# Copilot Instructions for SmartCane Codebase

## Big Picture Architecture
- **Three main components:**
  - `r_app/`: R scripts for crop analysis, package management, and reporting
  - `python_app/` & `python_scripts/`: Python notebooks and scripts for satellite data download and preprocessing
  - `laravel_app/`: Laravel PHP web application for user-facing features
- **Data Flow:**
  - Satellite data is downloaded/preprocessed in Python, stored in `python_scripts/data/`
  - R scripts in `r_app/` analyze, visualize, and report on this data
  - Reports and outputs are saved in `output/`
  - Laravel app may consume outputs for web display (integration is project-specific)

## Critical Developer Workflows
- **R Package Management:**
  - Always run `r_app/package_manager.R` after pulling changes or before analysis
  - Commit `renv.lock` but NOT the `renv/` folder
  - Use `source("r_app/package_manager.R")` in RStudio or `Rscript r_app/package_manager.R` in terminal
- **Crop Analysis:**
  - Main script: `r_app/crop_analysis_messaging.R`
  - Usage: `Rscript crop_analysis_messaging.R [week1] [week2] [farm]`
  - Output: Alerts, summary stats, and recommendations (see `PACKAGE_MANAGEMENT.md` for logic)
- **SAR Analysis & Reporting:**
  - Main report: `r_app/experiments/interactive_sar_visualization/Interactive_SAR_Report.Rmd`
  - Generate with: `rmarkdown::render("Interactive_SAR_Report.Rmd", output_file = "../../../output/Interactive_SAR_Report.html")`
  - Data source: `python_scripts/data/aura/weekly_SAR_mosaic/`
- **Python Data Download:**
  - Notebooks/scripts in `python_app/` and `python_scripts/` handle satellite data acquisition
  - Check `requirements_*.txt` for dependencies
- **Laravel App:**
  - Standard Laravel conventions (see `laravel_app/README.md`)
  - Use `artisan` for migrations, tests, etc.

## Project-Specific Conventions
- **Field Uniformity & Alerting:**
  - Uniformity thresholds and alert logic are defined in `PACKAGE_MANAGEMENT.md`
  - Message categories: 🚨 URGENT, ⚠️ ALERT, ✅ POSITIVE, 💡 OPPORTUNITY
  - Spatial pattern analysis uses Moran's I (see R scripts)
- **Package Management:**
  - Minimum versions enforced for critical R packages (see `PACKAGE_MANAGEMENT.md`)
  - All package changes go through `package_manager.R`
- **Output Files:**
  - Reports and logs go in `output/`
  - Do NOT commit logs or cache folders

## Integration Points & Dependencies
- **R ↔ Python:**
  - R scripts expect preprocessed data from Python scripts
  - Data location conventions: `python_scripts/data/`, `pivot.geojson`
- **R ↔ Laravel:**
  - Laravel may read outputs from R analysis (integration is custom)
- **External:**
  - Sentinel-1 SAR data, field boundaries (GeoJSON), R/Python packages

## Examples
- To run a full crop analysis workflow:
  ```powershell
  Rscript r_app/package_manager.R ; Rscript r_app/crop_analysis_messaging.R 32 31 simba
  ```
- To generate SAR report:
  ```r
  rmarkdown::render("r_app/experiments/interactive_sar_visualization/Interactive_SAR_Report.Rmd", output_file = "output/Interactive_SAR_Report.html")
  ```

## Key Files & Directories
- `r_app/package_manager.R`, `PACKAGE_MANAGEMENT.md`: Package logic & workflow
- `r_app/crop_analysis_messaging.R`: Crop analysis logic
- `r_app/experiments/interactive_sar_visualization/`: SAR analysis & reporting
- `python_scripts/`, `python_app/`: Data download/preprocessing
- `output/`: All generated reports
- `laravel_app/`: Web application

## Environment Notes
- On Windows, R can be found at: `C:\Program Files\R\R-4.4.3\bin\x64\R.exe`

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