| Stock class objects | Albacore Bluefin_tuna Bluefin_tuna_WAtl Blue_shark Butterfish Herring Mackerel Porgy Rockfish Snapper Sole Stock-class-objects Toothfish |
| MOM class objects | Albacore_TwoFleet MOM-class-objects |
| Apply multi Management Procedures (class MMP) to a hierarchical list of Data class objects | applyMMP |
| Apply Management Procedures to an object of class Data | applyMP |
| Convert ASAP 3 assessments into an operating model | ASAP2Data ASAP2OM |
| Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model. | Assess2MOM |
| Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. 'Assess2OM' is identical to 'VPA2OM'. | Assess2OM VPA2OM |
| Data class objects | Atlantic_mackerel China_rockfish Cobia Data-class-objects Example_datafile Gulf_blue_tilefish ourReefFish Red_snapper Simulation_1 |
| What objects of this class are available | avail |
| Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model | Awatea2OM |
| Import a multi-stock, multi-fleet OM from a BAM object | BAM2MOM BAM2OM |
| Boxplot of TAC recommendations | boxplot.Data |
| Calculate Reference Yield | calcRefYield |
| Simplifies the CAL slot of data object | CALsimp |
| Identify management procedures (MPs) based on data availability | Can Cant DLMdiag Needed |
| Check for duplicated MPs names | CheckDuplicate |
| Check that specified MPs are valid and will run on MSEtool::SimulatedData | CheckMPs |
| Utility functions for MSE objects | addMPs checkMSE joinHist joinMSE updateMSE |
| Check OM object is complete | CheckOM |
| Manually map parameters for the historical period of operating model | Choose ChooseEffort ChooseM ChooseSelect |
| Create a blank MP recommendations object (class Rec) of the right dimensions | CombineMMP |
| Check Convergence | Converge |
| Current default thresholds for COSEWIC satisficing | Cos_thresh_tab |
| Internal function for checking that the 'OM@cpars' is formatted correctly | cparscheck |
| Plot the median biomass and yield relative to last historical year | Cplot |
| Read in Data object from Excel spreadsheet | Data_xl |
| Class ''Data'' | Data-class |
| Converts a Data object into a .csv data file | Data2csv |
| DataDescription | DataDescription |
| Directory of the data in the installed package on your computer | DataDir |
| Initialize Data Input Files | DataInit |
| DataSlots | DataSlots |
| Fleet class objects | DecE_Dom DecE_HDom DecE_NDom FlatE_Dom FlatE_HDom FlatE_NDom Fleet-class-objects Generic_DecE Generic_FlatE Generic_Fleet Generic_IncE IncE_HDom IncE_NDom Low_Effort_Non_Target Targeting_Small_Fish Target_All_Fish |
| Department of Fisheries and Oceans stock status bar plot | DFO_bar |
| Department of Fisheries and Oceans historical plot | DFO_hist |
| Department of Fisheries and Oceans trade-off plot | DFO_plot |
| Department of Fisheries and Oceans default plot 2 | DFO_plot2 |
| Department of Fisheries and Oceans projection plot | DFO_proj |
| Department of Fisheries and Oceans biomass quantile plot | DFO_quant |
| Create a standard DFO MSE report | DFO_report |
| DFO performance spider plot (top three MPs) | DFO_spider |
| Create a standard DFO performance table | DFO_tab |
| A formatted version of the standard DFO performance plot, color coded by thresholds | DFO_tab_formatted |
| Directory of the installed package on your computer | DLMDataDir |
| Double-normal selectivity curve | dnormal |
| Hockey Stick Harvest control rule that modifies TAC. | doHCR |
| Create indices that are sampled at various frequencies | doIfreq |
| Determine dominate MPs | Dom |
| Calculate a management recommendation given constraints | doRec |
| A flexible empirical management procedure. | Emp |
| MP feasibility diagnostic | Fease |
| Class ''Fleet'' | Fleet-class |
| FleetDescription | FleetDescription |
| Reference management procedures | curEref FMSYref FMSYref50 FMSYref75 NFref |
| Obs class objects | Generic_Obs Imprecise_Biased Imprecise_Unbiased Obs-class-objects Perfect_Info Precise_Biased Precise_Unbiased |
| get object class | getclass |
| Get part of an MP specific data-list | getDataList |
