Updated allometric equations (incl. generic mangrove ELSE option), planting schedule defaults, and documentation

README.md

@@ -23,21 +23,18 @@ This project implements a flexible, modular dashboard for mangrove carbon seques
 
 ## Usage
 
-1. **Install dependencies:**
+1. **Access the Dashboard (Recommended):**
+   - The Mangrove ER Model Dashboard is hosted online.
+   - **Access it here:** [https://huggingface.co/spaces/mowcom/er-model](https://huggingface.co/spaces/mowcom/er-model)
+
+2. **(Optional) Run Locally for Development:**
    ```bash
-   # Method 1: Using conda (recommended)
+   # Using conda (recommended)
    conda env create -f environment.yml
    conda activate er-model
-   
-   # Method 2: Using pip in existing environment
-   pip install -r requirements.txt
-   ```
-2. **Run the dashboard:**
-   ```bash
-   conda activate er-model  # if using conda
    python dashboard/app.py
    ```
-   The terminal will display a public share link.
+   - To stop the local server, press `Ctrl+C` in the terminal.
 
 ## Growth Models
 - **Declining Increment (ACTIVE):**

configs/declining_increment.yaml

@@ -24,7 +24,7 @@ species:
         r0: 0.43  # m/yr
         T_m: 40  # years
     allometry:
-      equation: "Zanvo et al. 2023: Total = 1.938 × (DBH² H)^0.67628"
+      equation: "Zanvo et al. 2023: Total = 2.0738 × (DBH² H)^0.67628"
     initial_values:
       dbh: 0.1    # cm
       height: 0.2  # m
@@ -51,7 +51,7 @@ species:
         r0: 0.46  # m/yr
         T_m: 40
     allometry:
-      equation: "Zanvo et al. 2023: Total = 1.486 × (DBH² H)^0.55864"
+      equation: "Zanvo et al. 2023: Total = 1.5595 × (DBH² H)^0.55864"
     initial_values:
       dbh: 0.1    # cm
       height: 0.2  # m
@@ -59,11 +59,11 @@ species:
 project:
   duration_years: 30  # matches project_years
   planting_schedule:
-    year_1: 2500  # ha
-    year_2: 2500  # ha
-    year_3: 0  # ha
-    year_4: 0  # ha
-    year_5: 0  # ha
+    year_1: 500
+    year_2: 1500
+    year_3: 1500
+    year_4: 1500
+    year_5: 0
 
 carbon:
   biomass_to_carbon: 0.47  # IPCC default

dashboard/app.py

@@ -276,11 +276,11 @@ The model follows these steps to estimate net CO2 emission reductions:
 **1. Biomass Calculation:** Total above-ground and below-ground biomass per tree is calculated using allometric equations, which typically relate DBH and Height to biomass. For example, using equations from Zanvo et al. (2023):
 - For *Rhizophora spp.* (Species A):
   $$
-  \mathrm{Biomass}_{\mathrm{total}} = 1.938 \times (\mathrm{DBH}^2 \cdot H)^{0.67628}
+  \mathrm{Biomass}_{\mathrm{total}} = 2.0738 \times (\mathrm{DBH}^2 \cdot H)^{0.67628}
   $$
 - For *Avicennia germinans* (Species B):
   $$
-  \mathrm{Biomass}_{\mathrm{total}} = 1.486 \times (\mathrm{DBH}^2 \cdot H)^{0.55864}
+  \mathrm{Biomass}_{\mathrm{total}} = 1.5595 \times (\mathrm{DBH}^2 \cdot H)^{0.55864}
   $$
   *(Note: The specific equations are defined in the model configuration.)*
 

er_model_core/allometry.py

@@ -21,14 +21,16 @@ def calculate_biomass(dbh: float, height: float, species_name: str, params: Dict
     if base <= 0:
         print(f"[ERROR] Non-positive base in calculate_biomass: dbh={dbh}, height={height}, base={base}, species={species_name}")
     # Use Zanvo et al. 2023 equations that include both DBH and height
+    # Use Komiyama et al. 2005 generic mangrove equation for the else statement, the generic for all other mangroves
+    # Note that Komiyama generic equation is used with the average density value of 0.71 g/cm3 found across various mangrove species
     if species_name == "species_A":  # Rhizophora
-        # Total = 1.938 × (DBH² H)^0.67628
-        total_biomass = 1.938 * (dbh**2 * height)**0.67628
+        # Total = 2.0738 × (DBH² H)^0.67628
+        total_biomass = 2.0738 * (dbh**2 * height)**0.67628
     elif species_name == "species_B":  # Avicennia
-        # Total = 1.486 × (DBH² H)^0.55864
-        total_biomass = 1.486 * (dbh**2 * height)**0.55864
+        # Total = 1.5595 × (DBH² H)^0.55864
+        total_biomass = 1.5595 * (dbh**2 * height)**0.55864
     else:
         # Use a conservative generic equation if species not recognized
-        total_biomass = 1.712 * (dbh**2 * height)**0.61746
+        total_biomass = 0.251 * 0.71 * (dbh**2.46)
     
     return total_biomass 

tests/test_er_model.py

@@ -177,11 +177,11 @@ def test_allometric_equation_species_A_B():
     dbh = 10.0  # cm
     height = 5.0  # m
     # species_A (Rhizophora spp.)
-    expected_A = 1.938 * (dbh**2 * height)**0.67628
+    expected_A = 2.0738 * (dbh**2 * height)**0.67628
     result_A = calculate_biomass(dbh, height, "species_A", {})
     assert np.isclose(result_A, expected_A, rtol=1e-6), f"species_A: got {result_A}, expected {expected_A}"
     # species_B (Avicennia germinans)
-    expected_B = 1.486 * (dbh**2 * height)**0.55864
+    expected_B = 1.5595 * (dbh**2 * height)**0.55864
     result_B = calculate_biomass(dbh, height, "species_B", {})
     assert np.isclose(result_B, expected_B, rtol=1e-6), f"species_B: got {result_B}, expected {expected_B}"