model-dev/Example-a4aSCA.R at master · a4a/model-dev · GitHub

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@examples
data(ple4)
data(ple4.index)
#'
# fishing mortality by age and year (~separable) AND catchability at age without year trend
fmodel <- ~factor(age) + factor(year)
qmodel <- list(~factor(age))
fit1 <-  a4aSCA(fmodel=fmodel, qmodel=qmodel, stock=ple4, indices=FLIndices(ple4.index))

# fishing mortality as a smoother by age and year AND catchability at age without year trend
fmodel <- ~ s(age, k=4) + s(year, k=10)
fit2 <-  a4aSCA(fmodel=fmodel, qmodel=qmodel, stock=ple4, indices=FLIndices(ple4.index))

# fishing mortality as a smoother by age and year AND catchability at age without year trend
fmodel <- ~ s(age, k=4) + s(year, k=10)
qmodel <- list(~s(age, k=4) + year)
fit3 <-  a4aSCA(fmodel=fmodel, qmodel=qmodel, stock=ple4, indices=FLIndices(ple4.index))

# fishing mortality as a smoother by age and year AND catchability at age with year trend
fmodel <- ~ te(age, year, k=c(4, 10))
qmodel <- list(~s(age, k=4))
fit4 <-  a4aSCA(fmodel=fmodel, qmodel=qmodel, stock=ple4, indices=FLIndices(ple4.index))

# It's a statistical model
BIC(fit1, fit2, fit3)

# fit3 + smoother in recruitment
fmodel <- ~ s(age, k=4) + s(year, k=20)
qmodel <- list(~s(age, k=4))
rmodel <- ~s(year, k=20)
fit5 <-  a4aSCA(fmodel=fmodel, qmodel=qmodel, srmodel=rmodel, ple4, FLIndices(ple4.index))

# fit3 + bevholt
rmodel <- ~ bevholt(CV=0.05)
fit6 <-  a4aSCA(fmodel=fmodel, qmodel=qmodel, srmodel=rmodel, ple4, FLIndices(ple4.index))