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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