| AAVE |
Performance Metrics Methods |
| AAVY |
Performance Metrics Methods |
| addMPs |
Utility functions for MSE objects |
| Albacore |
Stock class objects |
| Albacore_TwoFleet |
MOM class objects |
| applyMMP |
Apply multi Management Procedures (class MMP) to a hierarchical list of Data class objects |
| applyMP |
Apply Management Procedures to an object of class Data |
| ASAP2Data |
Convert ASAP 3 assessments into an operating model |
| ASAP2OM |
Convert ASAP 3 assessments into an operating model |
| Assess2MOM |
Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model. |
| Assess2OM |
Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. 'Assess2OM' is identical to 'VPA2OM'. |
| Atlantic_mackerel |
Data class objects |
| avail |
What objects of this class are available |
| Awatea2OM |
Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model |
| calcRefYield |
Calculate Reference Yield |
| CALsimp |
Simplifies the CAL slot of data object |
| Can |
Identify management procedures (MPs) based on data availability |
| Cant |
Identify management procedures (MPs) based on data availability |
| CheckDuplicate |
Check for duplicated MPs names |
| CheckMPs |
Check that specified MPs are valid and will run on MSEtool::SimulatedData |
| checkMSE |
Utility functions for MSE objects |
| CheckOM |
Check OM object is complete |
| China_rockfish |
Data class objects |
| Choose |
Manually map parameters for the historical period of operating model |
| ChooseEffort |
Manually map parameters for the historical period of operating model |
| ChooseM |
Manually map parameters for the historical period of operating model |
| ChooseSelect |
Manually map parameters for the historical period of operating model |
| Cobia |
Data class objects |
| CombineMMP |
Create a blank MP recommendations object (class Rec) of the right dimensions |
| Converge |
Check Convergence |
| COSEWIC_Blow |
COSEWIC MSE run using the correct MPs and projected time horizon |
| COSEWIC_Dplot |
COSEWIC MSE run using the correct MPs and projected time horizon |
| COSEWIC_Hplot |
COSEWIC MSE run using the correct MPs and projected time horizon |
| COSEWIC_Pplot |
COSEWIC MSE run using the correct MPs and projected time horizon |
| COSEWIC_report |
COSEWIC MSE run using the correct MPs and projected time horizon |
| COSEWIC_tab |
COSEWIC MSE run using the correct MPs and projected time horizon |
| COSEWIC_tab_formatted |
COSEWIC MSE run using the correct MPs and projected time horizon |
| Cos_thresh_tab |
Current default thresholds for COSEWIC satisficing |
| cparscheck |
Internal function for checking that the 'OM@cpars' is formatted correctly |
| Cplot |
Plot the median biomass and yield relative to last historical year |
| curEref |
Reference management procedures |
| Data-class |
Class "Data" |
| Data-class-objects |
Data class objects |
| Data2csv |
Converts a Data object into a .csv data file |
| DataDescription |
DataDescription |
| DataDir |
Directory of the data in the installed package on your computer |
| DataInit |
Initialize Data Input Files |
| DataSlots |
DataSlots |
| Data_xl |
Read in Data object from Excel spreadsheet |
| DecE_Dom |
Fleet class objects |
| DecE_HDom |
Fleet class objects |
| DecE_NDom |
Fleet class objects |
| DFO_bar |
Department of Fisheries and Oceans stock status bar plot |
| DFO_hist |
Department of Fisheries and Oceans historical plot |
| DFO_plot |
Department of Fisheries and Oceans trade-off plot |
| DFO_plot2 |
Department of Fisheries and Oceans default plot 2 |
| DFO_proj |
Department of Fisheries and Oceans projection plot |
| DFO_quant |
Department of Fisheries and Oceans biomass quantile plot |
| DFO_report |
Create a standard DFO MSE report |
| DFO_spider |
DFO performance spider plot (top three MPs) |
| DFO_tab |
Create a standard DFO performance table |
| DFO_tab_formatted |
A formatted version of the standard DFO performance plot, color coded by thresholds |
| DLMDataDir |
Directory of the installed package on your computer |
| DLMdiag |
Identify management procedures (MPs) based on data availability |
| dnormal |
Double-normal selectivity curve |
| Dom |
Determine dominate MPs |
| Mackerel |
Stock class objects |
| makeMOM |
Utility for making multi-OMs |
| makemov |
Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob) |
| makemov2 |
Calculates movement matrices from user inputs for fraction in each area (fracs) the relative fraction moving to other areas, plus a mean probability of staying in any given area. |
| makeRel |
MICE relationships for multi-OM |
| makeTransparent |
Make colors transparent |
| ML2D |
Depletion and F estimation from mean length of catches |
| MMSE-class |
Class "MMSE" |
| MOM-class |
Class "MOM" |
| MOM-class-objects |
MOM class objects |
| MOM_agg_fleets |
Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) |
| movestockCPP |
Apply the movement model to the stock for one time-step |
| movfit_Rcpp |
Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters. |
| MPCalcsNAs |
Fill any NAs arising from MPCalcs (hermaphroditism mode) |
| MPtype |
Management Procedure Type |
| MSE-class |
Class "MSE" |
| MSEDescription |
MSEDescription |
| MSEextra |
Load more data from MSEextra package |
| MSYCalcs |
Internal function to calculate MSY Reference Points |
| multiData |
Combine data among fleets |
| multiDataS |
Combine data among stocks |
| multidebug |
A basic comparison of runMSE output (MSE) and multiMSE (MMSE) |
| multiMSE |
