MarineSensitivity Workflows

Reproducible Quarto / R notebooks that ingest marine species distribution models onto a global 0.05° cell grid, merge them per taxon, score marine sensitivity over the US study area, and publish the v8 marine-atlas as partitioned Parquet on S3 (served via titiler + a STAC catalog). Reusable logic lives in the msens R package; these notebooks orchestrate it via targets.

36 pipeline notebooks · generated 2026-09-15 11:34

Grid 2

Build the global 0.05° cell grid — the v8 sampling unit that every model is rasterized onto.

build_cell_grid

Build global 0.05° cell grid (v8 sampling unit)

Global ocean 0.05° raster cells in [-180,180] with env covariates + US study-area / Program-Area membership

deps: bootstrap_version
notebook ↗code ↗ ran 2026-09-15 11:32

Ingest 15

Acquire a source dataset and rasterize it onto the global cell grid as (mdl_key, cell_id, val). Each card's first chip is the data provider.

ingest_aquamaps

amAquaMapssuitabilityrasterstatic

Ingest AquaMaps → global 0.05° cells (bilinear-weight interpolation)

deps: build_cell_grid
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_aquax

axAquaXsuitabilityrasterstatic

Ingest AquaX → global 0.05° cells (position-mapped) · supersedes AquaMaps in US waters

v9: 10,536 AquaX ensemble suitability rasters, delivered on the v8 grid and masked to US waters, as dataset `ax`

deps: build_cell_grid, ingest_aquamaps
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_ca_nmfs

ca_nmfsNOAA NMFSrangevectorstatic

Ingest NMFS Core Distribution Areas → global 0.05° cells

deps: build_cell_grid
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_ch_nmfs

ch_nmfsNOAA NMFSrangevectorstatic

Ingest NMFS ESA Critical Habitat → global 0.05° cells

deps: build_cell_grid
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_dps_nmfs

dps_nmfsNOAA NMFSrangevectorstatic

Ingest NMFS listed entities (DPS / ESU / subspecies) → per-cell extinction risk on the global 0.05° grid

From the authoritative NOAA Fisheries critical-habitat service, with the IUCN range as the baseline outside listed DPSs

deps: build_cell_grid, ingest_rng_iucn, ingest_worms
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_sdm_nc

ncNOAA NCCOSdensityrasterseasonal

Ingest SDMs: NCCOS Atlantic & Pacific Seabird Densities

Seasonal seabird density (#/km²) → suitability [0,100] on the global 0.05° grid

deps: build_cell_grid
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_sdm_gm

gmNOAA SEFSCdensityvectormonthly

Ingest SDMs: NOAA SEFSC GoMex Cetacean & Sea-Turtle Densities

Monthly hexagon abundance (#/40 km²) → density → suitability [0,100] on the global 0.05° grid

deps: build_cell_grid
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_ch_fws

ch_fwsUSFWSrangevectorstatic

Ingest USFWS ESA Critical Habitat → global 0.05° cells

deps: build_cell_grid
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_rng_fws

rng_fwsUSFWSrangevectorstatic

Ingest USFWS species ranges → global 0.05° cells (v7-matched + marine-relevance)

deps: build_cell_grid
notebook ↗code ↗ ran 2026-09-15 11:32

ingest_taxon

ingest_taxon

deps: ingest_worms
code ↗

Merge 4

Crosswalk each model to a taxon, combine per-taxon models per cell, and derive validity / range / rarity flags.

merge_models

Merge models — combine each taxon's models per cell (max-merge + range mask; turtles ×)

deps: merge_models_prep
notebook ↗code ↗ ran 2026-09-15 11:32

merge_models_prep

Merge prep — taxon crosswalk (each model → WORMS / BOTW taxon)

deps: ingest_worms, ingest_aquamaps, ingest_aquax, ingest_dps_nmfs, ingest_rng_iucn, ingest_birdlife_botw, ingest_rng_fws, ingest_ch_nmfs, ingest_ch_fws, ingest_turtles_swot_dps, ingest_ca_nmfs, ingest_listings
notebook ↗code ↗ ran 2026-09-15 11:32

merge_taxon

Merge taxon metrics — validity flags + range / rarity / endemism / pct_marine

deps: merge_models, build_cell_grid, ingest_worms
notebook ↗code ↗ ran 2026-09-15 11:32

Score 3

Compute marine-sensitivity metrics per cell and per zone (program areas + ecoregions) over the US study area.

Registry & schema 3

Consolidate the dataset + model registry and support tables the pipeline and apps depend on.

Release & publish 9

Freeze a versioned marine-atlas release to S3, build the view-DB + STAC, and publish native serving surfaces.

release_marine_atlas

Release marine-atlas — versioned Parquet → S3, view-DB serving, STAC

deps: build_registry, score_zone_metrics, publish_native, build_common_names
notebook ↗code ↗ ran 2026-09-15 11:32

Pipeline DAG

The full targets dependency graph (from _targets.R via msens::build_targets_list()), rendered with tar_mermaid(). 

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