Downscale management scenarios to field scale

000-config.R

@@ -35,6 +35,26 @@ pecan_outdir <- file.path(ccmmf_dir, "modelout", "ccmmf_phase_2b_mixed_pfts_2025
 # PEcAn model output to be analyzed
 pecan_archive_tgz <- file.path(ccmmf_dir, "lebauer_agu_2025_20251210.tgz")
 
+# -----Management scenarios config -----
+# set to TRUE to use Phase 3 management scenario outputs
+USE_PHASE_3_SCENARIOS <- TRUE
+
+phase_3_outdir <- file.path(ccmmf_dir, "modelout", "ccmmf_phase_3_scenarios_20251210")
+
+management_scenarios <- c(
+  "baseline",
+  "compost",
+  "reduced_till",
+  "zero_till",
+  "reduced_irrig_drip",
+  "stacked"
+)
+
+# override paths if using Phase 3
+if (USE_PHASE_3_SCENARIOS) {
+  pecan_outdir <- phase_3_outdir
+}
+
 # **Variables to extract**
 # see docs/workflow_documentation.qmd for complete list of outputs
 outputs_to_extract <- c("TotSoilCarb", "AGB")

docs/CHANGELOG.md

@@ -6,20 +6,31 @@ Once a new release is made this file will be updated to create a new `Unreleased
 
 For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
 
-<!-- 
+
 sections to include in release notes:
 
 ## [Unreleased]
 
 ### Added
 
+- Management scenario support for comparing agricultural practices
+  - Configuration flag `USE_PHASE_3_SCENARIOS` in `000-config.R`
+  - Six scenarios: baseline, compost, reduced_till, zero_till, reduced_irrig_drip, stacked
+  - Scenario-aware extraction from pre-aggregated `.Rdata` files
+  - `scenario` column added to all output CSVs
+  - `scenarios` array in metadata JSON
+- Early exit in `031_aggregate_sipnet_output.R` for single-PFT runs
+- Parquet output for large files (>100k rows) via `write_output()` helper
+
 ### Fixed
 
+- Empty vector handling in mixed-scenario logic (`040_downscale.R`)
+
 ### Changed
 
 ### Removed
 
--->
+
 
 ## 0.2.0-2a
 

docs/workflow_documentation.md

@@ -75,6 +75,26 @@ git clone git@github.com:ccmmf/downscaling
   - detect and use resources for parallel processing (with future package); default is `available cores - 1`
   - PRODUCTION mode setting. For testing, set `PRODUCTION` to `FALSE`. This is _much_ faster and requires fewer computing resources because it subsets large datasets. Once a test run is successful, set `PRODUCTION` to `TRUE` to run the full workflow.
 
+#### Management Scenario Configuration
+
+To compare carbon outcomes under different agricultural practices, enable management scenario mode:
+```r
+USE_PHASE_3_SCENARIOS <- TRUE
+```
+
+When enabled, the workflow processes multiple management scenarios in a single run. Each scenario represents a different combination of practices applied to annual croplands.
+
+**Available Management Scenarios:**
+
+| Scenario | Description |
+|----------|-------------|
+| baseline | Conventional management practices |
+| compost | Compost application replacing mineral N fertilizer |
+| reduced_till | Reduced tillage intensity (0.10) |
+| zero_till | No tillage (0.00) |
+| reduced_irrig_drip | Drip irrigation replacing canopy irrigation |
+| stacked | Combined: compost + reduced tillage + drip irrigation |
+
 ### 1. Data Preparation
 
 ```sh
@@ -235,9 +255,13 @@ Extracts and formats SIPNET outputs for downscaling:
 
 **Inputs:**
 - `out/ENS-<ensemble_number>-<site_id>/YYYY.nc`
+- `results_monthly_<variable>.Rdata` (management scenario mode)
+- `site_info.csv` (management scenario mode)
 
 **Outputs:**
-- `out/ensemble_output.csv`: Long format data
+- `out/ensemble_output.csv`: Long format data with columns:
+  - `scenario`: Management scenario identifier (when scenarios enabled)
+  - `datetime`, `site_id`, `lat`, `lon`, `pft`, `parameter`, `variable`, `prediction`
 
 ### 5. Mixed Cropping Systems
 
@@ -277,12 +301,13 @@ Builds Random Forest models to predict carbon pools for all fields; aggregates t
 - `data/site_covariates.csv`: Environmental covariates
 
 **Outputs from `040_downscale.R`:**
-- `model_outdir/downscaled_preds.csv`: Per-site, per-ensemble predictions with totals and densities
-- `model_outdir/downscaled_preds_metadata.json`: Metadata for predictions
-- `model_outdir/training_sites.csv`: Training site list per PFT and pool
+- `model_outdir/downscaled_preds.csv`: Per-site, per-ensemble predictions with columns:
+  - `site_id`, `scenario`, `pft`, `ensemble`, `c_density_Mg_ha`, `total_c_Mg`, `area_ha`, `county`, `model_output`
+- `model_outdir/downscaled_preds_metadata.json`: Metadata including scenarios list
+- `model_outdir/downscaled_deltas.csv`: Carbon change from simulation start to end per scenario
+- `model_outdir/training_sites.csv`: Training site list per scenario, PFT, and pool
 - `cache/models/*_models.rds`: Saved RF models per spec
 - `cache/training_data/*_training.csv`: Training covariate matrices per spec
-- `model_outdir/downscaled_deltas.csv`: Optional start→end deltas when available
 
 **Outputs from `041_aggregate_to_county.R`:**
 - `model_outdir/county_summaries.csv`: County statistics (means/SDs across ensembles for stocks and densities)