Run a multi-fleet multi-stock Management Strategy Evaluation |
| P10 |
Performance Metrics Methods |
| P100 |
Performance Metrics Methods |
| P50 |
Performance Metrics Methods |
| Perfect_Imp |
Imp class objects |
| Perfect_Info |
Obs class objects |
| PerformanceMetric |
Performance Metrics Methods |
| plot-method |
Standard plot for an object of class MOM |
| plot.Data |
Plot Data object |
| plot.Fleet |
Plot Operating Model Object |
| plot.Hist |
Plot Operating Model Object |
| plot.Imp |
Plot Operating Model Object |
| plot.MMSE |
Standard plot for an object of class MMSE (multi MSE) |
| plot.MOM |
Standard plot for an object of class MOM |
| plot.MSE |
Plot MSE object |
| plot.Obs |
Plot Operating Model Object |
| plot.OM |
Plot Operating Model Object |
| plot.pars |
Plot Operating Model Object |
| plot.Stock |
Plot Operating Model Object |
| plotFun |
Print out plotting functions |
| plotmulti |
A basic SSB plot for debugging runMSE output |
| plotOFL |
A generic OFL plot for NOAA use |
| plotquant |
A fairly tidy time-series quantile plot |
| plotRel |
Plot a relationship between stocks |
| plot_mov |
Calculates movement matrices from user inputs |
| plot_SS2MOM |
Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) |
| plot_SS2OM |
Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) |
| PMLimit |
Create a table of Performance Limits and Performance Objectives |
| PMObj |
Create a table of Performance Limits and Performance Objectives |
| PMobj-class |
An object for storing data for analysis using data-limited methods |
| PNOF |
Performance Metrics Methods |
| Porgy |
Stock class objects |
| Pplot |
A projection by projection plot of F/FMSY and B/BMSY |
| Pplot2 |
A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield |
| Precise_Biased |
Obs class objects |
| Precise_Unbiased |
Obs class objects |
| predict.Rel |
MICE relationships for multi-OM |
| predictLH |
Predict missing life-history parameters |
| print.Rel |
MICE relationships for multi-OM |
| Project |
Run a Management Strategy Evaluation |
| ProjectMOM |
Run a multi-fleet multi-stock Management Strategy Evaluation |
| PWhisker |
Performance Whisker Plot |
| R0conv |
Stock recruit parameterization |
| read.control.file |
Reads iSCAM files into a hierarchical R list object |
| read.data.file |
Reads iSCAM files into a hierarchical R list object |
| read.mcmc |
Reads iSCAM files into a hierarchical R list object |
| read.par.file |
Reads iSCAM files into a hierarchical R list object |
| read.projection.file |
Reads iSCAM files into a hierarchical R list object |
| read.report.file |
Reads iSCAM files into a hierarchical R list object |
| RealFease |
MP feasibility diagnostic using real data |
| Rec-class |
Class "Rec" |
| Red_snapper |
Data class objects |
| Replace |
Replace an existing Stock, Fleet, Obs, or Imp object |
| replic8 |
Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing |
| Report |
Generate a Data Report |
| ReqData |
ReqData |
| Required |
What management procedures need what data |
| Rockfish |
Stock class objects |
| runCOSEWIC |
COSEWIC MSE run using the correct MPs and projected time horizon |
| runInMP |
Runs input control MPs on a Data object. |
| runMP |
Run a Management Procedure |
| runMSE |
Run a Management Strategy Evaluation |
| Sense |
Sensitivity analysis |
| setup |
Setup parallel processing |
| show |
Show MSEtool S4 objects |
| show-method |
Show the output of a PM |
| show-method |
Show MSEtool S4 objects |
| show-method |
Show the output of a single MP recommendation |
| show-MSEtool |
Show MSEtool S4 objects |
| SIL |
Slot in list: get the slot values from a list of objects |
| simCAA |
Simulate Catch-at-Age Data |
| simCAL |
Simulate Catch-at-Length Data |
| simmov |
Calculates movement matrices from user inputs |
| simmov2 |
Calculates movement matrices from user specified distribution among other areas |
| Simulate |
Run a Management Strategy Evaluation |
| simulate.Rel |
MICE relationships for multi-OM |
| SimulatedData |
SimulatedData Data |
| SimulateMOM |
Run a multi-fleet multi-stock Management Strategy Evaluation |
| Simulation_1 |
Data class objects |
| SketchFun |
Manually map the historical relative fishing effort trajectory. |
| Snapper |
Stock class objects |
| Sole |
Stock class objects |
| SRalphaconv |
Stock recruit parameterization |
| SRbetaconv |
Stock recruit parameterization |
| SS2Data |
Reads data Stock Synthesis file structure into a Data object using package r4ss |
| SS2DataMOM |
Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE |
| SS2MOM |
Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) |
| SS2OM |
Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) |
| SSBrefplot |
Plot Spawning stock biomass and reference points for both historical and projected period |
| SSMOM2OM |
Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) |
| Stock-class |
Class "Stock" |
| Stock-class-objects |
Stock class objects |
| StockDescription |
StockDescription |
| STY |
Performance Metrics Methods |
| Sub |
Subset MSE object by management procedure (MP) or simulation. |
| SubCpars |
Subset the cpars slot in an operating model |
| SubCpars-method |
Subset the cpars slot in an operating model |
| SubOM |
Subset a Stock, Fleet, Obs, or Imp object from an OM object |
| summary-method |
Summary of Data object |
| summary-method |
Summary of MMSE object |
| summary-method |
Summary of MSE object |
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