Specify the stock-recruit relationship (SRR) for Rceattle

Stock recruitment relationships currently implemented in Rceattle:

srr_fun = 0 or "mean": No stock recruit relationship. Recruitment is a function of R0 and annual deviates (i.e. steepness = 0.99). $$R_y = exp(R0 + R_{dev,y})$$
srr_fun = 2 or "BevertonHolt": Beverton-holt stock-recruitment relationship $$R_y = \frac{\alpha_{srr} * SB_{y-minage}}{1+\beta_{srr} * SB_{y-minage}}$$
srr_fun = 4 or "Ricker": Ricker stock-recruitment relationship $$R_y = \alpha_{srr} * SB_{y-minage} * exp(-\beta_{srr} * SB_{y-minage})$$

When srr_pred_fun > 0 and srr_fun = 0 recruitment in the hindcast is estimated as in srr_fun = 0 $$R_y = exp(R0 + R_{dev,y})$$, but an additional stock recruitment relationship defined by srr_pred_fun is estimated between srr_hat_styr and srr_hat_endyr and treated as an additional penalty. The stock recruitment relationship defined by srr_pred_fun is then used in the projection.

Usage

build_srr(
  srr_fun = 0,
  srr_pred_fun = srr_fun,
  proj_mean_rec = TRUE,
  srr_mse_switchyr = NULL,
  srr_hat_styr = NULL,
  srr_hat_endyr = NULL,
  srr_est_mode = 1,
  srr_prior = 4,
  srr_prior_sd = 1,
  srr_indices = NA,
  Bmsy_lim = NA,
  linkages = NULL
)

Arguments

srr_fun: Stock recruit function to be used for hindcast estimation of Rceattle (see @description below). Default = 0
srr_pred_fun: stock recruit function for projection, reference points, and penalties to be used for Rceattle (see below). When srr_fun == 0, it treats the stock-recruit curve as an additional penalty onto the annualy estimated recruitment from the hindcast (sensu AMAK and Jim Ianelli's pollock model). If srr_fun > 0 then srr_pred_fun = srr_fun and no additional penalty is included.
proj_mean_rec: Project the model using: 0 = mean recruitment (average R of hindcast) or 1 = SRR(omega, srr_devs)
srr_mse_switchyr: is used for MSEs to deal with AMAK and Jim Ianelli's estimation where a stock recruit function is estimated as an additional penalty (srr_fun = 0 and srr_pred_fun > 0). It tells the model in what year to switch to the stock recruit function.
srr_hat_styr: Integer. The first year used for estimating the recruitment function as an additional penalty. It will add additional penalties sensu AMAK and Jim Ianelli's pollock model when srr_pred_fun > 0 and srr_fun = 0, starting at styr + 1. Defaults to $styr + 1$ in $data_list$. Useful if environmental data used to condition stock-recruit relationships is not available until end-year, but projections are desired.
srr_hat_endyr: Integer. The last year used for estimating the recruitment function as an additional penalty. It will add an additional penalties sensu AMAK and Jim Ianelli's pollock model when srr_pred_fun > 0 and srr_fun = 0. Recruitment Defaults to $endyr$ in $data_list$. Useful if environmental data used to condition stock-recruit relationships is not available for the full time-series, but projections are desired.
srr_est_mode: Switch to determine estimation mode. 0 = fix alpha to prior mean, 1 = freely estimate R0, alpha, and/or beta (default), 2 = use lognormally distributed prior for alpha (Ricker) or steepness (Beverton), 3 = use beta distributed prior for steepness (Beverton) given mean and sd.
srr_prior: mean for normally distributed prior for stock-recruit parameter
srr_prior_sd: Prior standard deviation for stock-recruit parameter
srr_indices: Soft-deprecated. Use the linkages argument instead. See vignette("environmental-linkages").
Bmsy_lim: Upper limit for Ricker based SSB-MSY (e.g 1/Beta). Will add a likelihood penalty if beta is estimated above this limit. Default NA is not used.
linkages: Optional named list of linkage_spec() objects keyed by recruitment parameter name (must be one of "log_R0", "log_alpha", "log_beta"). Each spec describes how that parameter depends on environmental covariates and on stratifying factors (species, sex). The offset enters additively (on the log scale) inside the recruitment compute. See vignette("environmental-linkages") for details.

Value

A list containing the stock recruitment relationship settings