WIP: update files before testing hugging-er build

README.md

@@ -98,6 +98,3 @@ er-chapman-richards/
 - Jimenez, J.A. & Lugo, A.E. (1985, 1987)
 - Zanvo et al. (2023) for allometric equations
 - Field data from Nigeria mangrove sites (2024)
-
-## License
-[License details to be added] 

configs/linear.yaml

@@ -1,74 +0,0 @@
-growth_model: linear
-
-species:
-  - name: "species_A"  # Rhizophora spp.
-    planting_density: 4000  # trees/ha
-    mortality_rates:
-      year_1: 15  # %
-      year_2: 12  # %
-      year_3: 6   # %
-      year_4: 5   # %
-      year_5: 5   # %
-      year_6: 5   # %
-      year_7: 5   # %
-      year_8: 5   # %
-      year_9: 5   # %
-      year_10: 5  # %
-      subsequent: 1.5  # % (years 11-30)
-    linear:
-      dbh:
-        r: 1.83  # cm/yr
-      height:
-        r: 0.61  # m/yr
-    allometry:
-      equation: "Zanvo et al. 2023: Total = 1.938 × (DBH² H)^0.67628"
-    initial_values:
-      dbh: 1.0    # cm
-      height: 0.5  # m
-
-  - name: "species_B"  # Avicennia germinans
-    planting_density: 444  # trees/ha
-    mortality_rates:
-      year_1: 15  # %
-      year_2: 12  # %
-      year_3: 6   # %
-      year_4: 5   # %
-      year_5: 5   # %
-      year_6: 5   # %
-      year_7: 5   # %
-      year_8: 5   # %
-      year_9: 5   # %
-      year_10: 5  # %
-      subsequent: 1.5  # % (years 11-30)
-    linear:
-      dbh:
-        r: 1.2  # cm/yr (example, adjust as needed)
-      height:
-        r: 0.4  # m/yr (example, adjust as needed)
-    allometry:
-      equation: "Zanvo et al. 2023: Total = 1.486 × (DBH² H)^0.55864"
-    initial_values:
-      dbh: 1.0    # cm
-      height: 0.5  # m
-
-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
-
-carbon:
-  biomass_to_carbon: 0.47  # IPCC default
-  carbon_to_co2: 3.67     # molecular weight ratio
-  buffer_percentage: 20    # risk buffer
-  leakage_percentage: 0    # no leakage assumed
-  baseline_emissions: 0    # tCO2/ha/year
-
-scenarios:
-  area: 1000.0  # ha
-  dbh_range: [1.0, 25.0]  # cm
-  height_range: [0.5, 15.0]  # m
-  growth_rate_factor: 1.0 

configs/linear_plateau.yaml

@@ -1,82 +0,0 @@
-growth_model: linear_plateau
-
-species:
-  - name: "species_A"  # Rhizophora spp.
-    planting_density: 4000  # trees/ha
-    mortality_rates:
-      year_1: 15  # %
-      year_2: 12  # %
-      year_3: 6   # %
-      year_4: 5   # %
-      year_5: 5   # %
-      year_6: 5   # %
-      year_7: 5   # %
-      year_8: 5   # %
-      year_9: 5   # %
-      year_10: 5  # %
-      subsequent: 1.5  # % (years 11-30)
-    linear_plateau:
-      dbh:
-        r: 1.83  # cm/yr
-        T_p: 30  # plateau at 30 years
-        a: 11.07  # asymptote from params.yaml
-      height:
-        r: 0.61  # m/yr
-        T_p: 12  # plateau at 12 years
-        a: 11.58  # asymptote from params.yaml
-    allometry:
-      equation: "Zanvo et al. 2023: Total = 1.938 × (DBH² H)^0.67628"
-    initial_values:
-      dbh: 1.0    # cm
-      height: 0.5  # m
-
-  - name: "species_B"  # Avicennia germinans
-    planting_density: 444  # trees/ha
-    mortality_rates:
-      year_1: 15  # %
-      year_2: 12  # %
-      year_3: 6   # %
-      year_4: 5   # %
-      year_5: 5   # %
-      year_6: 5   # %
-      year_7: 5   # %
-      year_8: 5   # %
-      year_9: 5   # %
-      year_10: 5  # %
-      subsequent: 1.5  # % (years 11-30)
-    linear_plateau:
-      dbh:
-        r: 1.2  # cm/yr (example, adjust as needed)
-        T_p: 30
-        a: 17.0
-      height:
-        r: 0.4  # m/yr (example, adjust as needed)
-        T_p: 12
-        a: 8.8
-    allometry:
-      equation: "Zanvo et al. 2023: Total = 1.486 × (DBH² H)^0.55864"
-    initial_values:
-      dbh: 1.0    # cm
-      height: 0.5  # m
-
-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
-
-carbon:
-  biomass_to_carbon: 0.47  # IPCC default
-  carbon_to_co2: 3.67     # molecular weight ratio
-  buffer_percentage: 20    # risk buffer
-  leakage_percentage: 0    # no leakage assumed
-  baseline_emissions: 0    # tCO2/ha/year
-
-scenarios:
-  area: 1000.0  # ha
-  dbh_range: [1.0, 25.0]  # cm
-  height_range: [0.5, 15.0]  # m
-  growth_rate_factor: 1.0 

