Extract AmeriFlux BASE-BADM/BIF crop management records into EcoSIM-editable plant-management and soil-management Excel workbooks that can be converted to EcoSIM NetCDF files. Use when asked to derive EcoSIM planting, harvest, fertilizer, or tillage management inputs from AMF *_BIF_*.xlsx or BIF CSV files, especially for crop sites where management details live in GRP_DM_* records and DM_COMMENT fields.
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Review the instructions the agent will receive before you install.
Use this skill to convert AmeriFlux BADM/BIF management metadata into two editable EcoSIM workbooks:
*_plant_mgmt.xlsx, matching $ecosim-natural-plant-mgmt.*_soil_mgmt.xlsx, matching $ecosim-soil-mgmt.The extractor also writes companion JSON files and a *_management_extraction_review.xlsx workbook. Always review assumptions before converting the generated Excel files to NetCDF, because many AmeriFlux management quantities are stored in free-text comments.
Read references/mapping_rules.md when you need the exact parsing and default mapping rules.
AMF-BIF sheet..venv-cmip6/bin/python \
.agents/skills/ameriflux-bif-ecosim-mgmt/scripts/extract_bif_mgmt_to_ecosim_excel.py \
/path/to/AMF_SITE_BIF_YYYYMMDD.xlsx \
--pftpar-nc /path/to/ecosim_pftpar_YYYYMMDD.nc \
--koppen-code 41 \
--out-dir result/SITE/ecosim_mgmt_from_bif
corn=maiz41, soybean=soyb41 by default);NH4Soil, NH3Soil, UreaSoil, and NO3Soil;FractionCut assumptions..venv-cmip6/bin/python .agents/skills/ecosim-natural-plant-mgmt/scripts/plant_mgmt_excel_bridge.py \
xlsx-to-nc SITE_plant_mgmt.xlsx SITE_pft_mgmt.nc --json-output SITE_pft_mgmt.json
.venv-cmip6/bin/python .agents/skills/ecosim-soil-mgmt/scripts/soil_mgmt_excel_bridge.py \
xlsx-to-nc SITE_soil_mgmt.xlsx SITE_soil_mgmt.nc --json-output SITE_soil_mgmt.json
--start-year and --end-year: limit the output years.--pftpar-nc: EcoSIM PFT parameter NetCDF used to validate pft_type against pfts.--koppen-code: two-digit EcoSIM climate number used to compose <pfts_short><koppen>.--crop-pft-map crop=pftcode: explicit crop mapping override, repeatable.--planting-depth-m: default planting depth used when BIF only provides seed rate.--topo NH1,NV1,NH2,NV2: set EcoSIM topo-unit bounds.--default-fertilizer-n-g-m2: placeholder N rate when a fertilizer event lacks a parseable rate.--tillage-depth-m and --tillage-type: placeholders for BIF tillage records.The plant workbook has the exact sheets required by plant_mgmt_excel_bridge.py: control, topo_units, pft_years, and management.
The soil workbook has the exact sheets required by soil_mgmt_excel_bridge.py: control, topo_units, year_selectors, event_files, fertilizer, tillage, and irrigation.
The review workbook is not consumed by EcoSIM. It exists to protect unit consistency and mass-flow assumptions before NetCDF conversion.
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Extract EPA/NADP tDEP atmospheric deposition and NADP precipitation chemistry rasters for an AmeriFlux or EcoSIM site. Use when deriving atmospheric chemistry inputs such as NH4, NO3, SO4, Ca, or precipitation pH for EcoSIM forcing workflows.
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Sort AmeriFlux BASE-BADM BIF variables from Excel or CSV files into observation, management-event, static metadata, and plotting-ready target time-series tables. Use when Codex is asked to sort AmeriFlux BIF variables into time series; organize BADM/BIF variables by date; pivot AMF *_BIF_*.xlsx files by GROUP_ID; output total LAI, leaf mass per area, above-ground biomass, canopy height, fruit yield, or total yield time series; write MATLAB readers for BIF time-series plotting; or prepare dated AmeriFlux site observations and management records for EcoSIM workflows.
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Convert AmeriFlux ERA5 half-hourly meteorological CSV files into EcoSIM hourly climate forcing NetCDF files, compare generated forcing against overlapping measured tower meteorology when a FULLSET file is available, and report large biases or errors. Use when preparing or validating EcoSIM climate inputs for AmeriFlux sites, checking ERA5 against in situ records, diagnosing forcing discrepancies, or writing climate-quality reports. For non-AmeriFlux paper sites that need a fresh Copernicus CDS ERA5 point download by longitude/latitude, use era5-cds-point-download first.
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Create EcoSIM Fortran namelist files and workable EcoSIM run folders for AmeriFlux site runs from site-specific grid, plant management, climate forcing, and greenhouse-gas inputs. Use when preparing or updating an EcoSIM `.namelist`, run folder, runfolder, run directory, or executable-ready site case for AmeriFlux or FLUXNET sites, especially after generating `*_ecosim_grid.nc`, `*_ecosim_climate_<first>-<last>.nc`, and `*_pft_mgmt.nc` inputs.
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Extract AmeriFlux site metadata and map it to EcoSIM JSON variables. Use when a task needs site latitude, longitude, elevation, mean annual temperature, Koppen climate code, or vegetation type for an AmeriFlux site ID or flux-site name.
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Extract dominant-component soil profile variables for EcoSIM grid or template inputs from gSSURGO, with FAO HWSD v2.0 fallback when gSSURGO data are unavailable or incomplete. Use when deriving soil depth, bulk density, field capacity, wilting point, hydraulic conductivity, texture, rock fraction, pH, CEC, or soil organic carbon; or when converting EcoSIM grid NetCDF files to editable Excel workbooks and back.
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