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nwfscDeltaGLM Is an R package for implementing a Bayesian stratified delta-GLMM for use when standardizing fishery-independent index data for U.S. West Coast surveys. Has built in diagnostic functions and model-comparison tools * Is intended to improve analysis speed, replicability, peer-review, and interpretation of index standardization methods


First, please install JAGS (Just Another Gibbs Sampler) here:

Next, please use R version >=3.1.1 and install the package:

# Install package
# Current releases can be installed with
# Specific version can be installed as
# install_github("nwfsc-assess/nwfscDeltaGLM", ref="1.0.0") 
# Load package

Please see vignettes folder (i.e., for an example of how to run the model. Or for an example of how to simulate and fit some different data structures.

Known installation/usage issues

Please read the following list of known problems and solutions * Users sometimes have trouble loading the package, with R throwing an error about package "rjags". Please reinstall the latest version of JAGS and then re-install nwfscDeltaGLM

Further reading

For more details regarding development and testing of this delta-GLMM software please see: Shelton, A. O., J. T. Thorson, E. J. Ward, and B. E. Feist. 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: Thorson, J. T., and E. J. Ward. 2014. Accounting for vessel effects when standardizing catch rates from cooperative surveys. Fisheries Research 155:168–176. Thorson, J. T., and E. Ward. 2013. Accounting for space-time interactions in index standardization models. Fisheries Research 147:426–433. 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. 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. Helser, T. E., A. E. Punt, and R. D. Methot. 2004. A generalized linear mixed model analysis of a multi-vessel fishery resource survey. Fisheries Research 70:251–264.

nwfsc-assess/nwfscDeltaGLM documentation built on April 4, 2018, 3:06 p.m.