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fixing ref points and projections when there are multiple fleets
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@timjmiller
timjmiller committed Nov 9, 2022
1 parent 56b95fe commit b4c1ca3
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Showing 5 changed files with 306 additions and 57 deletions.
7 changes: 2 additions & 5 deletions R/fit_wham.R
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Expand Up @@ -228,7 +228,7 @@ check_projF = function(mod)
{
redo_SPR_years = mod$years_full[y[bad]]
warning(paste0("Changing initial values for estimating FXSPR used to define F in projection years ", paste(redo_SPR_years, collapse = ","), "."))
mod$env$data$F_init_proj[ind[bad]] = mod$env$data$FXSPR_init_proj[y[bad]]
mod$env$data$F_proj_init[ind[bad]] = mod$env$data$FXSPR_init_proj[y[bad]]
mod$fn(mle)
mod$rep = mod$report()
correct_F = round(mod$env$data$percentFXSPR * exp(mod$rep$log_FXSPR[y])/100, 4)
Expand All @@ -242,17 +242,14 @@ check_projF = function(mod)
if(length(ind))
{
y = mod$env$data$n_years_model + ind
#print(y)
#print(dim(mod$rep$pred_catch))
bad = which(round(mod$env$data$proj_Fcatch[ind],4) != round(rowSums(mod$rep$pred_catch[y,,drop=F]),4))
if(length(bad))
{
for(i in 1:2)
{
redo_Catch_years = mod$years_full[y[bad]]
#print(redo_Catch_years)
warning(paste0("Changing initial values for finding F from Catch in projection years ", paste(redo_Catch_years, collapse = ","), , "."))
mod$env$data$F_init_proj[ind[bad]] = mod$env$data$F_init_proj[ind[bad]]*0.5
mod$env$data$F_proj_init[ind[bad]] = mod$env$data$F_proj_init[ind[bad]]*0.5
mod$fn(mle)
mod$rep = mod$report()
bad = which(round(mod$env$data$proj_Fcatch[ind],4) != round(sum(mod$rep$pred_catch[y,,drop=F]),4))
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6 changes: 3 additions & 3 deletions R/prepare_projection.R
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Expand Up @@ -9,7 +9,7 @@
#' \item \code{$n.yrs} (integer), number of years to project/forecast. Default = \code{3}.
#' \item \code{$use.last.F} (T/F), use terminal year F for projections. Default = \code{TRUE}.
#' \item \code{$use.avg.F} (T/F), use average of F over certain years for projections. Default = \code{FALSE}. Years to average over determined by $avg.yrs defined below.
#' \item \code{$use.FXSPR} (T/F), calculate and use F at X% SPR for projections. Default = \code{FALSE}.
#' \item \code{$use.FXSPR} (T/F), calculate and use F at X\% SPR for projections. Default = \code{FALSE}.
#' \item \code{$use.FMSY} (T/F), calculate and use FMSY for projections. Default = \code{FALSE}.
#' \item \code{$proj.F} (vector), user-specified fishing mortality for projections. Length must equal \code{n.yrs}.
#' \item \code{$proj.catch} (vector), user-specified aggregate catch for projections. Length must equal \code{n.yrs}.
Expand All @@ -20,9 +20,9 @@
#' \item \code{$proj.ecov} (matrix), user-specified environmental covariate(s) for projections. \code{n.yrs x n.ecov}.
#' \item \code{$cont.Mre} (T/F), continue M random effects (i.e. AR1_y or 2D AR1) for projections. Default = \code{TRUE}. If \code{FALSE}, M will be averaged over \code{$avg.yrs} (which defaults to last 5 model years).
#' \item \code{$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).
#' \item \code{$percentFXSPR} (scalar), percent of F_XSPR to use for calculating catch in projections, only used if $use.FXSPR = TRUE. For example, GOM cod uses F = 75% F_40%SPR, so \code{proj.opts$percentFXSPR = 75}. Default = 100.
#' \item \code{$percentFXSPR} (scalar), percent of F_XSPR to use for calculating catch in projections, only used if $use.FXSPR = TRUE. For example, GOM cod uses F = 75\% F_40\%SPR, so \code{proj.opts$percentFXSPR = 75}. Default = 100.
