nwfscDeltaGLM-package: Package for conducting Bayesian estimation of CPUE index...

In nwfsc-assess/nwfscDeltaGLM: Bayesian delta-GLM package for constructing indices of CPUE data

Package for conducting Bayesian estimation of CPUE index standardization (fisheries, ecology).

Description

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.

Author(s)

Maintainer: Eric Ward <[e-mail]>

References

Thorson, J.T. and E.J. Ward. 2013. Accounting for space-time interactions in index standardization models. Fisheries Research, 147, 426-433.

Thorson, J.T., A.O. Shelton, E.J. Ward, and H.J. Skaug. 2015. Geostatistical delta-generalized linear mixed models improve precision for estimated abundance indices for West Coast groundfishes. ICES J Mar Sci, 72, 1297-1310.

Examples

data(Example_Species) # raw haul data
data(SA3) # raw strata areas
data(defaultLimits) # default limits

masterDat = Example_Species

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

# Preliminary data processing
DataList = processData(masterDat = masterDat, strata.limits=defaultLimits)

# Define settings
mcmc.control = list(chains=3, thin=1, burnin=500, iterToSave=1000)

modelStructure1 = list("StrataYear.positiveTows"="fixed",
"VesselYear.positiveTows"="zero",
"StrataYear.zeroTows"="fixed",
"VesselYear.zeroTows"="zero",
"Vessel.positiveTows"="zero",
"Vessel.zeroTows"="zero",
"Catchability.positiveTows"="one",
"Catchability.zeroTows"="zero",
"year.deviations"="fixed",
"strata.deviations"="fixed")

# Define models
fitted_models = list()
fitted_models[[1]] = fitDeltaGLM(datalist=DataList, modelStructure=modelStructure1,
mcmc.control=mcmc.control,
Species=species,
Parallel=FALSE)

#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)

nwfsc-assess/nwfscDeltaGLM documentation built on July 8, 2023, 4:49 a.m.