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Build per-segment per-species mapping_code tokens from schema tables

Source: R/lnk_mapping_code.R
lnk_mapping_code.Rd

Schema-aware portable wrapper around lnk_pipeline_mapping_code(). Queries table_access, table_habitat (long form), and table_streams.feature_code, assembles the inputs (pivot habitat long → wide, build feature_code lookup), calls lnk_pipeline_mapping_code() for the per-segment token compute, and optionally writes the result to table_to.

Usage

lnk_mapping_code(
  conn,
  table_access,
  table_habitat,
  table_streams,
  aoi,
  table_to = NULL,
  presence = NULL,
  species_resident = c("bt", "wct"),
  species_anadromous = c("ch", "cm", "co", "pk", "sk", "st"),
  species_spawn_only = c("cm", "pk")
)

Arguments

conn

A DBI::DBIConnection to the local pipeline DB.

table_access

Character. Schema-qualified name of the streams_access table (e.g. "working_pars.streams_access" or "fresh_default.streams_access").

table_habitat

Character. Schema-qualified name of a long-form habitat source — either the working-schema streams_habitat table or the persist streams_habitat_long_vw view. Must have columns id_segment, watershed_group_code, species_code, spawning, rearing.

table_streams

Character. Schema-qualified name of the streams table, queried for id_segment + feature_code.

aoi

Character. Watershed group code (e.g. "PARS") — filters all input queries to one WSG.

table_to

Character or NULL. Optional schema-qualified destination table for the result. When non-NULL, lnk_pipeline_mapping_code() writes the tibble via dbWriteTable(overwrite = TRUE). Default NULL — returns-only.

presence

Named logical vector or NULL. Per-species presence flag for aoi. When NULL the function derives presence from the data: a species is present iff it has at least one habitat row with spawning = TRUE or rearing = TRUE. Pass explicit values to override (e.g. force-include a species for QGIS symbology even when no segments are accessible).

species_resident

Character. Species using the resident flavor of mapping_code_barrier. Default c("bt", "wct"). Pass-through to lnk_pipeline_mapping_code()'s resident_species arg.

species_anadromous

Character. Species using the anadromous flavor. Default c("ch", "cm", "co", "pk", "sk", "st"). Pass-through to lnk_pipeline_mapping_code()'s anadromous_species arg.

species_spawn_only

Character. Species without rearing semantics. Default c("cm", "pk"). Pass-through to lnk_pipeline_mapping_code()'s spawn_only_species arg.

Value

Invisibly, the per-segment per-species mapping_code tibble keyed by id_segment with one mapping_code_<sp> text column per species in union(species_resident, species_anadromous).

Details

Decouples the mapping_code build from any specific schema layout. Caller passes explicit table names — the function works against working-schema tables (mid-pipeline) or persist-schema tables (ad-hoc rebuild) without modification. The companion view <persist_schema>.streams_habitat_long_vw (created by lnk_persist_init()) presents the per-species split as a long-form shape so table_habitat can point at either layout.

This function replaces the inline assembly previously buried inside lnk_compare_wsg(). The compare wrapper now goes through this function via lnk_pipeline_run(..., mapping_code = TRUE). Operators can also call this directly against persist schema with the tunnel down — the build is tunnel-independent (the diff vs reference is separate, see .lnk_compare_wsg_mapping_code_diff).

Tracks link#187 (tunnel decouple + portable build).

See also

Other compare: lnk_compare_rollup(), lnk_compare_wsg(), lnk_parity_annotate()

Examples

if (FALSE) { # \dontrun{
conn <- DBI::dbConnect(
  RPostgres::Postgres(),
  host = "localhost", port = 5432, dbname = "fwapg",
  user = "postgres", password = "postgres")

# Working-schema build during a pipeline run:
lnk_mapping_code(
  conn,
  table_access  = "working_pars.streams_access",
  table_habitat = "working_pars.streams_habitat",
  table_streams = "working_pars.streams",
  aoi           = "PARS",
  table_to      = "working_pars.streams_mapping_code")

# Ad-hoc rebuild against persist (tunnel-free) for QGIS symbology:
lnk_mapping_code(
  conn,
  table_access  = "fresh_default.streams_access",
  table_habitat = "fresh_default.streams_habitat_long_vw",
  table_streams = "fresh_default.streams",
  aoi           = "PARS",
  table_to      = "fresh_default.streams_mapping_code")
} # }