Classify Habitat for One Species

Copy a base stream network, apply pre-computed access barriers, then classify spawning, rearing, and lake rearing habitat for a single species. Each species gets its own output table because break points modify segment geometry.

Usage

frs_habitat_species(
  conn,
  species_code,
  base_tbl,
  breaks,
  breaks_habitat = NULL,
  params_sp,
  fresh_sp,
  to = NULL
)

Arguments

conn

A DBI::DBIConnection object (from frs_db_conn()).

species_code

Character. Uppercase species code (e.g. "CO", "BT").

base_tbl

Character. Schema-qualified base table with the enriched stream network (from frs_extract() + frs_col_join()).

breaks

Character. Schema-qualified access breaks table from frs_habitat_access().

breaks_habitat

Character or NULL. Schema-qualified habitat gradient breaks table. When provided, skips the per-species gradient scan and applies this pre-computed table instead. Default NULL computes on the fly.

params_sp

Named list. Species parameters from frs_params() (e.g. frs_params()$CO).

fresh_sp

Data frame row. Species row from parameters_fresh.csv with access_gradient_max, spawn_gradient_min.

to

Character or NULL. Output table name. Default NULL uses working.streams_{sp}.

Value

conn invisibly, for pipe chaining.

See also

Other habitat: frs_aggregate(), frs_break(), frs_break_apply(), frs_break_find(), frs_break_validate(), frs_categorize(), frs_classify(), frs_col_generate(), frs_col_join(), frs_extract(), frs_habitat(), frs_habitat_access(), frs_habitat_partition()

Examples

if (FALSE) { # \dontrun{
conn <- frs_db_conn()
params <- frs_params(csv = system.file("extdata",
  "parameters_habitat_thresholds.csv", package = "fresh"))
fresh <- read.csv(system.file("extdata",
  "parameters_fresh.csv", package = "fresh"))

frs_habitat_species(conn, "CO", "working.streams_bulk",
  breaks = "working.breaks_access_bulk_015",
  breaks_habitat = "working.breaks_habitat_bulk_00549",
  params_sp = params$CO,
  fresh_sp = fresh[fresh$species_code == "CO", ],
  to = "working.streams_bulk_co")

DBI::dbDisconnect(conn)
} # }