| Extract the first dimension of a hierarchical list of recommendation objects | getfirstlev |
| Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp. | getmov2 |
| Search R session for MP | getMP |
| Count independent variables for a MICE relationship at position x in a Rel list | getnIVs |
| Calculate selectivity curve | getsel |
| Stock recruit parameterization | hconv R0conv SRalphaconv SRbetaconv |
| Internal Herm functions | checkHerm expandHerm Herm-int subsetHerm |
| Class ''Hist'' | Hist-class |
| Wrapper for histogram function | hist2 |
| HistDescription | HistDescription |
| Class ''Imp'' | Imp-class |
| ImpDescription | ImpDescription |
| ~~ Methods for Function 'initialize' ~~ | initialize initialize,Data-method initialize,DLM_general-method initialize,Fease-method initialize,Fleet-method initialize,MSE-method initialize,Obs-method initialize,OM-method initialize,Stock-method initialize-methods |
| Function to run a set of input control methods | Input |
| Reads iSCAM files into a hierarchical R list object | fetch.file.names iSCAM load.iscam.files read.control.file read.data.file read.mcmc read.par.file read.projection.file read.report.file |
| Reads MPD or MCMC estimates and data from iSCAM file structure into an operating model | iSCAM2Data iSCAM2OM |
| Combines all iSCAM age composition data across fleets | iSCAMcomps |
| Combines indices into a single index using linear modelling (** Deprecated **) | iSCAMinds |
| Plot several plots with a shared legend | join_plots |
| Join Data objects present in a list | joinData |
| KOBE plot: a projection by projection plot of F/FMSY and B/BMSY | Kplot |
| Lag the time-series slots in a 'Data' object by a specified number of time-steps | Lag_Data |
| Dimensions of a hierarchical list object | ldim |
| Predict missing life-history parameters | LH2OM predictLH |
| LHdatabase | LHdatabase |
| Utility for making multi-OMs | makeMOM |
| Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob) | makemov |
| 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. | makemov2 |
| MICE relationships for multi-OM | makeRel predict.Rel print.Rel simulate.Rel |
| Make colors transparent | makeTransparent |
| Depletion and F estimation from mean length of catches | ML2D |
| Class ''MMSE'' | MMSE-class |
| Class ''MOM'' | MOM-class |
| Apply the movement model to the stock for one time-step | movestockCPP |
| Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters. | movfit_Rcpp |
| Fill any NAs arising from MPCalcs (hermaphroditism mode) | MPCalcsNAs |
| Management Procedure Type | MPtype |
| Class ''MSE'' | MSE-class |
| MSEDescription | MSEDescription |
| Load more data from MSEextra package | MSEextra |
| Internal function to calculate MSY Reference Points | MSYCalcs |
| Combine data among fleets | multiData |
| Combine data among stocks | multiDataS |
| A basic comparison of runMSE output (MSE) and multiMSE (MMSE) | multidebug |
| Item in list: get the list values from a list of lists | NIL |
| National Oceanographic and Atmospheric Administration default plot 1 | NOAA_plot |
| Class ''Obs'' | Obs-class |
| ObsDescription | ObsDescription |
| Class ''OM'' | OM-class |
| OMDescription | OMDescription |
| Generate OM Documentation Report | OMdoc |
| Copy example OM XL and OM Documentation | OMexample |
| Initialize Operating Model | OMinit |
| Determine optimal number of cpus | optCPU |
| Imp class objects | Imp-class-objects Overages Perfect_Imp |
| Performance Metrics Methods | AAVE AAVY LTY P10 P100 P50 PerformanceMetric PGK PNOF STY Yield |
| Plot Data object | plot.Data |
| Standard plot for an object of class MMSE (multi MSE) | plot.MMSE |
| Standard plot for an object of class MOM | plot,MOM,missing-method plot.MOM |
| Plot MSE object | plot.MSE |
| Plot Operating Model Object | plot.Fleet plot.Hist plot.Imp plot.Obs plot.OM plot.pars plot.Stock |
| Print out plotting functions | plotFun |
| A basic SSB plot for debugging runMSE output | plotmulti |
| A generic OFL plot for NOAA use | plotOFL |
| A fairly tidy time-series quantile plot | plotquant |
