Description

VAST

Is an R package for implementing a spatial delta-generalized linear mixed model (delta-GLMM) for multiple categories (species, size, or age classes) when standardizing survey or fishery-dependent data.
Builds upon a previous R package SpatialDeltaGLMM (public available here), and has unit-testing to automatically confirm that VAST and SpatialDeltaGLMM give identical results (to the 3rd decimal place for parameter estimates) for several varied real-world case-study examples
Has built in diagnostic functions and model-comparison tools
Is intended to improve analysis speed, replicability, peer-review, and interpretation of index standardization methods

Background

This tool is designed to estimate spatial variation in density using spatially referenced data, with the goal of habitat associations (correlations among species and with habitat) and estimating total abundance for a target species in one or more years.
The model builds upon spatio-temporal delta-generalized linear mixed modelling techniques (Thorson Shelton Ward Skaug 2015 ICESJMS), which separately models the proportion of tows that catch at least one individual ("encounter probability") and catch rates for tows with at least one individual ("positive catch rates").
Submodels for encounter probability and positive catch rates by default incorporate variation in density among years (as a fixed effect), and can incorporate variation among sampling vessels (as a random effect, Thorson and Ward 2014) which may be correlated among categories (Thorson Fonner Haltuch Ono Winker In press).
Spatial and spatiotemporal variation are approximated as Gaussian Markov random fields (Thorson Skaug Kristensen Shelton Ward Harms Banante 2014 Ecology), which imply that correlations in spatial variation decay as a function of distance.

Database

Regions available in the example script: and see FishViz.org for visualization of results for regions with a public API for their data.

Installation Instructions

This function depends on R version >=3.1.1 and a variety of other tools.

First, install the "devtools" package from CRAN

# Install and load devtools package
install.packages("devtools")
library("devtools")

Second, please install the following:

TMB (Template Model Builder): https://github.com/kaskr/adcomp
INLA (integrated nested Laplace approximations): http://www.r-inla.org/download

Note: at the moment, TMB and INLA can be installed using the commands

# devtools command to get TMB from GitHub
install_github("kaskr/adcomp/TMB") 
# source script to get INLA from the web
source("http://www.math.ntnu.no/inla/givemeINLA.R")

Next, please install the geostatistical_delta-GLMM package from this GitHub repository using a function in the "devtools" package:

# Install package
install_github("james-thorson/VAST") 
# Load package
library(VAST)

Known installation/usage issues

none

Example code

Please see examples folder for single-species and multi-species examples of how to run the model. This folder also contains a User Manual

This code illustrates how to loop through different default model configurations, plot diagnostics for each model, and obtain the AIC for each model.

Please also read the instructions from the single-species SpatialDeltaGLMM package, Guidelines for West Coast users wiki page, which is a living document and will evolve over time as best practices become apparent.

Description of package

Please cite if using the software

Thorson, J.T., and Barnett, L.A.K. In press. Comparing estimates of abundance trends and distribution shifts using single- and multispecies models of fishes and biogenic habitat. ICES J. Mar. Sci. URL: https://academic.oup.com/icesjms/article-abstract/2907795/Comparing-estimates-of-abundance-trends-and

Description of individual features

Correlated spatio-temporal variation among species

Thorson, J.T., Ianelli, J.N., Larsen, E., Ries, L., Scheuerell, M.D., Szuwalski, C., and Zipkin, E. 2016. Joint dynamic species distribution models: a tool for community ordination and spatiotemporal monitoring. Glob. Ecol. Biogeogr. 25(9): 1144–1158. doi:10.1111/geb.12464. url: http://onlinelibrary.wiley.com/doi/10.1111/geb.12464/abstract.
Thorson, J.T., Scheuerell, M.D., Shelton, A.O., See, K.E., Skaug, H.J., and Kristensen, K. 2015. Spatial factor analysis: a new tool for estimating joint species distributions and correlations in species range. Methods Ecol. Evol. 6(6): 627–637. doi:10.1111/2041-210X.12359. url: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12359/abstract

Index of abundance

Thorson, J.T., Shelton, A.O., Ward, E.J., Skaug, H.J., 2015. Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES J. Mar. Sci. J. Cons. 72(5), 1297–1310. doi:10.1093/icesjms/fsu243. URL: http://icesjms.oxfordjournals.org/content/72/5/1297

