Ebedthan/asda

An interactive web atlas for exploring predicted soil bacterial diversity across Sub-Saharan Africa # Africa Soil Diversity Atlas An interactive web atlas for exploring predicted soil bacterial diversity across Sub-Saharan Africa, derived from 16S rRNA amplicon sequencing of ~810 soil samples across 9 countries. Built with R and Shiny. Deployed on Posit Connect. ## Overview This atlas serves spatially continuous predictions of Hill diversity indices and evenness at 0.05° resolution (~5 km), estimated from Bayesian hierarchical models fitted to soil microbiome data from BioProject PRJNA807934. Users can query predicted diversity values at any location in Sub-Saharan Africa by clicking the map or hovering the cursor over it. ### Countries covered Benin, Botswana, Côte d'Ivoire, Kenya, Mozambique, Namibia, South Africa, Zambia, Zimbabwe ### Diversity indices available | Layer | Symbol | Unit | |---|---|---| | Species richness | q = 0 | ASVs | | Shannon diversity | q = 1 | Effective species | | Simpson diversity | q = 2 | Effective species | | Evenness | logE | - | All layers are served as **mean prediction** alongside a **90% posterior predictive interval (PPI)**, reflecting the full uncertainty from the underlying Bayesian model. ## Repository structure ``` . ├── global.R # Startup: loads rasters, defines metadata & helpers ├── ui.R # Full-screen map layout with floating panels ├── server.R # Reactive logic: layer swap, map click, cursor tooltip ├── R/ │ ├── mod_map.R # Map Shiny module │ ├── mod_predict.R # Prediction Shiny module │ └── utils.R # Utility functions ├── www/ │ └── atlas.css # Custom CSS (dark forest-green theme) ├── data/ # Pre-computed raster predictions (not tracked by git) │ ├── pred_mean_D0.tif │ ├── pred_mean_D1.tif │ ├── pred_mean_D2.tif │ ├── pred_mean_logE.tif │ ├── pred_mean_D0_even.tif │ ├── pred_ppi90_D0.tif │ ├── pred_ppi90_D1.tif │ ├── pred_ppi90_D2.tif │ ├── pred_ppi90_logE.tif │ └── pred_ppi90_D0_even.tif └── sda.Rproj ``` > **Note:** The …