eqsim_run2: simulates the equilibrium results for a population

In einarhjorleifsson/mac: Miscalaneous set of functions related fish stock assessment work

Description

An amended function from the msy-package

Usage

eqsim_run2(fit, bio.years = c(2008, 2012), bio.const = FALSE,
  sel.years = c(2008, 2012), sel.const = FALSE, Fscan = seq(0, 1, len =
  20), Fcv = 0, Fphi = 0, Blim, Bpa, recruitment.trim = c(3, -3),
  Btrigger = 0, Nrun = 200, process.error = TRUE, verbose = TRUE,
  extreme.trim)

Arguments

fit	A list returned from the function fitModels
bio.years	The years to sample maturity, weights and M from
bio.const	A flag, if FALSE mean of the biological values from the years selected are used
sel.years	The years to sample the selection patterns from
sel.const	A flag, if FALSE mean of the selection patterns from the years selected are used
Fscan	F values to scan over
Fcv	Assessment error in the advisory year
Fphi	Autocorrelation in assessment error in the advisory year
Blim	This we know
Bpa	This we know
recruitment.trim	A numeric vector with two log-value clipping the extreme recruitment values from a continuous lognormal distribution. The values must be set as c("high","low").
Btrigger	If other than 0 (default) the target F applied is reduced by SSB/Btrigger
Nrun	The number of years to run in total (last 50 years from that will be retained)
process.error	Use stochastic recruitment or mean recruitment? (TRUE = predictive)
verbose	Flag, if TRUE (default) indication of the progress of the simulation is provided in the console. Useful to turn to FALSE when knitting documents.
extreme.trim	Call John Simmonds :-)

Author(s)

Colin Millar [e-mail]

einarhjorleifsson/mac documentation built on May 16, 2019, 1:29 a.m.