| Plot a relationship between stocks | plotRel |
| Create a table of Performance Limits and Performance Objectives | PMLimit PMObj |
| An object for storing data for analysis using data-limited methods | PMobj-class |
| A projection by projection plot of F/FMSY and B/BMSY | Pplot |
| A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield | Pplot2 |
| Performance Whisker Plot | PWhisker |
| A quantile plot | quantile_plot |
| MP feasibility diagnostic using real data | RealFease |
| Class ''Rec'' | Rec-class |
| Replace an existing Stock, Fleet, Obs, or Imp object | Replace |
| Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing | replic8 |
| Generate a Data Report | Report |
| ReqData | ReqData |
| What management procedures need what data | Required |
| COSEWIC MSE run using the correct MPs and projected time horizon | COSEWIC_Blow COSEWIC_Dplot COSEWIC_Hplot COSEWIC_Pplot COSEWIC_report COSEWIC_tab COSEWIC_tab_formatted runCOSEWIC |
| Runs input control MPs on a Data object. | runInMP |
| Run a Management Procedure | runMP |
| Select DataList for an MP from 'MMSE@PPD' | select_MP |
| Sensitivity analysis | Sense |
| Setup parallel processing | setup |
| Show MSEtool S4 objects | show show,Data-method show,Hist-method show,MMSE-method show,MSE-method show,OM-method show-MSEtool |
| Show the output of a PM | show,PMobj-method |
| Show the output of a single MP recommendation | show,Rec-method |
| Slot in list: get the slot values from a list of objects | SIL |
| Simulate Catch-at-Age Data | simCAA |
| Simulate Catch-at-Length Data | simCAL |
| Calculates movement matrices from user inputs | plot_mov simmov |
| Calculates movement matrices from user specified distribution among other areas | simmov2 |
| Run a Management Strategy Evaluation | Project runMSE Simulate |
| SimulatedData Data | SimulatedData |
| Run a multi-fleet multi-stock Management Strategy Evaluation | multiMSE ProjectMOM SimulateMOM |
| Manually map the historical relative fishing effort trajectory. | SketchFun |
| General purpose polynomial smoother | smoothy |
| Standard MSE projection plot | Splot |
| Reads data Stock Synthesis file structure into a Data object using package r4ss | SS2Data |
| Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE | SS2DataMOM |
| Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) | MOM_agg_fleets plot_SS2MOM plot_SS2OM SS2MOM SS2OM SSMOM2OM |
| Plot Spawning stock biomass and reference points for both historical and projected period | SSBrefplot |
| Class ''Stock'' | Stock-class |
| StockDescription | StockDescription |
| Subset MSE object by management procedure (MP) or simulation. | Sub |
| Subset the cpars slot in an operating model | SubCpars SubCpars,MOM-method SubCpars,OM-method |
| Subset a Stock, Fleet, Obs, or Imp object from an OM object | SubOM |
| Summary of Data object | summary,Data-method |
| Summary of MMSE object | summary,MMSE-method |
| Summary of MSE object | summary,MSE-method |
| Calculate TAC recommendations for more than one MP | TAC |
| TAC Filter | TACfilter |
| Taxa_Table | Taxa_Table |
| Tom's expand grid | TEG |
| OM class objects | OM-class-objects testOM |
| Current default thresholds for DFO satisficing | Thresh_tab |
| Remove observation, implementation, and process error | tinyErr tinyErr,OM-method |
| Generic Trade-Plot Function | NOAA_plot2 Tplot Tplot2 Tplot3 TradePlot |
| Tune MP | tune_MP |
| Turing Test | Turing TuringMOM |
| Find the Management Procedures that use a particular data slot | Uses |
| Valid custom parameters (cpars) | validcpars |
| Calculate Value Of Information | VOI |
| Calculate Value Of Information 2 | VOI2 |
| Yet another Value of Information Plot | VOIplot |
| Takes a fitted SAM model and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix. | WHAM2OM |
| Biomass wormplot | wormplot |
| Internal function to write CSVs for objects | writeCSV |
| Import a Data object from Excel file | XL2Data |
| Import Fleet Object from Excel file | XL2Fleet |
| Load OM from Excel file | XL2OM |
| Import Stock Object from Excel file | XL2Stock |
