sca: Statistical catch-at-age method

In flr/FLa4a: A Simple and Robust Statistical Catch at Age Model

Statistical catch-at-age method

Description

Statistical catch-at-age method of the a4a stock assessment framework.

Usage

sca(stock, indices, ...)

## S4 method for signature 'FLStock,FLIndex'
sca(stock, indices, ...)

## S4 method for signature 'FLStock,FLIndices'
sca(
  stock,
  indices,
  fmodel = missing,
  qmodel = missing,
  srmodel = missing,
  n1model = missing,
  vmodel = missing,
  covar = missing,
  wkdir = missing,
  verbose = FALSE,
  fit = "assessment",
  center = TRUE,
  mcmc = missing
)

Arguments

stock	an FLStock object containing catch and stock information
indices	an FLIndices object containing survey indices
...	additional argument list that might never be used
fmodel	a formula object depicting the model for log fishing mortality at age
qmodel	a list of formula objects depicting the models for log survey catchability at age
srmodel	a formula object depicting the model for log recruitment
n1model	a formula object depicting the model for the population in the first year of the time series
vmodel	a list of formula objects depicting the model for the variance of fishing mortality and the indices
covar	a list with covariates to be used by the submodels. The formula must have an element with the same name as the list element.
wkdir	used to set a working directory for the admb optimiser; if wkdir is set, all admb files are saved to this folder, otherwise they are deleted.
verbose	if true, admb fitting information is printed to the screen.
fit	character with type of fit: 'MP' or 'assessment'; the former does not require the hessian to be computed, while the latter does.
center	logical defining if the data should be centered before fitting.
mcmc	an SCAMCMC object with the arguments to run MCMC

Details

[REQUIRES REVISION] This method is the advanced method for stock assessment, it gives the user access to a set of arguments that the sca method doesn't. In particular, the default for the fit argument is 'assessment'. For detailed information about using the sca read the vignette 'The a4a Stock Assessment Modelling Framework' (vignette('sca')).

Value

an a4aFit object if fit is "MP" or an a4aFitSA object if fit is "assessment"

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 <-  sca(fmodel=fmodel, qmodel=qmodel, stock=ple4, indices=FLIndices(ple4.index))

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

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

# fishing mortality as a smoother by age and year (but still separable) AND
# catchability as a smoother by age with year trend
fmodel <- ~ s(age, k=4) + s(year, k=10)
qmodel <- list(~s(age, k=4) + year)
fit4 <-  sca(fmodel=fmodel, qmodel=qmodel, stock=ple4, indices=FLIndices(ple4.index))

# It's a statistical model
BIC(fit1, fit2, fit3, fit4)

# fishing mortality as a smoother by age and year with interactions (i.e. non-separable) AND
# catchability as a smoother by age without year trend
fmodel <- ~ te(age, year, k=c(4, 10))
qmodel <- list(~s(age, k=4))
fit5 <-  sca(fmodel=fmodel, qmodel=qmodel, stock=ple4, indices=FLIndices(ple4.index))

# fit3 + smoother in recruitment
fmodel <- ~ s(age, k=4) + s(year, k=20)
qmodel <- list(~s(age, k=4))
rmodel <- ~s(year, k=20)
fit6 <-  sca(fmodel=fmodel, qmodel=qmodel, srmodel=rmodel, ple4, FLIndices(ple4.index))

# fit3 + bevholt
rmodel <- ~ bevholt(CV=0.05)
fit7 <-  sca(fmodel=fmodel, qmodel=qmodel, srmodel=rmodel, ple4, FLIndices(ple4.index))

flr/FLa4a documentation built on Dec. 21, 2024, 9:28 p.m.