Description Usage Arguments Details

View source: R/getRunCommands.R

Function to generate a script to make a tcsam02 model run

1 2 3 4 5 6 7 | ```
getRunCommands(os = "osx", model = "tcsam02", path2model = "",
configFile = "", pin = FALSE, pinFile = NULL, mseMode = NULL,
hess = FALSE, minPhase = NULL, maxPhase = NULL, mcmc = FALSE,
mc.N = 1e+06, mc.save = 1000, mc.scale = 1000, jitter = FALSE,
jit.seed = NULL, calcOFL = FALSE, calcTAC = FALSE, HCR = 1,
calcDynB0 = FALSE, fullClean = TRUE, cleanup = TRUE,
verbose = FALSE)
``` |

`os` |
- 'win', 'mac', 'osx', or 'linux' |

`model` |
- admb model name |

`path2model` |
- path to model |

`configFile` |
- filename (including path) to model configuration file |

`pin` |
- flag (T/F) to use a pin file |

`pinFile` |
- name of pin file (if different from default) |

`mseMode` |
- mse mode for model run (NULL [off: default], "opModMode", "estModMode") |

`hess` |
- flag (T/F) to calculate the hessian |

`minPhase` |
- start phase (or NULL) for minimization calculations |

`maxPhase` |
- last phase (or NULL) for minimization calculations |

`mcmc` |
- flag (T/F) to do mcmc calculations |

`mc.N` |
- number of mcmc iterations to do |

`mc.save` |
- number of iterations to skip when saving mcmc calculations |

`mc.scale` |
- number of iterations to adjust scale for mcmc calculations |

`jitter` |
- flag (T/F) to use jitter initial values |

`jit.seed` |
- value for random number seed to generate jitter |

`calcOFL` |
- flag (T/F) to do OFL calculations |

`calcTAC` |
- flag (T/F) to calculate the TAC for the next fishing year |

`HCR` |
- integer indicating the Harvest Control Rule used to calculate the TAC |

`calcDynB0` |
- flag (T/F) to do dynamic B0 calculations |

`fullClean` |
- flag to clean up almost all files (use when making multiple jitter runs) |

`cleanup` |
- flag (T/F) to clean up unnecessary files |

`verbose` |
- flag (T/F) to print diagnostic info |

. If `cleanup`

is TRUE, then .bar, .b0*, .p0*, .r0*, variance,
EchoOut.dat, CheckFile.dat, and fimn.log files are deleted.

If the path associated with `configFile`

is a relative one, it should
be relative to the path for model output.

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