README.md

In nwfsc-assess/VAST_WestCoast: Estimation and simulation with VAST for the US West Coast

VASTWestCoast

The Northwest Fisheries Science Center (NWFSC) uses VAST to generate indicies of abundance from survey data. This package, VASTWestCoast, acts as a wrapper for VAST, where the input arguments are specific to those needed for the NWFSC.

Installing

Install issues are always troublesome, for which I am sorry. The best guidance I can give you is to close all of your current R sessions and open a new R session before trying to install any of the following packages. Lastly, use the internal check functions to see if TMB is properly installed prior to running other VASTWestCoast functions.

remotes::install_github("James-Thorson-NOAA/FishStatsUtils")
remotes::install_github("James-Thorson-NOAA/VAST")
remotes::install_github("pfmc-assessments/VASTWestCoast")
library(VASTWestCoast)

Using VASTWestCoast

Configuration of the VAST package is complex, and the intent of VASTWestCoast was to simplify and standardize the code needed to generate indices of abundance for species managed by the Pacific Fisheries Management Council (PFMC). Settings that should be specified the same regardless of species and of survey are set behind the scenes to ensure their consistency. For example, all results are corrected for retransformation bias to account for nonlinear transformation of random effects (Thorson and Kristensen, 2016).

The simplest way to run VAST is to use

?VASTWestCoast::VAST_spp
VAST_spp(dir = getwd(), species = "sablefish")

where the species argument is the common name for the species of interest.

Issues

Please post all issues to the github issues board such that other users can benefit from the conversation generated. The use of appropriately labelled issues is extremely beneficial to developers in that current needs can be both tracked and prioritized for everyone's benefit.

nwfsc-assess/VAST_WestCoast documentation built on July 4, 2023, 5:45 p.m.