df_expansion: Expansion and Species Composition of an expansion domain

In PIFSCstockassessments/expalg.cie: Expansion Algorithm

Expansion and Species Composition of an expansion domain

Description

Expansion and Species Composition of an expansion domain

Usage

df_expansion(
  year,
  pool_f,
  species,
  bl,
  bl2,
  bl_unknown_method,
  bl_unknown_fished,
  bl_known_fished,
  p1,
  p2,
  sample_days,
  days,
  interviews,
  interviews_raw,
  catch,
  catch_raw,
  methods_refer,
  ports_refer,
  reference
)

Arguments

year	Year of the expansion
pool_f	Whether to pool interviews when fewer than 3 are available for a domain
species	a vector of species or all species (when spcies = NA)
bl	boat log entries ...
bl2	squared counts of boat log entries with known fishing method for each domain ([PORT_FK, TYPE_OF_DAY, METHOD_FK, CHARTER_F])
bl_unknown_method	counts of boat log entries with unknown fishing method for each domain ([PORT_FK, TYPE_OF_DAY, CHARTER_F])
bl_unknown_fished	counts of boat log entries with unknown fishing status for each domain ([PORT_FK, TYPE_OF_DAY, CHARTER_F])
bl_known_fished	counts of boat log entries with known fishing status for each domain ([PORT_FK, TYPE_OF_DAY, CHARTER_F])
p1	adjustment factors to account for missed vessels outside of shift times for each domain ([PORT_FK, METHOD_FK, CHARTER_F])
p2	adjustment factor to account for vessels outside of the sampled ports
sample_days	the number of sample days for each domain ([PORT_FK, TYPE_OF_DAY])
days	the number of calendar days for each domain ([TYPE_OF_DAY])
interviews	interviews for the expansion period
interviews_raw	all interviews for all years, for use when pooling
catch	interview catch data for the expansion period
catch_raw	interview catch data for all years
methods_refer	vector to convert method keys to method indices
ports_refer	vector to convert port keys to port indices
reference	reference values for use when insufficient interviews are available for a domain

Value

Two data frames containing all expansion and species composition fields for each expansion domain

PIFSCstockassessments/expalg.cie documentation built on June 15, 2022, 1:41 a.m.