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:

# Download development branch (or perhaps master branch in future releases)
devtools::install_github("james-thorson/VAST", ref="development")
devtools::install_github("james-thorson/FishStatsUtils", ref="development")

# Load packages
library(TMB)
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$Region, purpose="index",
  strata.limits=example$strata.limits )

# Change settings from defaults
settings$ObsModel = c(2,0)
settings$use_anisotropy = FALSE
settings$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'], model_args=list("Npool"=20),
  newtonsteps=0, optimize_args=list("getsd"=FALSE) )

# Plot results
plot_results( settings=settings, fit=fit )

• Note: this result differs somewhat from the result used for backwards-compatibility checks, due to differences in the k-means locations for knots between earlier reposited results and newer version of FishStatsUtils.