| alphaconv | Calculate parameters for beta distribution from mean and... |
| applyMP | Apply Management Procedures to an object of class Data |
| avail | What objects of this class are available |
| AvC | