# Install package install.packages("devtools", repos = "http://cran.us.r-project.org") library("devtools") install_github("pfmc-assessments/nwfscDeltaGLM") # Load package library(nwfscDeltaGLM)
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 = data.frame( STRATA = LETTERS[1:15], NLat = seq(1.5, 15.5, 1), SLat = seq(0.5, 14.5, 1), MinDepth = 0, MaxDepth = 100, stringsAsFactors = FALSE )
species = "Simulated_Species" names(masterDat)[which(names(masterDat)=="SPECIES_WT_KG")] = species masterDat = cbind(masterDat, AREA_SWEPT_MSQ=masterDat$AREA_SWEPT_HA*1e4)
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)
This looks for an object named \code{masterDat} in the global environment,
DataList = processData(masterDat = masterDat, strata.limits = strata.limits, X.bin=X.bin, X.pos=X.pos)
mcmc.control = list(chains=3, thin=1, burnin=100, iterToSave=200) 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") 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")
Create a list that could be used to hold additional models,
fitted_models = list() fitted_models[[1]] = fitDeltaGLM(datalist=DataList, likelihood = "gamma", modelStructure=modelStructure1, mcmc.control=mcmc.control, covariates=Covariates, Species=species) fitted_models[[2]] = fitDeltaGLM(datalist=DataList, likelihood = "gamma", modelStructure=modelStructure2, mcmc.control=mcmc.control, covariates=Covariates, Species=species)
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