations │ ├── figure3publicationtrend.png ← temporal trend chart │ └── READMEfigures.md ← naming and generation notes ├── supplementary/ │ ├── supplementary-1prisma-scr.pdf ← completed prisma-scr checklist │ ├── supplementary-2included-studies.xlsx← final table of included studies │ └── supplementary-3search-strategy.pdf ← formatted search strategy ├── docs/ │ ├── contributing.md ← guide for issues & pull requests │ ├── codeofconduct.md ← contributor covenant │ └── citation.md ← how to cite this repository └── .github/ ├── workflows/ci.yml ← github actions for ci and link checks ├── ISSUETEMPLATE/bugreport.md ← template for reporting bugs └── PULLREQUESTTEMPLATE.md ← template for pull requests data description screening log (data/raw/screening_log.csv) purpose: records counts at each screening stage: identified, deduplicated, screened, full-text assessed, and included

columns:

stage – screening stage name

count – number of records

included studies (data/raw/includedstudiesraw.xlsx) purpose: initial extraction of study details from peer-reviewed clinical/epidemiological publications

columns:

author_year – lead author and publication year

country – study location

design – study design (cohort, case-control, descriptive)

population – age group or clinical setting

n_cases – number of BWF cases

n_controls – number of comparison or control subjects

cfr – case fatality ratio (%)

features – main clinical or diagnostic findings

notes – additional context

After running scripts/parseincludedstudies.R, you will find data/processed/includedstudiesclean.csv with standardized column names, computed CFR percentages, and cleaned notes.

installation & environment setup system requirements operating system: windows, macos, or linux

r: version ≥ 4.0.0 (https://cran.r-project.org/)

r packages: readxl, janitor, dplyr, PRISMAstatement, yaml, sf, ggplot2

clone the repository bash Copy git clone https://github.com/YourUser/bwf-scoping-review.git cd bwf-scoping-review install r dependencies r Copy install.packages(c( "readxl", "janitor", "dplyr", "PRISMAstatement", "yaml", "sf", "ggplot2" )) workflow 1: data management & table preparation see scripts/parseincludedstudies.R for detailed steps to:

read raw excel table

clean column names and formats

calculate case fatality ratios

export data/processed/includedstudiesclean.csv

workflow 2: prisma flow diagram see scripts/generateprismaflow.R for instructions to:

load screening counts from data/processed/screening_counts.yaml

generate a prisma-scr flow diagram object

save as figures/figure1prismaflow.png

running the pipeline after setting up data and r environment:

bash Copy Rscript scripts/parseincludedstudies.R Rscript scripts/generateprismaflow.R verify that:

data/processed/includedstudiesclean.csv exists

figures/figure1prismaflow.png was generated

how to cite if you use any data or code from this repository, please cite:

Paasi, G.; Okwware, S.; Olupot-Olupot, P. (2025). the resurgence of Blackwater Fever among children in sub–Saharan Africa: a scoping review Zenodo. https://doi.org/10.5281/zenodo.15647335

license this repository is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0). see LICENSE.md for full terms.

zenodo deposition after creating a release (e.g., v1.0.0), zenodo will archive it and mint a DOI. update zenodo.json with:

json Copy { "title": "Blackwater Fever scoping review repository", "upload_type": "dataset", "description": "Data and code for a scoping review on blackwater fever among children in sub–Saharan Africa, including search strategies, extracted tables, prisma-scr flow diagram, and analysis scripts. Licensed under CC BY 4.0.", "creators": [ { "name": "Paasi, George", "https://orcid.org/0000-0001-6360-0589" }, { "name": "Olupot-Olupot, Peter" } ], "license": "CC-BY-4.0" }

contact information lead author george paasi, MPH, Advanced-FETP clinical trials dept., mbale clinical research institute busitema university faculty of health sciences mbale, uganda email: georgepaasi8@gmail.com

for issues or suggestions, please open an issue or pull request.

vbnet Copy

LICENSE.md

```markdown Creative Commons Attribution 4.0 International License

Copyright (c) 2025 George Paasi