Description Details Note Author(s) References See Also

Import and plot results from statistical catch-at-age models, used in fisheries stock assessments.

*Import model results:*

`importADCAM` | ADCAM model results |

`importCol` | Coleraine model results |

*Plot model fit to data:*

`plotCA` | catch at age |

`plotCL` | catch at length |

`plotIndex` | abundance index |

`plotLA` | length at age |

*Plot derived quantities:*

`plotB` | biomass, recruitment, and landings |

`plotN` | numbers at age |

`plotSel` | selectivity and maturity |

*Sigmas and sample sizes:*

`getN` , `getSigmaI` , `getSigmaR`
| extract |

`estN` , `estSigmaI` , `estSigmaR`
| estimate |

`iterate` | combine all `get*` and
`est*` |

*Import MCMC results:*

`importMCMC` | traces of likelihoods, parameters, biomass and recruitment |

`importProj` | medium-term projections of biomass and catch |

*Examples:*

`x.cod` , `x.ling` , `x.oreo` ,
`x.saithe` , `x.sbw` | cod, ling, oreo, and whiting assessments |

`xmcmc` , `xproj` | MCMC results |

`browseVignettes()`

shows the vignettes, found in the
‘scape/doc’ directory.

Arni Magnusson.

Magnusson, A. (2005) *R goes fishing: Analyzing fisheries data
using AD Model Builder and R.* Proceedings of the 4th International
Workshop on Distributed Statistical Computing.

Magnusson, A. and Hilborn, R. (2007) What makes fisheries data
informative? *Fish and Fisheries* **8**, 337–358.

Magnusson, A., Punt, A. E., and Hilborn, R. (2013) Measuring
uncertainty in fisheries stock assessment: the delta method,
bootstrap, and MCMC. *Fish and Fisheries* **14**, 325–342.

Most scape graphics are `trellis`

plots, rendered with the
lattice package.

The functions `Args`

and `ll`

(package gdata) can be
useful for browsing unwieldy functions and objects.

The plotMCMC package can be used to diagnose the results of MCMC analysis.

scape documentation built on May 2, 2018, 1:04 a.m.

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