ibagur/moz-cholera

Shinny app to run data modelling and analysis on daily cholera data in Mozambique # Mozambique Cholera Monitoring Dashboard ## Overview This R-based system provides a comprehensive ETL (Extract, Transform, Load) pipeline and interactive dashboard for monitoring cholera outbreaks in Mozambique. The system processes epidemiological data, generates visualizations, and creates an interactive Shiny web application for real-time cholera surveillance. ## System Architecture The system follows a modular approach with numbered scripts that execute in sequence: ### Core Workflow Scripts | Script | Purpose | Description | |--------|---------|-------------| | `00-init.R` | Initialization | Sets up the tool name and handles file renaming from templates | | `01-moz-cholera-required.R` | Dependencies | Loads all required R packages for mapping, visualization, and data processing | | `02-moz-cholera-functions.R` | Custom Functions | Contains project-specific utility functions | | `03-moz-cholera-config.R` | Configuration | Defines paths, Azure settings, fonts, and system parameters | | `04-moz-cholera-dataload.R` | Data Loading | ETL process for importing and cleaning multiple data sources | | `05-moz-cholera-process.R` | Data Processing | Transforms raw data into analysis-ready formats | | `06-moz-cholera-analysis.R` | Data Analysis | Statistical analysis and calculations | | `07-moz-cholera-plot.R` | Visualization | Creates maps, charts, and interactive plots | | `08-moz-cholera-output.R` | Data Export | Exports processed data to Excel and updates Azure storage | | `09-moz-cholera-render.R` | Report Generation | Renders reports and documentation | ### Main Entry Points - **`moz-cholera.R`** - Main script that orchestrates the entire workflow - **`app.R`** - Shiny web application for the interactive dashboard ## Data Sources The system processes multiple data sources: ### Input Data Types - **Bulletin Files** (PDF/Excel): Daily cholera surveillance reports from DVS - **Partnership Files** (Excel): Information about partner organizations and coverage …