nwfscDeltaGLM-package: Package for conducting Bayesian estimation of CPUE index...
In nwfscDeltaGLM: Bayesian delta-GLM package for constructing indices of CPUE data

Description Details Author(s) References Examples

The nwfscDeltaGLM package is developed by the Northwest Fisheries Science Center, National Oceanic Administration, USA. It's primary purpose is for application to stock assessment, where it can be used to generate time series of CPUE indices from raw trawl data. Optional model components include vessel, strata, and year effects, as well as their interactions. A number of likelihoods are included for the positive component of the model, including both continuous (lognormal, gamma, inverse Gaussian) and discrete (Poisson, Negative Binomial) distributions.

Package:
Type:	Package
Version:	1.0
Date:	2013-12-05
License:	What license is it under?

~~ An overview of how to use the package, including the most important functions ~~

Eric J Ward

Maintainer: Eric Ward <eric.ward@noaa.gov>

Thorson, J.T. and E.J. Ward. 2013. Accounting for space<e2><80><93>time interactions in index standardization models. Fisheries Research, 147, 426:433.

#data(Example_Species)
#masterDat = Example_Species
#LoadFn(paste(DataFile,"RandomSpecies.dmp",sep=""))
#strata.limits <- readIn(ncol=5,nlines=6)
#  STRATA  NLat SLat MinDepth MaxDepth
#  A      49.0 36.0  55        183
#  B      49.0 36.0  183       549
#  C      49.0 34.5  549       700
#  D      36.0 34.5  55        549
#  E      34.5 32.0  55        549

# Modify data slightly
#species = "Example_Species"
#names(masterDat)[9] = species

# Preliminary data processing
#processData()

# Define settings
#mcmc.control = list(chains=2, thin=2, burnin=2e3, iterToSave=2e3)
#Parallel = TRUE   # If having trouble, try turning off parallel
#modelStructure1 = list("StrataYear.positiveTows"="fixed", "VesselYear.positiveTows"="random", "StrataYear.zeroTows"="fixed", "VesselYear.zeroTows"="random", "Catchability.positiveTows"="one", "Catchability.zeroTows"="zero", "year.deviations"="fixed", "strata.deviations"="fixed")
modelStructure1 = list("StrataYear.positiveTows"="fixed", "VesselYear.positiveTows"="fixed", "StrataYear.zeroTows"="fixed", "VesselYear.zeroTows"="fixed", "Catchability.positiveTows"="one", "Catchability.zeroTows"="zero", "year.deviations"="fixed", "strata.deviations"="fixed")
#modelStructure2 = list("StrataYear.positiveTows"="correlated", "VesselYear.positiveTows"="correlated", "StrataYear.zeroTows"="correlated", "VesselYear.zeroTows"="correlated", "Catchability.positiveTows"="one", "Catchability.zeroTows"="zero", "year.deviations"="fixed", "strata.deviations"="fixed")

# Define models
#attach(Data)
#mods = list()
#mods[[1]] = fitDeltaGLM(modelStructure=modelStructure1, mcmc.control=mcmc.control,Parallel=Parallel, Species=species)
#mods[[2]] = fitCPUEModel(modelStructure=modelStructure2, mcmc.control=mcmc.control, Parallel=Parallel, Species=species)

# Process MCMC output
# Make sure that Data is attached prior to running
#doMCMCDiags(my.wd,mods)