YFT MAIN DATASET: 100 simulated YFT datasets at the 1 area scale — YFT_1area_observations_1_100

This R data file contains 100 data sets for a one area YFT model. 100 simulations of the YFT 1 area aggregated catch, cpue, length frequencies, and tagging data (along with biological data).

data('YFT_1area_observations_1_100_v2')

Format

A data frame 'YFT_1area_observations_1_100_v2.Rdata' with variables:

dat_1A_X: Simulated aggregated 1 area datasets for YFT; X=1:100
biol_dat: Biological data for YFT

The key lists in YFT_1area_observations_1_100_v2$ (e.g., dat_1A_1$lencomp) include:

lencomp: (list) 1 area dataframe of aggregated length frequencies by length bin with columns corresponding to pseudo-year (Yr), season(Seas), fleet/survey index (FltSvy), sex (Gender), partition – length data come from all fish encountered (Part=0), number of lengths sampled (Nsamp), and the set of length bins.

catch: (list) 1 area dataframe of catch by fishery, including pseudo-year (year), and season (seas)

CPUE/cpu: (list) 1 area cpue with columns for pseudo-year (year), season (seas), cpue (cpu), standard deviation associated with lognormal error in cpue (cv), and survey index (index); note that CPUE is for longline only

tag_releases: 1 area tag release data with columns corresponding to generic tag release event number (tg), area of release (reg), pseudo-year (yr), season (season), sex (Gender), age (age), and number of releases (nrel) adjusted for initial tag mortality

tag_recaps: 1 area tag recapture data with columns corresponding to generic tag release event number (tg), pseudo-year (yr), season (season), fleet index (fleet), and the number of recaptures (recaps)

Explanations of list object items in the provided data files that analysts may find additionally useful.

Much of these follow, or closely follow, Stock Synthesis (version SS3.24Z) naming conventions. The name is the list identifier in each Rdata object (e.g., the name styr is found using dat_1A_4$styr).

styr Start year (pseudo-year)

endyr End year (pseudo-year)

nseas Number of seasons

spawn_seas Season when spawning occurs

Nfleet Number of fishing fleets

Nsurveys Number of surveys (fishery-dependent CPUE)

N_areas Number of spatial areas

fleetnames Specific fleet and survey index names

surveytiming Timing of fleet and surveys

areas Areas where each fleet or survey operate

units_of_catch Specifies units for catch (2=numbers of fish)

se_log_catch Standard error associated with catch

Ngenders Number of sexes

Nages Number of ages

lbin_vector_pop Vector of length bins in the population (cm)

lbin_vector Vector of length bins in the data (cm)

N_tag_groups Number of tag release events

N_recap_events Number of recapture events

mixing_latency_period Length of time units (psudo-years) necessary to allow for tag mixing

The lists in biol_dat include:

M: age varying natural mortality

age: first age to last age (pseudo-years)

maturity: maturity at age ogive (pseudo-years)

k: age varying growth coefficients

L: length (cm)

Linf: length infinity (cm)

Lmin: length minimum (cm)

a: length-weight scaling coefficient

b: length-weight shape parameter

LenAge_cv: length-age coefficient of variability

Examples

data('YFT_1area_observations_1_100_v2')
#> Warning: data set 'YFT_1area_observations_1_100_v2' not found
head(dat_1A_1$catch)
#> Error in head(dat_1A_1$catch): object 'dat_1A_1' not found
head(biol_dat)
#> Error in head(biol_dat): object 'biol_dat' not found