Intended for conditioning operating models for data-limited stocks. From a historical time series of total catch or effort, and potentially age/length compositions and multiple indices of abundance, the SRA returns a range of values for depletion, selectivity, unfished recruitment (R0), historical fishing effort, and recruitment deviations for the operating model. This is done by sampling life history parameters provided by the user and fitting to the data in a statistical catch-at-age model (with the predicted catch equal to the observed catch). This function is intended to generate a range of potential depletion scenarios that could be supported from sparse data. Either a full catch (conditioned on catch) or effort (conditioned on effort) time series is needed but missing data (as NAs) are allowed for all other data types.
SRA_scope(OM, Chist = NULL, Ehist = NULL, condition = c("catch",
"effort"), Index = NULL, I_sd = NULL, CAA = NULL, CAL = NULL,
ML = NULL, length_bin = NULL, C_eq = 0, E_eq = 0, ML_sd = NULL,
selectivity = "logistic", I_type = NULL, LWT = list(),
ESS = c(30, 30), fix_dome = FALSE, max_F = 3, cores = 1L,
integrate = FALSE, mean_fit = FALSE, ...)plot_SRA_scope(...)
Sub_cpars(OM, sims = 1:OM@nsim)
A vector of historical catch, should be of length OM@nyears. If there are multiple fleets: a matrix of OM@nyears rows and nfleet columns.
Ideally, the first year of the catch series represents unfished conditions (see also C_eq).
A vector of historical effort, should be of length OM@nyears (see also E_eq).
String to indicate whether the SRA model is conditioned on catch or effort.
A vector of values of an index (of length OM@nyears). If there are multiple surveys: a matrix of historical indices of abundances, with rows indexing years and columns indexing surveys.
A vector or matrix of standard deviations (lognormal distribution) for the indices corresponding to the entries in Index.
If NULL, this function will use values from OM@Iobs.
Age composition matrix with nyears rows and OM@maxage columns. If multiple fleets: an array with dimension: nyears, OM@maxage, and nfleets.
Length composition matrix with nyears rows and columns indexing the length bin. If multiple fleets: an array with dimension: nyears, length bins, and nfleets.
A vector of mean length observations (length OM@nyears), or if multiple fleets: matrix of dimension: nyears and nfleets. Generally, should not
be used if CAL is also provided, unless mean length and length comps are independently sampled.
A vector for the midpoints of the length bins for CAL. All length bin widths should be equal in size.
A numeric vector of length nfleet for the equilibrium catch for each fleet in Chist prior to the first year of the operating model.
Zero implies unfished conditions in year one. Otherwise, this is used to estimate depletion in the first year of the data.
The equilibrium effort for each fleet in Ehist prior to the first year of the operating model.
Zero implies unfished conditions in year one. Otherwise, this is used to estimate depletion in the first year of the data.
The standard deviation (normal distribution) of the observed mean lengths. If there are multiple fleets, a vector of length nfleet.
If NULL, default value is 0.1 * mean(ML).
A character vector of length nfleet to indicate "logistic" or "dome" selectivity for each fleet in Chist.
A character vector (length nsurvey) to indicate the type of biomass for which each index follows. Either "B" for
total biomass, or "SSB" for spawning biomass. If NULL, "B" is used. Use numbers if the index corresponds to a fleet in Chist.
A named list of likelihood weights for the SRA model. See details.
A numeric vector of length two for the maximum effective samples size of the age and length compositions, respectively for the multinomial likelihood function. The annual sample size of an age or length composition sample is the minimum of ESS or the number of observations.
Logical, if selectivity = "dome", determines whether the descending limb of selectivity is fixed or not.
The maximum F for any fleet in the scoping model (higher F's in the model are penalized in the objective function).
Integer for the number of CPU cores for the stock reduction analysis.
Logical, whether to treat recruitment deviations as penalized parameters (FALSE) or random effects (TRUE).
Logical, whether to run an additional with mean values of life history parameters from the OM.
Other arguments to add in the future.
A logical vector of length OM@nsim or a numberic vector indicating which simulations to keep.
One of indices, age compositions, or length compositions should be provided in addition to the historical catch.
Selectivity is fixed to values sampled from OM if no age or length compositions are provided.
LWT is a named list containing the likelihood weights (values > 0) with the possible options:
Chist: A vector of length nfleet.
Index: A vector of length nsurvey.
CAA, CAL, ML, C_eq: A vector of length nfleet for each.
By default, all likelihood weights are equal to one if not specified by the user. Likelihoods for CAA and CAL can also be adjusted by changing the
multinomial sample size. See argument ESS.
plot_SRA_scope is now deprecated in favor of plot.SRA
Output from SRA_scope is placed in objects in OM@cpars. Sub_cpars is a convenient function to subset simulations
for the operating model, for example, to remove simulations from unconverged model fits or outlier simulations.
plot.SRA '>SRA