Man pages for szuwalski/GeMS
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'.... |
