Index standardization

This example will provide an abundance index for Alaska pollock in the eastern Bering Sea.

It’s useful for reproducibility to record and use a specific VAST release number, while noting your system specifications. This example is run under VAST 3.9.1.
Retrieve system and package version numbers with sessionInfo()

Set up

Install the latest version of VAST

devtools::install_github("James-Thorson-NOAA/VAST")

Set local working directory (change for your machine)

setwd( "Enter directory location here" )

Load VAST and the example data set

library(VAST)

# examples installed with VAST
example = load_example( data_set="EBS_pollock" )

Additional datasets are available in load_example. See ?load_example for list of stocks with example data. To use a new data set, input new data in the same format as example data. See ?make_data for more details.

Configure model settings

Make settings, with defaults defined by the specified purpose argument. Here, we use purpose="index2" which reflects current “good practices” for standardizing an abundance index for use in a subsequent stock-assessment model.

settings = make_settings( n_x = 100, 
  Region = example$Region, 
  purpose = "index2" )

Run the model

Run model, where default settings can be overridden by passing additional arguments to fit_model

fit = fit_model( settings = settings, 
  Lat_i = example$sampling_data[,'Lat'], 
  Lon_i = example$sampling_data[,'Lon'], 
  t_i = example$sampling_data[,'Year'], 
  b_i = example$sampling_data[,'Catch_KG'], 
  a_i = example$sampling_data[,'AreaSwept_km2'] )

See the model results

Plot results. Add some more info here.

plot( fit )

Predicted density of Alaska pollock in the eastern Bering Sea for each year

Works cited

Thorson, J. T., Shelton, A. O., Ward, E. J., and Skaug, H. J. 2015. Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES Journal of Marine Science: Journal du Conseil, 72: 1297–1310.