nwfscDeltaGLM: Bayesian delta-GLM package for constructing indices of CPUE data

The nwfscDeltaGLM package provides a Bayesian framework for constructing CPUE indices out of stratified survey (or commercial) fisheries landings data. The model can also be applied to similarly stratified bycatch data. The model is very flexible, optionally allowing the incorporation of strata, year, and vessel effects, strata x year and vessel x year interactions, and fixed covariates. Several parameterization for including offsets (effort) are also included. Each of these can be included in the presence-absence (occupancy) model or the positive component of the delta-GLM model.

AuthorEric Ward, Jim Thorson, NOAA, NWFSC, Seattle, USA
Date of publication2014-08-11 05:17:29
MaintainerEric Ward - NOAA Federal <eric.ward@noaa.gov>
LicenseGPL-2
Version1.0

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Files in this package

nwfscDeltaGLM/DESCRIPTION
nwfscDeltaGLM/NAMESPACE
nwfscDeltaGLM/R
nwfscDeltaGLM/R/ComputeIndices.R nwfscDeltaGLM/R/ComputeMleIndices.R
nwfscDeltaGLM/R/ConvergencePlot.r
nwfscDeltaGLM/R/LoadFn.r
nwfscDeltaGLM/R/MCMCDiagnosticsPlot.R
nwfscDeltaGLM/R/MapData.r
nwfscDeltaGLM/R/PlotData.R
nwfscDeltaGLM/R/PlotOffset.r
nwfscDeltaGLM/R/PosteriorPredictive.r
nwfscDeltaGLM/R/SimSimple.R nwfscDeltaGLM/R/cMx.R
nwfscDeltaGLM/R/corFunction.r
nwfscDeltaGLM/R/doMCMCDiags.r
nwfscDeltaGLM/R/fitDeltaGLM.R nwfscDeltaGLM/R/logDensity.R nwfscDeltaGLM/R/onLoad.R
nwfscDeltaGLM/R/processData.r
nwfscDeltaGLM/R/readIn.R
nwfscDeltaGLM/R/strata.fn.r
nwfscDeltaGLM/R/updateDeltaGLMcode.R
nwfscDeltaGLM/data
nwfscDeltaGLM/data/AFSCforeign_hauls.txt.gz
nwfscDeltaGLM/data/Example_Species.txt.gz
nwfscDeltaGLM/data/SA3.txt.gz
nwfscDeltaGLM/examples
nwfscDeltaGLM/examples/Example_Species.csv
nwfscDeltaGLM/examples/Example_delta-GLMM.R
nwfscDeltaGLM/examples/Example_delta-GLMM_simulation.R
nwfscDeltaGLM/examples/INPFCandStateLatitudeBounds.txt
nwfscDeltaGLM/examples/Testing_delta-GLMM_calibration.R
nwfscDeltaGLM/examples/bayesGLM_Writeup_2.15.docx
nwfscDeltaGLM/examples/defaultLimits.csv
nwfscDeltaGLM/man
nwfscDeltaGLM/man/ComputeIndices.Rd nwfscDeltaGLM/man/ComputeMleIndices.Rd nwfscDeltaGLM/man/ConvergencePlot.Rd nwfscDeltaGLM/man/MCMCDiagnosticsPlot.Rd nwfscDeltaGLM/man/MapData.Rd nwfscDeltaGLM/man/PlotData.Rd nwfscDeltaGLM/man/PlotOffset.Rd nwfscDeltaGLM/man/PosteriorPredictive.Rd nwfscDeltaGLM/man/SimSimple.Rd nwfscDeltaGLM/man/cMx.Rd nwfscDeltaGLM/man/corFunction.Rd nwfscDeltaGLM/man/doMCMCDiags.Rd nwfscDeltaGLM/man/fitDeltaGLM.Rd nwfscDeltaGLM/man/loadFn.Rd nwfscDeltaGLM/man/logDensity.Rd nwfscDeltaGLM/man/nwfscDeltaGLM-package.Rd nwfscDeltaGLM/man/processData.Rd nwfscDeltaGLM/man/readIn.Rd nwfscDeltaGLM/man/strata.fn.Rd
nwfscDeltaGLM/nwfscDeltaGLM.Rproj

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