Run salmonMSE — salmonMSE • salmonMSE

salmonMSE() runs a salmon management strategy evaluation from an operating model object (SOM or simpleSOM), by checking the operating model object with check_SOM(), running the projection in ProjectSOM() (parallel if called upon, then stitches together the output in a single object), and calculates reference points with calc_ref().

ProjectSOM() is the internal projection function.

Usage

salmonMSE(SOM, ncores = 1, silent = FALSE)

ProjectSOM(SOM, sims, check = FALSE)

Arguments

SOM: An object of class SOM. For salmonMSE(), can also be an object of class simpleSOM
ncores: Integer, maximum number of processors to run projection with parallel processing
silent: Logical, whether to report progress in console
sims: Optional integer vector to run projection for a subset of simulations. Intended for parallel processing.
check: Deprecated. Logical, whether to check the structure of the input object with check_SOM(). The check is now automated when needed.

Value

SMSE object

Examples

if (FALSE) { # \dontrun{
SMSE <- salmonMSE(simple_SOM)
} # }

SOM_simp <- new("simpleSOM")
simpleSMSE <- salmonMSE(SOM_simp)