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# Install dependencies
install.packages('rjags')
install.packages('R2jags')
install.packages('pscl')
install.packages('runjags')
install.packages('statmod')
install.packages('superdiag')
# Install package
install.packages("nwfscDeltaGLM", repos="http://R-Forge.R-project.org", type="source")
# Load package
library(nwfscDeltaGLM)
# updateDeltaGLMcode()
# File structure
my.wd <- "C:/Users/James.Thorson/Desktop/"
setwd(my.wd)
# Simulate data
# MeanEncounter=0.5; Nyears=10; Nstrata=15; Nvessels=4; Obsperyear=175; sigmaV=rep(1,2); sigmaVY=rep(1,2); sigmaS=rep(1,2); sigmaY=rep(1,2); sigmaSY=rep(1,2); sigmaResid=1
Sim_List = SimSimple( MeanEncounter=0.5, Nyears=10, Nstrata=15, Nvessels=4, Obsperyear=175, sigmaV=rep(0,2), sigmaVY=rep(1,2), sigmaS=rep(1,2), sigmaY=rep(1,2), sigmaSY=rep(1,2), sigmaResid=1 )
masterDat = Sim_List[["DF"]]
strata.limits <- readIn(ncol=5,nlines=16)
STRATA NLat SLat MinDepth MaxDepth
A 1.5 0.5 0 100
B 2.5 1.5 0 100
C 3.5 2.5 0 100
D 4.5 3.5 0 100
E 5.5 4.5 0 100
F 6.5 5.5 0 100
G 7.5 6.5 0 100
H 8.5 7.5 0 100
I 9.5 8.5 0 100
J 10.5 9.5 0 100
K 11.5 10.5 0 100
L 12.5 11.5 0 100
M 13.5 12.5 0 100
N 14.5 13.5 0 100
O 15.5 14.5 0 100
# Generate useless covariates (i.e., not in the true operating model)
Covariates = list(positive=TRUE, binomial=TRUE)
nX.binomial = 1
nX.pos = 1
X.bin = matrix( rnorm(nrow(masterDat)*nX.binomial, mean=0, sd=1), ncol=nX.binomial)
X.pos = matrix( rnorm(nrow(masterDat)*nX.pos, mean=0, sd=1), ncol=nX.pos)
# Modify data slightly
species = "Simulated_Species"
names(masterDat)[5] = species
masterDat = cbind(masterDat, AREA_SWEPT_MSQ=masterDat$AREA_SWEPT_HA*1e4)
processData()
# Define settings
#mcmc.control = list(chains=3, thin=1e1, burnin=1e4, iterToSave=1e4)
mcmc.control = list(chains=2, thin=1e0, burnin=1e3, iterToSave=1e3)
Parallel = FALSE # If having trouble, try turning off parallel
# Define models
mods = list()
modelStructure1 = list("StrataYear.positiveTows"="zero", "VesselYear.positiveTows"="random2", "StrataYear.zeroTows"="zero", "VesselYear.zeroTows"="random2", "Vessel.positiveTows"="zero", "Vessel.zeroTows"="zero", "Catchability.positiveTows"="one", "Catchability.zeroTows"="zero", "year.deviations"="fixed", "strata.deviations"="fixed")
mods[[1]] = fitDeltaGLM(likelihood = "gamma", modelStructure=modelStructure1, mcmc.control=mcmc.control, covariates=Covariates, Parallel=Parallel, Species=species)
modelStructure2 = list("StrataYear.positiveTows"="zero", "VesselYear.positiveTows"="zero", "Vessel.positiveTows"="random2", "StrataYear.zeroTows"="zero", "VesselYear.zeroTows"="zero", "Vessel.zeroTows"="random2", "Catchability.positiveTows"="one", "Catchability.zeroTows"="zero", "year.deviations"="fixed", "strata.deviations"="fixed")
mods[[2]] = fitDeltaGLM(likelihood = "gamma", modelStructure=modelStructure2, mcmc.control=mcmc.control, covariates=Covariates, Parallel=Parallel, Species=species)
save(mods, file=paste(my.wd,"mods.RData",sep=""))
# Process MCMC output
data(SA3)
doMCMCDiags(my.wd, mods, StrataWeights="Equal")
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