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
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.
33 pipeline notebooks · generated 2026-08-12 11:33
Grid 1
Build the global 0.05° cell grid — the v8 sampling unit that every model is rasterized onto.
Ingest 13
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
Ingest AquaMaps → global 0.05° cells (bilinear-weight interpolation)
deps: build_cell_grid
ingest_birdlife_botw
Ingest BirdLife BOTW → global 0.05° cells (whole range)
deps: build_cell_grid
ingest_rng_iucn
Ingest IUCN Red List expert ranges → global 0.05° cells
deps: build_cell_grid
ingest_ca_nmfs
Ingest NMFS Core Distribution Areas → global 0.05° cells
deps: build_cell_grid
ingest_ch_nmfs
Ingest NMFS ESA Critical Habitat → global 0.05° cells
deps: build_cell_grid
ingest_sdm_nc
Ingest SDMs: NCCOS Atlantic & Pacific Seabird Densities
Seasonal seabird density (#/km²) → suitability [0,100] on the global 0.05° grid
deps: build_cell_grid
ingest_sdm_gm
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
ingest_turtles_swot_dps
Ingest SWOT + NMFS-DPS sea turtle ranges → global 0.05° cells
deps: build_cell_grid
ingest_listings
Ingest US federal listings → MMPA / MBTA / ESA taxon attributes
ingest_ch_fws
Ingest USFWS ESA Critical Habitat → global 0.05° cells
deps: build_cell_grid
ingest_rng_fws
Ingest USFWS species ranges → global 0.05° cells (v7-matched + marine-relevance)
deps: build_cell_grid
ingest_worms
Ingest WoRMS — (re)build the spp.duckdb `worms` table from the monthly marinespecies.org DwC-A
ingest_taxon
ingest_taxon
deps: ingest_worms
Merge 4
Crosswalk each model to a taxon, combine per-taxon models per cell, and derive validity / range / rarity flags.
build_common_names
Build taxon common names — NMFS > FWS > BirdLife > WoRMS (English)
deps: merge_taxon, ingest_worms
merge_models
Merge models — combine each taxon's models per cell (max-merge + range mask; turtles ×)
deps: merge_models_prep
merge_models_prep
Merge prep — taxon crosswalk (each model → WORMS / BOTW taxon)
deps: ingest_worms, ingest_aquamaps, ingest_rng_iucn, ingest_birdlife_botw, ingest_rng_fws, ingest_ch_nmfs, ingest_ch_fws, ingest_turtles_swot_dps, ingest_ca_nmfs, ingest_listings
merge_taxon
Merge taxon metrics — validity flags + range / rarity / endemism / pct_marine
deps: merge_models, build_cell_grid, ingest_worms
Score 3
Compute marine-sensitivity metrics per cell and per zone (program areas + ecoregions) over the US study area.
score_cell_metrics
Score cell metrics — extrisk_{spcat} → ecoregion rescale → primprod → composite
deps: score_zones
score_zones
Score setup — zones (program areas + ecoregions) + taxon prep
deps: merge_taxon, build_cell_grid
score_zone_metrics
Score zone metrics — program-area composite + v7 equivalence gate
deps: score_cell_metrics
Registry & schema 3
Consolidate the dataset + model registry and support tables the pipeline and apps depend on.
build_registry
Build the model + dataset registry (`dataset` + `model` tables)
deps: merge_taxon
build_zone_sets
Build the zone-set registry (spatial units as vintages, not per-version copies)
deps: build_cell_grid
build_zone_cells
Build zone_cell once per (zone set × grid), not once per release
deps: build_zone_sets
Release & publish 9
Freeze a versioned marine-atlas release to S3, build the view-DB + STAC, and publish native serving surfaces.
backfill_versions
Backfill a past release into the multi-version atlas
deps: build_zone_cells
build_app_support
Build app support files — zone gpkgs, layers registry, metrics raster
deps: score_zone_metrics
build_v7_cell_model
Build cell_model — the cell-oriented twin of a release's model_cell
build_version_manifest
Build the version registry (`latest.txt`, `versions.json`, `manifest.json`)
deps: score_zone_metrics
publish_storage_index
Publish a browsable index for the public bucket (storage.marinesensitivity.org)
deps: release_marine_atlas
publish_stac_api
Publish a searchable STAC API — per-model Items over stac-geoparquet
deps: build_registry
publish_native
Publish native-format input surfaces — range PMTiles + AquaMaps COGs
deps: merge_taxon
publish_score_cogs
Publish score surfaces as COGs (retiring the SQL→tile factory)
deps: score_zone_metrics
release_marine_atlas
Release marine-atlas — versioned Parquet → S3, view-DB serving, STAC
deps: build_registry, score_zone_metrics, publish_native, build_common_names
Pipeline DAG
The full targets dependency graph (from _targets.R via
msens::build_targets_list()), rendered with
tar_mermaid().
