Description Usage Arguments Value Author(s) References Examples

View source: R/StochasticSRA.R

Specify an operating model, using catch composition data and a historical catch series. Returns and operating model with depletion (D), selectivity parameters (L5, LFS) and effort trajectory (Effyears, EffLower, EffUpper) filled.

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`OM` |
An operating model object with M, growth, stock-recruitment and maturity parameters specified. |

`CAA` |
A matrix nyears (rows) by nages (columns) of catch at age (age 1 to maxage in length) |

`Chist` |
A vector of historical catch observations (nyears long) going back to unfished conditions |

`Ind` |
A vector of historical abundance index observations (assumed proportional to SSB) |

`ML` |
A vector of historical mean length (in catch) observations |

`CAL` |
A matrix of nyears (row) by n length bins (columns) of catch at length samples |

`mulen` |
A vector mean length by length bin, a vector the same as the number of columns of CAL |

`wts` |
A vector of relative weights for the likelihood functions of CAA, Chist, Ind, ML and CAL |

`Jump_fac` |
A multiplier of the jumping distribution variance to increase acceptance (lower Jump_fac) or decrease acceptance rate (higher Jump_fac) |

`nits` |
The number of MCMC iterations |

`burnin` |
The number of initial MCMC iterations to discard |

`thin` |
The interval over which MCMC samples are extracted for use in graphing / statistics |

`ESS` |
Effective sample size - the weighting of the catch at age data |

`MLsd` |
The lognormal sd of the mean length observations |

`ploty` |
Do you want to see diagnostics plotted? |

`nplot` |
how many MCMC samples should be plotted in convergence plots? |

`SRAdir` |
A directory where the SRA diagnostics / fit are stored |

A list with three positions. Position 1 is the filled OM object, position 2 is the custompars data.frame that may be submitted as an argument to runMSE() and position 3 is the matrix of effort histories `[nyears x nsim]`

vector of objects of class`classy`

T. Carruthers (Canadian DFO grant)

Walters, C.J., Martell, S.J.D., Korman, J. 2006. A stochastic approach to stock reduction analysis. Can. J. Fish. Aqua. Sci. 63:212-213.

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