#TEST
#----------------------------------------------------------------------------------------------
# LLSIm BUM by trip, with 5% observer coverage including observed catch in totals April 17 2022
#----------------------------------------------------------------------------------------------
library(BycatchEstimator)
library(MuMIn)
#-------------------------------------------------
#Step 1. Run the setup file and review data inputs
setupObj<-bycatchSetup(
#modelTry = c("Lognormal","Delta-Lognormal","Delta-Gamma","TMBnbinom1","TMBnbinom2","TMBtweedie"),
modelTry = c("Delta-Lognormal", "TMBnbinom2"),
obsdat = LLSIM_BUM_Example_observer,
logdat = LLSIM_BUM_Example_logbook,
yearVar = "Year",
obsEffort = "hooks",
logEffort = "hooks",
logUnsampledEffort = "unsampledEffort",
includeObsCatch = TRUE,
matchColumn = "trip",
factorNames = c("Year","fleet","area","season"),
randomEffects= NULL,
randomEffects2= NULL,
EstimateIndex = TRUE,
EstimateBycatch = TRUE,
logNum = NA,
sampleUnit = "trips",
complexModel = formula(y~Year+fleet+hbf+area+season),
simpleModel = formula(y~Year+fleet+area),
indexModel = formula(y~Year+area),
designMethods =c("Ratio","Delta"),
designVars=c("Year","area"),
designPooling = FALSE,
minStrataUnit=1,
minStrataEffort=1,
baseDir = getwd(),
runName = "LLSIMBUMtrip2022Aprilobs05mc",
runDescription = "LLSIm BUM by trip, with 5% observer coverage including observed catch in totals April 17 2022",
common = c("Swordfish","Blue marlin")[2],
sp = c("Xiphias gladius","Makaira nigricans")[2],
obsCatch = c("SWO","BUM")[2],
catchUnit = "number",
catchType = "catch"
)
#----------------------------------------------------------------------------
#Optionally, instead of running setup, you can read-in a previous model setup
setupObj<-readRDS(file=paste0(getwd(), paste("/Output", "LLSIMBUMtrip2022Aprilobs05mc"),"/", "2022-05-02","_BycatchModelSpecification.rds"))
#-------------
#Step 2. Model Fitting
bycatchFit(
setupObj = setupObj,
selectCriteria = "BIC",
DoCrossValidation = FALSE,
DredgeCrossValidation = FALSE,
ResidualTest = FALSE,
CIval = 0.05,
VarCalc = "None",
useParallel = TRUE,
nSims = 1000,
baseDir = getwd(),
plotValidation = FALSE,
trueVals = NULL,
trueCols = NULL,
doReport = FALSE
)
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