graph LR
style Graph fill:#FFFFFF00,stroke:#000000;
subgraph Graph
direction LR
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x49fc1e0d72360909(["ingest_worms"]):::ingest --> x9497f70f25af06d7(["build_common_names"]):::merge
x49b111dbddc718dd(["merge_taxon"]):::merge --> x9497f70f25af06d7(["build_common_names"]):::merge
x49b111dbddc718dd(["merge_taxon"]):::merge --> x353f9ddf9886075c(["build_registry"]):::schema
x41a1875ace44021e(["build_cell_grid"]):::grid --> x1a1f66f07f9fbe62(["ingest_aquamaps"]):::ingest
x41a1875ace44021e(["build_cell_grid"]):::grid --> x7de1c3460218a5c9(["ingest_birdlife_botw"]):::ingest
x41a1875ace44021e(["build_cell_grid"]):::grid --> x22c2dae0a5579fb1(["ingest_ca_nmfs"]):::ingest
x41a1875ace44021e(["build_cell_grid"]):::grid --> x4dfdc6a38879aeb4(["ingest_ch_fws"]):::ingest
x41a1875ace44021e(["build_cell_grid"]):::grid --> xa04f096eecbe6336(["ingest_ch_nmfs"]):::ingest
x41a1875ace44021e(["build_cell_grid"]):::grid --> x964ed8969f46bd55(["ingest_rng_fws"]):::ingest
x41a1875ace44021e(["build_cell_grid"]):::grid --> xe9b4164e4cddee29(["ingest_rng_iucn"]):::ingest
x41a1875ace44021e(["build_cell_grid"]):::grid --> xcba4944363cebc92(["ingest_turtles_swot_dps"]):::ingest
xaabdb461a9e32014(["merge_models_prep"]):::merge --> x6c4981172b9125c0(["merge_models"]):::merge
x4dfdc6a38879aeb4(["ingest_ch_fws"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
x7de1c3460218a5c9(["ingest_birdlife_botw"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
xe9b4164e4cddee29(["ingest_rng_iucn"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
x1a1f66f07f9fbe62(["ingest_aquamaps"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
xa0ef2b4c4b8deff2(["ingest_listings"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
x22c2dae0a5579fb1(["ingest_ca_nmfs"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
x49fc1e0d72360909(["ingest_worms"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
xa04f096eecbe6336(["ingest_ch_nmfs"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
x964ed8969f46bd55(["ingest_rng_fws"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
xcba4944363cebc92(["ingest_turtles_swot_dps"]):::ingest --> xaabdb461a9e32014(["merge_models_prep"]):::merge
x41a1875ace44021e(["build_cell_grid"]):::grid --> x49b111dbddc718dd(["merge_taxon"]):::merge
x6c4981172b9125c0(["merge_models"]):::merge --> x49b111dbddc718dd(["merge_taxon"]):::merge
x49fc1e0d72360909(["ingest_worms"]):::ingest --> x49b111dbddc718dd(["merge_taxon"]):::merge
x49b111dbddc718dd(["merge_taxon"]):::merge --> xb598afaf51898417(["publish_native"]):::release
x353f9ddf9886075c(["build_registry"]):::schema --> x645366053402e71c(["release_marine_atlas"]):::release
x9497f70f25af06d7(["build_common_names"]):::merge --> x645366053402e71c(["release_marine_atlas"]):::release
xa1369084a0260d9c(["score_zone_metrics"]):::score --> x645366053402e71c(["release_marine_atlas"]):::release
xb598afaf51898417(["publish_native"]):::release --> x645366053402e71c(["release_marine_atlas"]):::release
x484a4524379bfe98(["score_zones"]):::score --> xfb031dbd34cf644a(["score_cell_metrics"]):::score
xfb031dbd34cf644a(["score_cell_metrics"]):::score --> xa1369084a0260d9c(["score_zone_metrics"]):::score
x41a1875ace44021e(["build_cell_grid"]):::grid --> x484a4524379bfe98(["score_zones"]):::score
x49b111dbddc718dd(["merge_taxon"]):::merge --> x484a4524379bfe98(["score_zones"]):::score
end
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