Generic Management Strategy Evaluation

AgeAssPlot | Function to plot age-structured models Used within the 'GeMS'... |

AgeStructureComp | Age-Structure Comparison |

BevHolt | Function that calculates negative log-likelihood for... |

calcBHrec | Function that calculates recruitment values with... |

calcREF | Calculates... STUFF for use in Cody's brain. Probably related... |

calcRICKrec | Function that calculates recruitment values from Ricker... |

CalculateBias | Calculate Bias |

CalculateMohn | Calculates Mohn's Rho for use in 'AgeStructureComp' |

CheckGradient | Extracts gradients from age-structured model runs for use in... |

CheckReferencePoints | Reference Points Extracts reference points from... |

CheckRetro | Check Retrospective |

CleanInput | Clean up OM input (checks lengths of vectors for time-varying... |

FindF35 | Calculates F35 for 'GeMS' |

FindFMSY | Calculates yield at F, to be passed to optimizing function |

GeMS | Wrapper function to run an MSE. |

GeMSplots | More plots.. currently commented out from 'AgeStructureComp' |

get_exec | Get Executable Get SimAss binary/executable location in... |

HarvestControlRule | Harvest Control Rule Used within the 'GeMS' function. |

initialN | Calculate initial biomass using Recruitment *... |

MyBoxPlot | Customised Box Plot Used within the 'GeMSplots' function, not... |

PlotLifeHistory | Plot Life History |

PlotParam | Plot Life History Parameter |

plot_stuff_inside | Compare model estimates |

PolygonPlots | Plots polygons |

ProdMod | Production Model Fits a production model to input data |

ProdModPlot | Production Model Plot |

ProductionModelOutput | Compare Production Model Outputs |

ProjPopDym | Project population dynamics |

PullTimevary | Used to pull parameters from age-structured estimation model... |

PullTrueProj | Pull True Projections Not used anywhere... yet. |

ReadCTLfile | Read in CTL csv file |

ReadPar | Pull parameters from .PAR file. For use in 'AgeStructureComp' |

ReadRep | Pull parameters from .REP file. For use in 'AgeStructureComp' |

ReadTruDat | Pull parameters from TrueQuantities.DAT file. For use in... |

Recruitment | Recruitment function |

Ricker | Ricker function |

run_GeMS | Function to run GeMS |

SBPRfunc | Calculate spawning-biomass-per-recruit quantities for use in... |

selAtAgeFunc | Selectivity-at-age |

StockRecCheck | Stock-Recruitment Check |

StrLine | Negative log-likelihood |

TakeOut | Extract values from given string for use in 'ReadCTLfile'.... |

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