Bootstrap data sources to replicate bottom trawl survey age and length composition for computation of input sample size tailored to GOA stock complexes (i.e., rougheye-blackspotted and dusky rockfish; where length and age composition are expanded for each individual species in the complex, and combined post expansion)
srvy_iss_goa_cmplx(
iters = 1,
lfreq_data,
specimen_data,
cpue_data,
strata_data,
yrs = NULL,
bin = 1,
boot_hauls = FALSE,
boot_lengths = FALSE,
boot_ages = FALSE,
al_var = FALSE,
al_var_ann = FALSE,
age_err = FALSE,
len_samples = NULL,
age_samples = NULL,
plus_len = NULL,
plus_age = NULL,
cmplx_code = 3005012,
by_strata = FALSE,
global = FALSE,
cmplx = "rebs",
region = "goa",
save_interm = FALSE,
save_stats = FALSE,
save
)number of iterations (min of 500 recommended for full run)
length frequency input dataframe
age-length specimen input dataframe
catch-per-unit effort input dataframe
strata id and area size input dataframe
any year filter >= (default = NULL)
bin size (default = 1 cm), also can use custom length bins following ss3 bin convention
Boolean. Resample hauls w/replacement? (default = FALSE)
Boolean. Resample length frequency w/replacement? (default = FALSE)
Boolean. Resample ages w/replacement? (default = FALSE)
Boolean. Include age-length variability in resampled age data? (default = FALSE)
Boolean. Resample age-length variability annually or pooled across years? (default = FALSE)
Boolean. Include ageing error in resampled age data? (default = FALSE)
If set at a value, tests reductions in haul-level length sampling. To test, set this value at some smaller level than current sampling rate, i.e., 25 (default = NULL)
If set at a value, tests reductions (and increases) in survey-level number of ages collected. To test, set at a proportion of ages collected, i.e., 0.8 or 1.2 (default = NULL)
If set at a value, computes length expansion with a plus-length group (default = FALSE)
If set at a value, computes age expansion with a plus-age group (default = FALSE)
Numeric value to replace the individual species codes with a complex code shared across species. (default = 3005012)
Boolean. Should length/age pop'n values be computed at stratum level? (default = FALSE)
Boolean. Fill in missing length bins with global age-lenth key? (default = FALSE)
Complex name for saving results. (default = 'rebs')
Region will create a folder and place results in said folder. (default = 'goa')
Boolean. Save the intermediate results: resampled age/length comps and realized sample size per iteration? (default = FALSE)
Boolean. Save other statistics: base age/length comps without resampling, mean length-at-age, bootstrap bias? (default = FALSE)
Name to attach to and identify output files.
Dataframe of input sample size by year, complex (designated with cmplx_code), sex (0 - combined sex with age/length data combined prior to expansion, 1 - males, 2 - females, 3 - unsexed, 12 - female/male compositions that sum to one across both sexes combined, 4 - combined sex after summing sex-specific age/length composition after expansion; all with short description IDs in sex_desc column) for age composition (output saved with 'iss_age' in file name) and length composition (output saved with 'iss_ln' in file name). For comparison, nominal sample size ('nss' - the number of age/length samples actually taken) and the number of sampled hauls for age/length ('nhls') are included. GOA complex output will be denoted with whatever is defined in cmplx argument within the file name. Will also produce other dataframes if desired (see save_intern and save_stats argument descriptions).