Update README and add model-specific READMEs for all growth models

README.md

@@ -1,6 +1,58 @@
-# Mangrove Emissions Reduction (ER) Modeling Suite
+# Mangrove Emissions Reduction Model & Dashboard
 
-A Python toolkit and interactive dashboard for modeling carbon sequestration and tree survival in mangrove restoration projects. Supports multiple growth and mortality models, including Chapman-Richards and Jimenez & Lugo parameterizations.
+This project implements a flexible, multi-model dashboard for mangrove carbon sequestration and emissions reduction, supporting several growth models:
+
+- **Chapman-Richards** (default/original)
+- **Simple Linear**
+- **Linear Plateau**
+- **Declining Increment**
+
+## Features
+- Compare multiple growth models side-by-side in a Gradio dashboard.
+- Each model is configured via a YAML file in `configs/`.
+- Each tab in the dashboard corresponds to a different model.
+- Planting schedule is editable for the Original Model tab.
+- All plots and tables update live.
+- Dashboard can be shared via a public link (`share=True`).
+
+## Usage
+
+1. **Install dependencies:**
+   ```bash
+   conda env create -f environment.yml
+   conda activate er-model
+   ```
+2. **Run the dashboard:**
+   ```bash
+   python dashboard/app.py
+   ```
+   The terminal will display a public share link.
+
+3. **Add new models:**
+   - Add a new YAML config to `configs/` (see examples for structure).
+   - Add an entry to `MODEL_CONFIGS` in `dashboard/app.py`.
+   - Optionally, add a README in the corresponding `models/` subfolder.
+
+## Growth Models
+- **Chapman-Richards:** Flexible sigmoidal growth, suitable for most mangrove species.
+- **Simple Linear:** Constant annual increment.
+- **Linear Plateau:** Linear growth up to a plateau.
+- **Declining Increment:** Annual increment declines linearly to zero; total size is the sum of non-negative increments (never decreases or goes negative).
+
+## File Structure
+- `dashboard/app.py` — Gradio dashboard UI and logic
+- `src/er_model.py` — Core model logic and growth functions
+- `configs/` — Model configuration YAMLs
+- `models/` — Reference model folders (see subfolder READMEs)
+
+## Notes
+- The dashboard is designed for easy extension: just add a config and a tab.
+- All growth models are robust to negative/complex values.
+- Diagnostics are included for debugging growth and biomass calculations.
+
+---
+
+For more details, see the README files in each `models/` subfolder.
 
 ---
 

models/declining_increment/README.md

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+# Declining Increment Model
+
+This folder documents the **Declining Increment** growth model used in the Mangrove ER Dashboard.
+
+- **Growth Model:** Declining Increment (annual increment declines linearly to zero; total size is the sum of non-negative increments)
+- **Parameters:** See `configs/declining_increment.yaml`
+- **Purpose:** For comparison with other models; may be appropriate for species or sites where growth slows with age.
+- **Usage:** Available as a tab in the dashboard for side-by-side comparison.
+
+**Note:** In this model, total DBH and height are calculated by summing annual increments, which decline to zero but never go negative. This ensures that size never decreases or becomes negative. 

models/jimenez_lugo/README.md

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+# Jimenez-Lugo Model
+
+This folder is reserved for the Jimenez-Lugo growth model and related files.
+
+- **Growth Model:** Jimenez-Lugo (alternative parameterization)
+- **Purpose:** For comparison with Chapman-Richards and other models; may be used for specific species or regions where this parameterization is justified.
+- **Status:** Deprecated/not currently used in the dashboard tabs. All references have been removed from the main app, but this folder is retained for archival and reproducibility purposes.
+
+If you wish to re-enable this model, add its config to `configs/` and update `MODEL_CONFIGS` in `dashboard/app.py`. 

models/linear/README.md

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+# Simple Linear Model
+
+This folder documents the **Simple Linear** growth model used in the Mangrove ER Dashboard.
+
+- **Growth Model:** Linear (constant annual increment)
+- **Parameters:** See `configs/linear.yaml`
+- **Purpose:** For comparison with other models; may be appropriate for young plantations or where growth is approximately linear.
+- **Usage:** Available as a tab in the dashboard for side-by-side comparison.
+
+This model is best used for demonstration or for species/sites where linear growth is justified by data. 

models/linear_plateau/README.md

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+# Linear Plateau Model
+
+This folder documents the **Linear Plateau** growth model used in the Mangrove ER Dashboard.
+
+- **Growth Model:** Linear Plateau (linear growth up to a plateau, then constant)
+- **Parameters:** See `configs/linear_plateau.yaml`
+- **Purpose:** For comparison with other models; may be appropriate for species or sites where growth levels off after a certain age.
+- **Usage:** Available as a tab in the dashboard for side-by-side comparison.
+
+This model is useful for scenarios where trees grow rapidly at first, then reach a maximum size. 

models/original/README.md

@@ -1,4 +1,15 @@
-# Original Model
+# Original Model (Chapman-Richards)
+
+**This is the default model and the only one with an editable planting schedule in the dashboard.**
+
+This folder contains reference files and documentation for the **Original Model** used in the Mangrove ER Dashboard.
+
+- **Growth Model:** Chapman-Richards (flexible sigmoidal growth)
+- **Purpose:** Baseline/reference for all comparisons
+- **Parameters:** See `configs/params.yaml`
+- **Usage:** Used in the 'Original Model' tab of the dashboard, with editable planting schedule.
+
+This is the default model for the project and is recommended for most mangrove species unless otherwise justified.
 
 ## Model Overview
 This is the default Chapman-Richards-based mangrove growth and carbon model for the project. It uses species-specific growth curves and DBH-dependent mortality to estimate carbon sequestration and tree survival over time.