Expand age and length composition

Expanding age/length composition data for use in stock assessments

It is possible to use VAST to expand subsamples of age/length composition obtained during bottom-trawl sampling. To do so, we first perform first-stage expansion and then fit a spatio-temporal model to those expanded samples:

# Load packages
library(VAST)

# load data set
# see `?load_example` for list of stocks with example data
# that are installed automatically with `FishStatsUtils`.
example = load_example( data_set="Lingcod_comp_expansion" )

# Make settings
settings = make_settings( n_x = 50,
  Region = example$Region,
  purpose = "index2",
  strata.limits = example$strata.limits,
  use_anisotropy = FALSE,
  fine_scale = FALSE )

# Run model
fit = fit_model( settings = settings,
  Lat_i = example$sampling_data[,'Lat'],
  Lon_i = example$sampling_data[,'Lon'],
  t_i = example$sampling_data[,'Year'],
  c_i = as.numeric(example$sampling_data[,'Length_bin'])-1,
  b_i = example$sampling_data[,'First_stage_expanded_numbers'],
  a_i = example$sampling_data[,'AreaSwept_km2'],
  Npool = 40,
  newtonsteps = 1,
  test_fit = FALSE )

# Plot results
results = plot( fit,
  check_residuals = FALSE )

# Calculate proportions
proportions = calculate_proportion( TmbData = fit$data_list,
  Index = results$Index,
  Year_Set = fit$year_labels )

Note: this code yields a slightly different result from those used for backwards-compatibility checks, due to differences in the k-means locations for knots between earlier reposited results and newer version of FishStatsUtils. Also, using "Npool"=20 using the newer k-means results in a noninvertible Hessian, so I here use "Npool"=40 instead.