#' \item \code{$percentFMSY} (scalar), percent of F_MSY to use for calculating catch in projections, only used if $use.FMSY = TRUE.
#' \item \code{$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.
#' \item \code{$proj_F_opt} (vector), integers specifying how to configure each year of the projection: 1: use terminal F, 2: use average F, 3: use F at X\% SPR, 4: use specified F, 5: use specified catch, 6: use Fmsy. Overrides any of the above specifications.
#' \item \code{$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.
#' }
#'
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8 changes: 4 additions & 4 deletions R/project_wham.R
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Expand Up @@ -7,7 +7,7 @@
#' \itemize{
#' \item Use last year F (default). Set \code{proj.opts$use.last.F = TRUE}. WHAM will use F in the terminal model year for projections.
#' \item Use average F. Set \code{proj.opts$use.avg.F = TRUE}. WHAM will use F averaged over \code{proj.opts$avg.yrs} for projections (as is done for M-, maturity-, and weight-at-age).
#' \item Use F at X% SPR. Set \code{proj.opts$use.FXSPR = TRUE}. WHAM will calculate F at X% SPR.
#' \item Use F at X\% SPR. Set \code{proj.opts$use.FXSPR = TRUE}. WHAM will calculate F at X\% SPR.
#' \item Specify F. Provide \code{proj.opts$proj.F}, an F vector with length = \code{n.yrs}.
#' \item Specify catch. Provide \code{proj.opts$proj.catch}, a vector of aggregate catch with length = \code{n.yrs}. WHAM will calculate F to get specified catch.
#' }
Expand Down Expand Up @@ -43,7 +43,7 @@
#' \item \code{$n.yrs} (integer), number of years to project/forecast. Default = \code{3}.
#' \item \code{$use.last.F} (T/F), use terminal year F for projections. Default = \code{TRUE}.
#' \item \code{$use.avg.F} (T/F), use average of F over certain years for projections. Default = \code{FALSE}. Years to average over determined by $avg.yrs defined below.
#' \item \code{$use.FXSPR} (T/F), calculate and use F at X% SPR for projections. Default = \code{FALSE}.
#' \item \code{$use.FXSPR} (T/F), calculate and use F at X\% SPR for projections. Default = \code{FALSE}.
#' \item \code{$use.FMSY} (T/F), calculate and use FMSY for projections. Default = \code{FALSE}.
#' \item \code{$proj.F} (vector), user-specified fishing mortality for projections. Length must equal \code{n.yrs}.
#' \item \code{$proj.catch} (vector), user-specified aggregate catch for projections. Length must equal \code{n.yrs}.
Expand All @@ -54,9 +54,9 @@
#' \item \code{$proj.ecov} (matrix), user-specified environmental covariate(s) for projections. \code{n.yrs x n.ecov}.
#' \item \code{$cont.Mre} (T/F), continue M random effects (i.e. AR1_y or 2D AR1) for projections. Default = \code{TRUE}. If \code{FALSE}, M will be averaged over \code{$avg.yrs} (which defaults to last 5 model years).
#' \item \code{$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).
#' \item \code{$percentFXSPR} (scalar), percent of F_XSPR to use for calculating catch in projections, only used if $use.FXSPR = TRUE. For example, GOM cod uses F = 75% F_40%SPR, so \code{proj.opts$percentFXSPR = 75}. Default = 100.
#' \item \code{$percentFXSPR} (scalar), percent of F_XSPR to use for calculating catch in projections, only used if $use.FXSPR = TRUE. For example, GOM cod uses F = 75\% F_40\%SPR, so \code{proj.opts$percentFXSPR = 75}. Default = 100.
#' \item \code{$percentFMSY} (scalar), percent of F_MSY to use for calculating catch in projections, only used if $use.FMSY = TRUE.
#' \item \code{$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.
#' \item \code{$proj_F_opt} (vector), integers specifying how to configure each year of the projection: 1: use terminal F, 2: use average F, 3: use F at X\% SPR, 4: use specified F, 5: use specified catch, 6: use Fmsy. Overrides any of the above specifications.
#' \item \code{$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.
#' }
#' @param n.newton integer, number of additional Newton steps after optimization. Passed to \code{\link{fit_tmb}}. Default = \code{0} for projections.
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