calc_df: Calculate expansion fields as a Data Frame

In PIFSCstockassessments/expalg.cie: Expansion Algorithm

Calculate expansion fields as a Data Frame

Description

Calculate expansion fields as a Data Frame

Usage

calc_df(
  year,
  pool_f,
  species,
  bl,
  bl2,
  bl_unknown_method,
  bl_unknown_fished,
  bl_known_fished,
  p1,
  p2,
  sample_days,
  days,
  interviews,
  interviews_raw,
  method_index,
  method_key,
  ports_refer,
  reference,
  port_index,
  type_of_day_index,
  charter_index,
  other_ports
)

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 species = NA)
bl	counts of boat log entries with known fishing method for each domain ([PORT_FK, TYPE_OF_DAY, METHOD_FK, CHARTER_F])
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 this domain
interviews_raw	all interviews for all years, for use when pooling
method_index	vector index of the current method
method_key	database key of the current method
ports_refer	vector to convert port keys to port indices
reference	reference values for the current method
port_index	vector index of the current port
type_of_day_index	vector index of the current type of day
charter_index	vector index of the current charter status
other_ports	boolean for whether this expansion is for the other (unsampled) ports (survey_zone = 24)

Value

Data frame with a single row containing all expansion fields for the current domain

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