`R/VPA2OM.R`

`VPA2OM.Rd`

A function that uses a set of VPA bootstrap estimates of numbers-at-age, fishing mortality rate-at-age, M-at-age, weight-at-age, length-at-age and Maturity-at-age to define a fully described MSEtool operating model. The user still needs to parameterize most of the observation and implementation portions of the operating model.

VPA2OM( Name = "A fishery made by VPA2OM", proyears = 50, interval = 2, CurrentYr = 2019, h = 0.999, Obs = MSEtool::Imprecise_Unbiased, Imp = MSEtool::Perfect_Imp, naa, faa, waa, Mataa, Maa, laa, nyr_par_mu = 3, LowerTri = 1, recind = 0, plusgroup = TRUE, altinit = 0, fixq1 = TRUE, report = FALSE, silent = FALSE, ... )

Name | Character string. The name of the operating model. |
---|---|

proyears | Positive integer. The number of projection years for MSE. |

interval | Positive integer. The interval at which management procedures will update the management advice in runMSE, e.g., 1 = annual updates. |

CurrentYr | Positive integer. The current year (final year of VPA fitting to data) |

h | The steepness of the stock-recruitment curve (greater than 0.2 and less than 1, assumed to be close to 1 to match VPA assumption). Either a single numeric or a length nsim vector. |

Obs | The observation model (class Obs). This function only updates the catch and index observation error. |

Imp | The implementation model (class Imp). This function does not update implementation parameters. |

naa | Numeric array |

faa | Numeric array |

waa | Numeric array |

Mataa | Numeric array |

Maa | Numeric array |

laa | Numeric array |

nyr_par_mu | Positive integer. The number of recent years that natural mortality, age vulnerability, weight, length and maturity parameters are averaged over for defining future projection conditions. |

LowerTri | Integer. The number of recent years for which model estimates of recruitment are ignored (not reliably estimated by the VPA) |

recind | Positive integer. The first age class that fish 'recruit to the fishery'. The default is 0 - ie the first position in the age dimension of naa is age zero |

plusgroup | Logical. Does the VPA assume that the oldest age class is a plusgroup? |

altinit | Integer. Various assumptions for how VPAs set up the initial numbers. 0: standard, 1: no plus group, 2: temporary fix for MSEtool plus group initialization |

fixq1 | Logical. Should q be fixed (ie assume the F-at-age array faa is accurate? |

report | Logical, if TRUE, a diagnostic will be reported showing the matching of the OM reconstructed numbers at age vs the VPA assessment. |

silent | Whether to silence messages to the console. |

... | Additional arguments, including R0 (unfished recruitment), phi0 (unfished spawners per recruit associated with R0 and h for calculating stock recruit parameters), Perr (recruitment standard deviation for sampling future recruitment), and AC (autocorrelation in future recruitment deviates). For all, either a numeric or a length nsim vector. |

An object of class OM.

Use a seed for the random number generator to sample future recruitment.

T. Carruthers