Chesapeake-Ecospace

R project to build spatial, environmental, and species preference inputs for a Chesapeake Bay ecosystem model in Ecopath with Ecosim (EwE) / Ecospace. Outputs are ESRI ASCII grids, NetCDF raster stacks, and CSV preference tables ready for import into Ecospace.

Ecospace grids: four resolutions sharing one extent (Chesapeake Bay, −77.4 to −75.55°W, 36.7 to 39.65°N, WGS84). The standard grid is F02 = 88×56 (56 columns × 88 rows, ~2-arcminute / ~3.5 km cells), with a finer option (F01 176×111) and coarser ones (F03 59×37, F04 44×28).

Quick Start

Most scripts are independent entry points. The environmental-driver module is the exception: it is a 3-stage pipeline whose stage scripts share cbefs-helpers.R and are driven by an orchestrator (run-environmental-drivers.R). Run pipelines in order; each can run independently once its prerequisites exist.

Pipeline A — Spatial Basemap (run once)

1. make-habitat-maps/make-baythymetry-basemap.R — downloads NOAA bathymetry, creates the Ecospace depth basemaps in output-for-ecospace/habitat/basemaps/ (base-depth-map-F01..F04-*.asc)
2. make-habitat-maps/make-jurisdictional-maps.R — creates binary MD/VA/Potomac ASC grids (requires basemap from step 1)

Pipeline B — Environmental Drivers (3-stage, long-running, requires ~43 GB CBEFS data)

A 3-stage pipeline that turns CBEFS hindcasts (1985–2024) into Ecospace drivers at all four resolutions. See make-environmental-drivers/README.md for the full technical reference, and docs/environmental-drivers-methods.md for the methods/rationale.

3. Stage 1 — make-environmental-drivers/process-CBEFS.R (run separately): raw CBEFS → native monthly-mean NC stacks (monthly computed in-process; native curvilinear grid, index space). run_mode <- "TEST" for a quick trial; write_daily_stack <- FALSE skips the ~47 GB daily archive (unused downstream).
4. Stages 2–3 — make-environmental-drivers/run-environmental-drivers.R (orchestrator): toggle do_regrid (Stage 2: regrid native → each basemap), do_ascii (Stage 3a: ASCII drivers), do_pdf / do_gif (Stage 3b/c: PDF/GIF visualizations). Select resolutions and variables_to_run (NULL = all).
5. (independent) make-environmental-drivers/make-atlas-climatology-maps.R — Bay Atlas climatology → monthly ASC files (separate from the 3-stage pipeline).

Pipeline C — Species Preference Functions

6. make-preference-functions/query-env-preference-parameters.R — queries FishBase API for species traits
7. make-preference-functions/Make-preference-functions.R — compiles data/derived/env-pref-parameters.csv → logistic preference curves

Note: make-preference-functions/query-aquamaps-data.R (AquaMaps HSPEN query) needs rework before use — see docs/INVENTORY.md.

Full Documentation

See docs/INVENTORY.md for:

• Complete R script inventory with inputs, outputs, and run order
• ASCII pipeline diagrams
• All final Ecospace output file paths
• Known issues and cleanup items