Classify Stream Segments into Habitat per Species

Fifth phase of the habitat classification pipeline. Builds the access-gating break table consumed by classification, then calls fresh::frs_habitat_classify() with the rules YAML, thresholds, per-species parameters, and barrier overrides from the config bundle.

Usage

lnk_pipeline_classify(
  conn,
  aoi,
  cfg,
  loaded,
  schema,
  species = NULL,
  thresholds_csv = NULL,
  method_csv = NULL
)

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 parameters_fresh, user_habitat_classification, and wsg_species_presence.

schema

Character. Working schema name.

species

Character vector. Species codes to classify. Default derives from loaded$parameters_fresh$species_code intersected with the species present in the AOI (via loaded$wsg_species_presence).

thresholds_csv

Path to the habitat thresholds CSV. Default NULL uses the config's own files$parameters_habitat_thresholds, falling back (with a message) to the copy shipped with fresh when the config declares none.

method_csv

Path to the per-watershed-group habitat model table (watershed_group_code, model = "cw" or "mad"), passed to fresh::frs_habitat_classify() as params_method. Default NULL uses the config's own files$parameters_habitat_method, falling back (with a message) to fresh's all-cw copy when the config declares none. A group the table does not list classifies on channel width. A mad group classifies on mad_m3s, which the prepare phase joins onto the working streams table (filling edge 1250 main stems with no value when cfg$pipeline$discharge_fill is set), and skips the stream-order rearing bypass. Read from the path, not from loaded$parameters_habitat_method, as the thresholds are, so editing loaded has no effect here.

Value

conn invisibly, for pipe chaining.

Details

The access-gating break table (fresh.streams_breaks) is assembled from the FULL gradient barrier set (not the minimal one used for segmentation), falls, user-identified definite barriers, and crossings with their AOI-filtered ltree values attached. Filtering to the AOI keeps the O(segments × breaks) access-gating join tractable.

Writes to:

• fresh.streams_breaks — access-gating breaks

• fresh.streams_habitat — per-species classification output (written by frs_habitat_classify)

See also

Other pipeline: lnk_pipeline_access(), lnk_pipeline_break(), 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)
lnk_pipeline_classify(conn, "BULK", cfg, loaded, schema)

DBI::dbDisconnect(conn)
} # }