/VAST

Spatio-temporal analysis of univariate or multivariate data, e.g., standardizing data for multiple species or stages

Primary LanguageC++GNU General Public License v3.0GPL-3.0

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.

User resources for learning about VAST

There are eight main resources for learning about VAST:

  • Model structure: Please see the User Manual for a document listing model equations and relating them to the input/output used in R.
  • Guidance for user decisions: Please see Thorson-2019 for guidance regarding the 15 major decisions needed in every VAST model
  • Examples: Please see examples folder for annoted Rmarkdown scripts that run single-species or multi-species examples for a variety of regions.
  • R-help documentation: Please see the standard R-help documentation, e.g., by typing ?VAST::Data_Fn in the R-terminal after installing the package.
  • Publications: Please see the publications list to identify peer-reviewed publications regarding individual features. These publications include statistical theory and model testing.
  • List-serv: Consider joining the FishStats listserve for 4-6 updates per year, including training classes.
  • Issue-tracker: Before posting new issues, users should explore the previous issues in the github issue tracker for VAST, SpatialDeltaGLMM, and FishStatsUtils, including a search for old and closed issues.
  • Wiki: Users should read and are encouraged to actively contribute to the wiki, which is housed at the github for SpatialDeltaGLMM

If there are questions that arise after this, please look for a VAST Point-of-Contact at your institution and consider contacting them prior to posting an issue.

Database

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

Installation Instructions

Build Status DOI

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:

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 VAST 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

Description of package

Please cite if using the software

  • Thorson, J.T., Barnett, L.A.K., 2017. Comparing estimates of abundance trends and distribution shifts using single- and multispecies models of fishes and biogenic habitat. ICES J. Mar. Sci. 74, 1311–1321. https://doi.org/10.1093/icesjms/fsw193
  • Thorson, J.T., 2019. Guidance for decisions using the Vector Autoregressive Spatio-Temporal (VAST) package in stock, ecosystem, habitat and climate assessments. Fish. Res. 210, 143–161. https://doi.org/10.1016/j.fishres.2018.10.013

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

Standardizing samples of size/age-composition data

Range shift metrics

Effective area occupied metric

Spatio-temporal statistical methods

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

Accounting for fisher targetting in fishery-dependent data

Bias-correction of estimated indices of abundance

Estimating and attributing variation in size-structured distribution

  • Kai, M., Thorson, J. T., Piner, K. R., and Maunder, M. N. 2017. Spatio-temporal variation in size-structured populations using fishery data: an application to shortfin mako (Isurus oxyrinchus) in the Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences. doi:10.1139/cjfas-2016-0327. URL: http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2016-0327#.W0olqjpKiUk.
  • Thorson, J. T., Ianelli, J. N., and Kotwicki, S. 2018. The relative influence of temperature and size-structure on fish distribution shifts: A case-study on Walleye pollock in the Bering Sea. Fish and Fisheries. doi:10.1111/faf.12225. URL: https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12225.

Estimating fishing impacts using spatial surplus production modelling

Estimating species interactions using multispecies Gompertz model

Estimating synchrony among species and locations as measure of risk-exposure

  • Thorson, J.T., Scheuerell, M.D., Olden, J.D., Schindler, D.E., 2018. Spatial heterogeneity contributes more to portfolio effects than species variability in bottom-associated marine fishes. Proc R Soc B 285, 20180915. https://doi.org/10.1098/rspb.2018.0915

Forecasting future changes in distribution or abundance

Thorson, In press. Forecast skill for predicting distribution shifts: A retrospective experiment for marine fishes in the Eastern Bering Sea. Fish Fish.

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.
  • Thorson, J., Ianelli, J., and O’Brien, L. 2015. 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