Segment the Stream Network at Configured Break Positions

Fourth phase of the habitat classification pipeline. Builds the remaining break-source tables (observations, habitat endpoints, crossings) that depend on AOI- and config-specific data, then runs fresh::frs_break_apply() sequentially over the break sources in the order defined by the config. After each round, id_segment is reassigned so downstream rounds see contiguous integer IDs.

Usage

lnk_pipeline_break(
  conn,
  aoi,
  cfg,
  loaded,
  schema,
  observations = "bcfishobs.observations"
)

Arguments

conn

A DBI::DBIConnection object.

aoi

Character. Watershed group code (today; extends to other spatial filters later).

cfg

An lnk_config object from lnk_config().

loaded

Named list of tibbles from lnk_load_overrides(). Carries observation_exclusions and wsg_species_presence.

schema

Character. Working schema name.

observations

Character. Schema-qualified observations table (default "bcfishobs.observations").

Value

conn invisibly, for pipe chaining.

Details

The break-source order matters. bcfishpass processes: observations → gradient_minimal → falls → barriers_definite → habitat_endpoints → crossings. This order is encoded in the bundled bcfishpass config (cfg$pipeline$break_order) and is the default when the config does not specify one.

Break sources

Valid entries for cfg$pipeline$break_order. Omit an entry to skip both segmentation and access-gating from that source.

name	source table	role	classify label
observations	<schema>.observations_breaks	fish observations from bcfishobs.observations, WSG- and species-filtered, exclusions applied	(informational; not a barrier)
gradient_minimal	<schema>.gradient_barriers_minimal	minimal-reduced gradient barriers (per-model 15/20/25/30%)	classify uses the FULL set with gradient_<NNNN> labels
falls	<schema>.falls	natural waterfalls from whse_basemapping.fwa_obstacles_sp (loaded by prep_load_aux); each fall is its own barrier (NOT minimal-reduced)	blocked
barriers_definite	<schema>.barriers_definite	user_barriers_definite.csv for the AOI	blocked
subsurfaceflow	<schema>.barriers_subsurfaceflow	FWA edge_type IN (1410, 1425) start points; honours user_barriers_definite_control. Opt-in (only built when listed)	blocked
habitat_endpoints	<schema>.habitat_endpoints	DRM and URM from user_habitat_classification.csv	(segmentation only; not a barrier)
crossings	<schema>.crossings_breaks	PSCIS + modelled crossings (any barrier_status)	classify maps barrier_status → barrier/potential/passable

Bcfishpass-bundle config opts in to subsurfaceflow for parity with bcfishpass natural access. Default-bundle leaves it off pending a NewGraph methodology decision.

Writes to (under the caller's working schema unless noted):

• <schema>.observations_breaks — WSG- and species-filtered observation positions, data-error exclusions applied

• <schema>.habitat_endpoints — both DRM and URM from the habitat classification table (matches bcfishpass convention)

• <schema>.crossings_breaks — crossing positions

• Mutates fresh.streams in place — adds segment boundaries at each break source position, reassigns id_segment

See also

Other pipeline: lnk_pipeline_access(), lnk_pipeline_classify(), lnk_pipeline_connect(), lnk_pipeline_crossings(), lnk_pipeline_load(), lnk_pipeline_mapping_code(), lnk_pipeline_prepare(), lnk_pipeline_run(), lnk_pipeline_setup(), lnk_pipeline_species(), lnk_presence()

Examples

if (FALSE) { # \dontrun{
conn   <- lnk_db_conn()
cfg    <- lnk_config("bcfishpass")
loaded <- lnk_load_overrides(cfg)
schema <- "working_bulk"

lnk_pipeline_setup(conn, schema)
lnk_pipeline_load(conn, "BULK", cfg, loaded, schema)
lnk_pipeline_prepare(conn, "BULK", cfg, loaded, schema)
lnk_pipeline_break(conn, "BULK", cfg, loaded, schema)

DBI::dbGetQuery(conn,
  "SELECT count(*) FROM fresh.streams")

DBI::dbDisconnect(conn)
} # }