Add support for continuous declining increment growth; use display names for species in dashboard

configs/declining_increment.yaml

@@ -1,4 +1,5 @@
 growth_model: declining_increment
+continuous_growth: true
 
 species:
   - name: "species_A"  # Rhizophora spp.

dashboard/app.py

@@ -25,6 +25,12 @@ MODEL_CONFIGS = {
     "Declining Increment": "configs/declining_increment.yaml"
 }
 
+# Add a mapping for display names
+SPECIES_DISPLAY_NAMES = {
+    'species_A': 'Rhizophora spp.',
+    'species_B': 'Avicennia germinans'
+}
+
 # Helper to update planting schedule in a config file
 def update_planting_schedule(config_path, year_areas):
     with open(config_path) as f:
@@ -39,7 +45,7 @@ def create_survival_table(model):
     """
     years = range(1, model.project.duration_years + 1)
     data = {"Year": []}
-    species_names = [s.name for s in model.species]
+    species_names = [SPECIES_DISPLAY_NAMES.get(s.name, s.name) for s in model.species]
     for name in species_names:
         data[name] = []
     data["Total Surviving Trees"] = []
@@ -113,8 +119,9 @@ def create_growth_increment_plots(config, model_type=None):
     years = np.arange(1, config["project"]["duration_years"] + 1)
     fig = make_subplots(rows=2, cols=2, subplot_titles=("DBH Growth", "HEIGHT Growth", "DBH Annual Increment", "HEIGHT Annual Increment"))
     from src.er_model import ERModel
+    use_continuous = config.get('continuous_growth', False)
     for sp in config["species"]:
-        name = sp["name"]
+        name = SPECIES_DISPLAY_NAMES.get(sp["name"], sp["name"])
         initial_dbh = sp["initial_values"]["dbh"]
         initial_height = sp["initial_values"]["height"]
         if model_type == "linear":
@@ -130,8 +137,12 @@ def create_growth_increment_plots(config, model_type=None):
         elif model_type == "declining_increment":
             dbh_params = sp["declining_increment"]["dbh"]
             height_params = sp["declining_increment"]["height"]
-            dbh = [ERModel.declining_increment_growth(t, dbh_params, initial_dbh) for t in years]
-            height = [ERModel.declining_increment_growth(t, height_params, initial_height) for t in years]
+            if use_continuous:
+                dbh = [ERModel.continuous_declining_increment_growth(t, dbh_params, initial_dbh) for t in years]
+                height = [ERModel.continuous_declining_increment_growth(t, height_params, initial_height) for t in years]
+            else:
+                dbh = [ERModel.declining_increment_growth(t, dbh_params, initial_dbh) for t in years]
+                height = [ERModel.declining_increment_growth(t, height_params, initial_height) for t in years]
         else:  # Default to Chapman-Richards
             dbh_params = sp["chapman_richards"]["dbh"]
             height_params = sp["chapman_richards"]["height"]
@@ -188,7 +199,7 @@ def create_all_plots(results, species_results, config):
     from src.er_model import ERModel
     growth_model = config.get('growth_model', 'chapman_richards')
     for sp in config["species"]:
-        name = sp["name"]
+        name = SPECIES_DISPLAY_NAMES.get(sp["name"], sp["name"])
         initial_dbh = sp["initial_values"]["dbh"]
         initial_height = sp["initial_values"]["height"]
         if growth_model == "linear":
@@ -251,14 +262,14 @@ def create_summary(results, species_results, config, model):
     for m in milestones:
         if m <= years:
             surv = model.calculate_total_surviving_trees(m)
-            surv_str = ", ".join([f"{k}: {v:,.0f}" for k, v in surv.items()])
+            surv_str = ", ".join([f"{SPECIES_DISPLAY_NAMES.get(k, k)}: {v:,.0f}" for k, v in surv.items()])
             survival_lines.append(f"Year {m} surviving trees: {surv_str}")
     # Per hectare (final year)
     surv_30 = model.calculate_total_surviving_trees(years)
     per_ha_lines = []
     for k, v in surv_30.items():
         per_ha = v / total_area if total_area > 0 else 0
-        per_ha_lines.append(f"{k}: {per_ha:,.0f} trees/ha")
+        per_ha_lines.append(f"{SPECIES_DISPLAY_NAMES.get(k, k)}: {per_ha:,.0f} trees/ha")
     summary = (
         f"Project Overview:\n----------------\nDuration: {years} years\nTotal Area Planted: {total_area:,.0f} ha\nBuffer Pool: {config['carbon']['buffer_percentage']}%\n\n"
         f"Carbon Sequestration:\n-------------------\nTotal Gross Carbon (Year {years}): {final_gross:,.0f} tCO2\nTotal Net Carbon (Year {years}): {final_net:,.0f} tCO2\nAverage Annual Gross: {avg_annual_gross:,.0f} tCO2/yr\nAverage Annual Net: {avg_annual_net:,.0f} tCO2/yr\n\n"
@@ -275,6 +286,12 @@ with gr.Blocks() as demo:
     gr.Markdown("# Mangrove ER Model Dashboard\nDeclining Increment Model Only")
     with gr.Tabs():
         with gr.Tab("Declining Increment"):
+            config = yaml.safe_load(open(MODEL_CONFIGS["Declining Increment"]))
+            use_continuous = config.get('continuous_growth', False)
+            if use_continuous:
+                gr.Markdown("**Mode:** Continuous declining increment growth (analytical formula)")
+            else:
+                gr.Markdown("**Mode:** Discrete declining increment growth (sum of annual increments)")
             gr.Markdown("## Planting Schedule (ha per year)")
             year_1 = gr.Number(value=2500, label="Year 1 Area (ha)")
             year_2 = gr.Number(value=2500, label="Year 2 Area (ha)")

src/er_model.py

@@ -203,6 +203,13 @@ class ERModel:
             total += frac * increment
         return total
 
+    @staticmethod
+    def continuous_declining_increment_growth(age: float, params: Dict[str, float], initial_value: float) -> float:
+        r0 = params["r0"]
+        T_m = params["T_m"]
+        # Continuous formula: initial + r0 * (age - age^2/(2*Tm))
+        return initial_value + r0 * (age - age**2 / (2 * T_m))
+
     def calculate_carbon_for_species(self, species: Species, age: int, area: float) -> float:
         """
         Calculate carbon sequestration for a single species and age.