Habitat eligibility override CSV with edge_type and feature_code defaults

[NewGraphEnvironment]

Context

link ships an override CSV for parameters_habitat.csv that defines what qualifies as habitat per species. The override starts from bcfishpass v0.5.0 defaults and departs where biological rationale supports it. Each departure tracked as a separate issue.

fresh#100 (fresh 0.9.0) adds edge_type filtering, fresh#105 adds feature_code categories, fresh#102 exposes params so link can pass its own CSV. This issue is about the link-side override.

bcfishpass v0.5.0 defaults (edge_types)

Species	spawn_edge_types	rear_edge_types	Notes
BT	stream, canal		No rearing edge filter. Rivers included via waterbody_type join.
CH	stream, canal	stream, canal	Rivers via waterbody_type.
CM	stream, canal		No freshwater rearing.
CO	stream, canal	stream, canal	CO wetland-flow carve-out (1050/1150). Rivers via waterbody_type.
PK	stream, canal		No freshwater rearing.
SK	stream, canal		Lake rearing via rear_lake_ha_min. No waterbody_type join.
ST	stream, canal	stream, canal	Rivers via waterbody_type.
WCT	stream, canal	stream, canal	Rivers via waterbody_type.

Note: bcfishpass v0.5.0 stream = 1000/1100 only (excludes 1050/1150 wetland-flow). fresh 0.9.0 stream category = 1000/1050/1100/1150. So fresh defaults already include wetland-flow streams.

bcfishpass v0.5.0 does not filter by feature_code.

Proposed link overrides

Edge types

Species	spawn_edge_types	rear_edge_types	Diff from bcfishpass v0.5.0
BT	stream, canal	stream, canal, river, lake	+river, +lake for rearing
CH	stream, canal, river	stream, canal, river, lake	+river for spawning, +river/lake for rearing
CM	stream, canal, river		+river for spawning
CO	stream, canal, river	stream, canal, river, lake, wetland	+river for spawning, +river/lake/wetland for rearing
PK	stream, canal, river		+river for spawning
SK	stream, canal	lake	Explicit lake rearing via edge_type (alongside rear_lake_ha_min)
ST	stream, canal, river	stream, canal, river, lake	+river for spawning, +river/lake for rearing
WCT	stream, canal, river	stream, canal, river, lake	+river for spawning, +river/lake for rearing

Feature types

Species	spawn_feature_types	rear_feature_types	Rationale
All	stream_definite, stream_intermittent	stream_definite, stream_intermittent, lake, reservoir	Include intermittent — fish use seasonal streams for spawning/rearing. Exclude ditch, industrial.

Key departures requiring evidence (separate issues)

1. Lakes for rearing (BT, CH, CO, ST, WCT) — bcfishpass v0.5.0 doesn't model lake rearing for most species. Many species rear in lakes (documented in Build fish passage connectivity literature RAG store #2 literature RAG).
2. Intermittent streams included — bcfishpass v0.5.0 doesn't filter on feature_code so these are implicitly included. We're explicit about it.
3. Wetland-flow streams for spawning — fresh 0.9.0 stream category includes 1050/1150. bcfishpass v0.5.0 excludes them. Streams through wetlands can be spawning habitat.
4. Rivers for spawning — bcfishpass v0.5.0 includes via waterbody_type join. We include via edge_type category directly.
5. Ditches excluded — not in any category. Fish may use ditches but we don't model them as habitat.

Implementation

Ship inst/extdata/parameters_habitat.csv as a complete override. Pass to fresh via:

frs_habitat(conn, "ADMS",
  params = frs_params(csv = system.file("extdata", "parameters_habitat.csv", package = "link")))

Relates to NewGraphEnvironment/fresh#100, NewGraphEnvironment/fresh#102, NewGraphEnvironment/fresh#105, #18

[NewGraphEnvironment]

Closing — superseded by the current overrides infrastructure:

• Per-species habitat eligibility lives in inst/extdata/configs/{bcfishpass,default}/dimensions.csv with the column-driven rule emission via lnk_rules_build(). The departures table in this issue (per-species edge_types) is now expressed via spawn_stream / rear_stream / rear_lake / rear_wetland columns + the edge_types / edge_types_explicit rule emission.
• Known-habitat overlay is wired via user_habitat_classification.csv consumed by fresh::frs_habitat_overlay() in lnk_pipeline_classify().

The "override CSV" framing has effectively become "the dimensions.csv + the overrides directory + the rules.yaml emission" together. Each named departure has its own column in dimensions.csv; the methodology research doc research/default_vs_bcfishpass.md documents the deltas.