R/prepare_projection.R
prepare_projection.Rdprepare_projection is an internal function called by project_wham,
which in turn is called by fit_wham if do.proj = TRUE.
prepare_projection(model, proj.opts)a previously fit wham model
a named list with the following components:
$n.yrs (integer), number of years to project/forecast. Default = 3.
$use.last.F (T/F), use terminal year F for projections. Default = TRUE.
$use.avg.F (T/F), use average of F over certain years for projections. Default = FALSE. Years to average over determined by $avg.yrs defined below.
$use.FXSPR (T/F), calculate and use F at X% SPR for projections. Default = FALSE.
$use.FMSY (T/F), calculate and use FMSY for projections. Default = FALSE.
$proj.F (vector), user-specified fishing mortality for projections. Length must equal n.yrs.
$proj.catch (vector), user-specified aggregate catch for projections. Length must equal n.yrs.
$avg.yrs (vector), specify which years to average over for calculating reference points. Default = last 5 model years, tail(model$years, 5).
$cont.ecov (T/F), continue ecov process (e.g. random walk or AR1) for projections. Default = TRUE.
$use.last.ecov (T/F), use terminal year ecov for projections.
$avg.ecov.yrs (vector), specify which years to average over the environmental covariate(s) for projections.
$proj.ecov (matrix), user-specified environmental covariate(s) for projections. n.yrs x n.ecov.
$cont.Mre (T/F), continue M random effects (i.e. AR1_y or 2D AR1) for projections. Default = TRUE. If FALSE, M will be averaged over $avg.yrs (which defaults to last 5 model years).
$avg.rec.yrs (vector), specify which years to calculate the CDF of recruitment for use in projections. Default = all model years. Only used when recruitment is estimated as fixed effects (SCAA).
$percentFXSPR (scalar), percent of F_XSPR to use for calculating catch in projections, only used if $use.FXSPR = TRUE. For example, GOM cod uses F = 75% F_40%SPR, so proj.opts$percentFXSPR = 75. Default = 100.
$percentFMSY (scalar), percent of F_MSY to use for calculating catch in projections, only used if $use.FMSY = TRUE.
$proj_F_opt (vector), integers specifying how to configure each year of the projection: 1: use terminal F, 2: use average F, 3: use F at X% SPR, 4: use specified F, 5: use specified catch, 6: use Fmsy. Overrides any of the above specifications.
$proj_Fcatch (vector), catch or F values to use each projection year: values are not used when using Fmsy, FXSPR, terminal F or average F. Overrides any of the above specifications of proj.F or proj.catch.
$proj_mature (matrix), user-supplied maturity values for the projection years with dimensions (n.yrs x n_ages).
$proj_waa (3-d array), user-supplied waa values for the projection years with first and third dimensions equal to that of model$input$data$waa (waa source x n.yrs x n_ages).
$proj_R_opt (integer), 1: continue any RE processes for recruitment, 2: make projected recruitment consistent with average recruitment in SPR reference points and cancel any bias correction for NAA in projection years.
same as prepare_wham_input, a list ready for fit_wham:
dataNamed list of data, passed to TMB::MakeADFun
parNamed list of parameters, passed to TMB::MakeADFun
mapNamed list of factors that determine which parameters are estimated, passed to TMB::MakeADFun
randomCharacter vector of parameters to treat as random effects, passed to TMB::MakeADFun
yearsNumeric vector of representing (non-projection) model years of WHAM model
years_fullNumeric vector of representing all model and projection years of WHAM model
ages.labCharacter vector of age labels, ending with plus-group
model_nameCharacter, name of stock/model (specified in call to prepare_wham_input)