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Build per-segment per-species mapping_code strings (bcfp parity)

Source: R/lnk_pipeline_mapping_code.R
lnk_pipeline_mapping_code.Rd

Mirrors bcfishpass.streams_mapping_code – a per-segment per-species semicolon-token compound describing the segment's habitat label, the most-relevant downstream barrier source, and an intermittent flag if applicable. Pure derivation over the bcfp-shape inputs (no SQL).

Usage

lnk_pipeline_mapping_code(
  access,
  habitat,
  feature_code,
  to = NULL,
  conn = NULL,
  presence = NULL,
  species_resident = c("bt", "wct"),
  species_anadromous = c("ch", "cm", "co", "pk", "sk", "st"),
  species_spawn_only = c("cm", "pk"),
  segment_id_col = "id_segment",
  intermittent_feature_code = "GA24850150",
  resident_species,
  anadromous_species,
  spawn_only_species
)

Arguments

access

A tibble or data.frame keyed by segment_id_col with has_barriers_<sp>_dnstr boolean per species, plus the bcfp-shape sources has_barriers_anthropogenic_dnstr, has_barriers_pscis_dnstr, has_barriers_dams_dnstr, and (optional) has_remediated_dnstr. Typically the output of lnk_pipeline_access() called with barrier_sources populated.

habitat

A tibble keyed by segment_id_col with spawning_<sp> and rearing_<sp> numeric columns per species. Mirrors bcfp's streams_habitat_linear shape.

feature_code

Named character or data.frame. Either a named character vector mapping segment_id -> feature_code, or a data.frame with segment_id_col and "feature_code" columns. Used for the INTERMITTENT flag.

to

Character or NULL. Optional schema-qualified destination table. When supplied, the result tibble is written via dbWriteTable(overwrite = TRUE) and the tibble is also returned (so callers can chain into lnk_pipeline_persist / build_species_views.R). Default NULL returns-only.

conn

A DBI::DBIConnection. Required only when to is supplied; ignored otherwise.

species_resident

Character. Species using the resident flavor of mapping_code_barrier. Default c("bt", "wct"). (Renamed from resident_species in v0.40.0; old name accepted with deprecation warning until v0.41.0.)

species_anadromous

Character. Species using the anadromous flavor. Default c("ch", "cm", "co", "pk", "sk", "st"). (Renamed from anadromous_species in v0.40.0.)

species_spawn_only

Character. Species without rearing semantics (token 1 only emits SPAWN, never REAR). Default c("cm", "pk"). Mirrors bcfp. (Renamed from spawn_only_species in v0.40.0.)

segment_id_col

Character. Default "id_segment".

intermittent_feature_code

Character. The feature_code value that flags an intermittent stream. Default "GA24850150" (bcfp).

resident_species

Deprecated alias for species_resident. Kept for one release (v0.40.0); removal in v0.41.0.

anadromous_species

Deprecated alias for species_anadromous. Kept for one release (v0.40.0); removal in v0.41.0.

spawn_only_species

Deprecated alias for species_spawn_only. Kept for one release (v0.40.0); removal in v0.41.0.

Value

A tibble keyed by segment_id_col with one mapping_code_<sp> character column per species in union(species_resident, species_anadromous).

Details

Vocabulary (per species):


{ACCESS|SPAWN|REAR|""} ; {NONE|DAM|MODELLED|ASSESSED|REMEDIATED} [;INTERMITTENT]

Token 1 (habitat) per bcfp:

  • ACCESS: species' barriers all upstream (i.e. accessible to species) AND segment has no spawning AND no rearing eligibility for the species

  • SPAWN: spawning eligibility > 0 (always wins over REAR)

  • REAR: rearing eligibility > 0 AND no spawning

  • "" (empty): species has at least one downstream barrier blocking it (so habitat label is suppressed – inaccessible).

  • For species without rearing semantics (CM, PK), the rearing conditions drop out – only ACCESS (no spawn, no barriers) and SPAWN (spawning > 0) emit.

Token 2 (barrier source) only emits when the species' barriers downstream is empty (i.e. accessible). Resident-flavor (BT, WCT) and anadromous-flavor (CH/CM/CO/PK/SK/ST) differ in their CASE order:

  • Resident: REMEDIATED > DAM > ASSESSED (anthropogenic + pscis + no dam) > MODELLED (anthropogenic + no pscis + no dam) > NONE (no anthropogenic).

  • Anadromous: REMEDIATED > DAM (any dam) > ASSESSED (any pscis) > MODELLED (any anthropogenic) > NONE.

Token 3 emits INTERMITTENT when the segment's feature_code matches the bcfp intermittent code (default "GA24850150") AND the species' barriers downstream is empty.

Empty / NULL tokens are dropped via paste(..., collapse = ";")-style composition so an inaccessible segment yields "" (empty string) and an accessible no-habitat-no-intermittent segment yields "ACCESS;NONE".

See also

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