Range shift metrics

Thorson, J.T., Pinsky, M.L., Ward, E.J., 2016. Model-based inference for estimating shifts in species distribution, area occupied, and center of gravity. Methods Ecol. Evol. 7(8), 990-1008. doi:10.1111/2041-210X.12567. URL: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12567/full

Effective area occupied metric

Thorson, J.T., Rindorf, A., Gao, J., Hanselman, D.H., and Winker, H. 2016. Density-dependent changes in effective area occupied for sea-bottom-associated marine fishes. Proc R Soc B 283(1840): 20161853. doi:10.1098/rspb.2016.1853. URL: http://rspb.royalsocietypublishing.org/content/283/1840/20161853.

Spatio-temporal statistical methods

Thorson, J.T., Skaug, H.J., Kristensen, K., Shelton, A.O., Ward, E.J., Harms, J.H., Benante, J.A., 2014. The importance of spatial models for estimating the strength of density dependence. Ecology 96, 1202–1212. doi:10.1890/14-0739.1. URL: http://www.esajournals.org/doi/abs/10.1890/14-0739.1
Shelton, A.O., Thorson, J.T., Ward, E.J., Feist, B.E., 2014. Spatial semiparametric models improve estimates of species abundance and distribution. Can. J. Fish. Aquat. Sci. 71, 1655–1666. doi:10.1139/cjfas-2013-0508. URL: http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2013-0508#.VMafDf7F_h4

Accounting for fish shoals using robust observation models

Thorson, J. T., I. J. Stewart, and A. E. Punt. 2012. Development and application of an agent-based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish (Sebastes spp.). ICES Journal of Marine Science 69:635–647. URL: http://icesjms.oxfordjournals.org/content/69/4/635
Thorson, J. T., I. Stewart, and A. Punt. 2011. Accounting for fish shoals in single- and multi-species survey data using mixture distribution models. Canadian Journal of Fisheries and Aquatic Sciences 68:1681–1693. URL: http://www.nrcresearchpress.com/doi/abs/10.1139/f2011-086#.VMafcf7F_h4

Accounting for variation among vessels

Helser, T.E., Punt, A.E., Methot, R.D., 2004. A generalized linear mixed model analysis of a multi-vessel fishery resource survey. Fish. Res. 70, 251–264. doi:10.1016/j.fishres.2004.08.007. url: http://www.sciencedirect.com/science/article/pii/S0165783604001705
Thorson, J.T., Ward, E.J., 2014. Accounting for vessel effects when standardizing catch rates from cooperative surveys. Fish. Res. 155, 168–176. doi:10.1016/j.fishres.2014.02.036. url: http://www.sciencedirect.com/science/article/pii/S0165783614000836

Accounting for fisher targetting in fishery-dependent data

Thorson, J.T., Fonner, R., Haltuch, M., Ono, K., and Winker, H. In press. Accounting for spatiotemporal variation and fisher targeting when estimating abundance from multispecies fishery data. Can. J. Fish. Aquat. Sci. doi:10.1139/cjfas-2015-0598. URL: http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2015-0598

Bias-correction of estimated indices of abundance

Thorson, J.T., and Kristensen, K. 2016. Implementing a generic method for bias correction in statistical models using random effects, with spatial and population dynamics examples. Fish. Res. 175: 66–74. doi:10.1016/j.fishres.2015.11.016. url: http://www.sciencedirect.com/science/article/pii/S0165783615301399

Funding and support for the tool

Ongoing: Support from Fisheries Resource Analysis and Monitoring Division (FRAM), Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA
Ongoing: Support from Danish Technical University (in particular Kasper Kristensen) for development of Template Model Builder software, URL: https://www.jstatsoft.org/article/view/v070i05
Generous support from people knowledgeable about each region and survey! Specific contributions are listed here.
1. Thorson, J., Ianelli, J., and O’Brien, L. Distribution and application of a new geostatistical index standardization and habitat modeling tool for stock assessments and essential fish habitat designation in Alaska and Northwest Atlantic regions. Habitat Assessment Improvement Plan 2014 RFP. URL: https://www.st.nmfs.noaa.gov/ecosystems/habitat/funding/projects/project15-027

andrewdeines/VAST