run.SIR: Run the SIR algorithm for a draws and stock (temporary)
In colemonnahan/sraplus:

Description Usage Arguments Details Value

Run the SIR algorithm for a draws and stock (temporary)

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run.SIR(nrep, Catch, Taxon, penalties = NULL, Kprior = 3, Kscale = 2,
  AgeVulnOffset = -1, years = NULL, pct.keep = 10, ProcessError = TRUE,
  simulation = NULL)

`nrep`	Number of replicates to run.
`Catch`	Vector of catches, one for each year.
`Taxon`	A list with taxonomic information, including 'Class', 'Order', 'Family', 'Genus', 'Species'. Any blanks will be converted to 'predictive' internally when querying FishLife.
`penalties`	A list specifying the penalties to use. See details for more information.
`Kprior`	Maybe a multiplier on K?
`Kscale`	Scalar to control the initial biomass which is generated
`AgeVulnOffset`	Optional parameter for offset of age of vulnerability from age of maturity. A value of 0 means knife edge selectivity starts at 50 before it. Thus (age of vulnerability = age of maturity + AgeVulnOffset). Defaults -1. Note that AgeMat is stochastic inside the function, so age at vulnerability will vary with it.
`years`	Optional vector of years which is used by plotting functions. Defaults to 1:length(Catch).
`pct.keep`	The percentage of "keepers" from the total. Default 10%.
`ProcessError`	Flag for whether to include process error deviations, passed on to model. Defaults to TRUE.
`simulation`	See documentation for AgeModel.

The penalties list provides penalties and priors for up to four components of the analysis: initial depletion, carrying capacity (K), terminal year B/BMSY ('bstatus') and terminal year U/UMSY ('ustatus'). The user specifies which distribution to use and two distributional arguments for each of these metrics. For instance a ustatus~N(.5, .75) would be specified with list elements: ustatus.mean=0.5, ustatus.sd=0.75 and ustatus.dist=1. 'dist' options are 1=normal, 2=lognormal and 3=uniform. The uniform case passes arguments min and max, while the other two the mean and SD. deviation, and distribution type. Currently if no initial distribution is provided one is calculated internally but this needs to be revisiting and thus throws a warning.

A list containing depletion, SSB, and harvest rate (U) for posterior draws, and a vector of Keepers

colemonnahan/sraplus documentation built on May 14, 2019, 3:10 a.m.