configs/params.yaml

@@ -1,86 +0,0 @@
-species:
-  - name: "species_A"  # Rhizophora spp.
-    planting_density: 4000  # trees/ha
-    mortality_rates:
-      year_1: 15  # %
-      year_2: 12  # %
-      year_3: 6   # %
-      year_4: 5   # %
-      year_5: 5   # %
-      year_6: 5   # %
-      year_7: 5   # %
-      year_8: 5   # %
-      year_9: 5   # %
-      year_10: 5  # %
-      subsequent: 1.5  # % (years 11-30)
-    chapman_richards:
-      dbh:
-        a: 11.07  # asymptotic maximum DBH (cm)
-        b: 0.4736   # growth rate parameter (yr^-1), back-solved from Aug 2024 data
-        c: 2.1    # shape parameter
-      height:
-        a: 11.58   # asymptotic maximum height (m)
-        b: 0.1335   # growth rate parameter (yr^-1), back-solved from Aug 2024 data
-        c: 1.5    # shape parameter
-    allometry:
-      equation: "Zanvo et al. 2023: Total = 1.938 × (DBH² H)^0.67628"
-    initial_values:
-      dbh: 1.0    # cm
-      height: 0.5  # m
-
-  - name: "species_B"  # Avicennia germinans
-    planting_density: 444  # trees/ha
-    mortality_rates:
-      year_1: 15  # %
-      year_2: 12  # %
-      year_3: 6   # %
-      year_4: 5   # %
-      year_5: 5   # %
-      year_6: 5   # %
-      year_7: 5   # %
-      year_8: 5   # %
-      year_9: 5   # %
-      year_10: 5  # %
-      subsequent: 1.5  # % (years 11-30)
-    chapman_richards:
-      dbh:
-        a: 17.0   # asymptotic maximum DBH (cm)
-        b: 0.4736  # growth rate parameter (yr^-1), back-solved from Aug 2024 data
-        c: 2.1    # shape parameter
-      height:
-        a: 8.8    # asymptotic maximum height (m)
-        b: 0.1335  # growth rate parameter (yr^-1), back-solved from Aug 2024 data
-        c: 1.5    # shape parameter
-    allometry:
-      equation: "Zanvo et al. 2023: Total = 1.486 × (DBH² H)^0.55864"
-    initial_values:
-      dbh: 1.0    # cm
-      height: 0.5  # m
-
-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
-
-carbon:
-  biomass_to_carbon: 0.47  # IPCC default
-  carbon_to_co2: 3.67     # molecular weight ratio
-  buffer_percentage: 20    # risk buffer
-  leakage_percentage: 0    # no leakage assumed
-  baseline_emissions: 0    # tCO2/ha/year
-
-# Note: b parameter is calculated using b = ln(c) / Tm
-# For both species:
-# - Tm = 6 years
-# - c = 2.1
-# Therefore: b = ln(2.1) / 6 ≈ 0.35 
-
-scenarios:
-  area: 1000.0  # ha
-  dbh_range: [1.0, 25.0]  # cm
-  height_range: [0.5, 15.0]  # m
-  growth_rate_factor: 1.0 

dashboard/plots/__init__.py

@@ -103,7 +103,7 @@ def create_all_plots(results, species_results, config):
     check_complex(arr, "annual_ers")
     fig2 = go.Figure()
     fig2.add_trace(go.Bar(x=results["year"], y=annual_ers, name="Annual Buffer ERs", marker_color="#2ecc71", opacity=0.7))
-    fig2.update_layout(title="Annual Emission Reductions (Buffer)", xaxis_title="Year", yaxis_title="Annual Buffer ERs (tCO2)", hovermode="x unified", template="plotly_white")
+    fig2.update_layout(title="Annual Emission Reductions (Post Buffer)", xaxis_title="Year", yaxis_title="Annual Buffer ERs (tCO2)", hovermode="x unified", template="plotly_white")
 
     # 3. Biomass per tree for all species (refactored to use model.species_metrics)
     years = results["year"]

models/jimenez_lugo/README.md

@@ -1,9 +0,0 @@
-# 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

@@ -1,10 +0,0 @@
-# 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

@@ -1,10 +0,0 @@
-# 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

@@ -1,41 +0,0 @@
-# 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.
-
-## Growth & Mortality Logic
-- **Growth:**
-  - Uses Chapman-Richards equations for both DBH and height for each species.
-  - Parameters are derived from field data and literature.
-- **Mortality:**
-  - Applies a DBH-dependent mortality rate, where annual mortality is a function of tree size (DBH) and its increment.
-  - This dynamic approach reflects higher mortality when trees are small, leveling off as they mature.
-
-## Parameters
-- See `configs/params.yaml` for all parameter values, including:
-  - Chapman-Richards parameters for DBH and height
-  - Initial values for DBH and height
-  - Planting density
-  - Mortality parameters (m_ref, DBH_ref, p)
-  - Allometric equations for biomass
-
-## References
-- Chapman-Richards growth model literature
-- Zanvo et al. (2023) for allometric equations
-- Field data from Nigeria mangrove sites (2024)
-
-## Usage
-- This model is available as the "Original Model" tab in the dashboard.
-- To modify parameters, edit `configs/params.yaml`.
-- For more details on running the dashboard, see the top-level README.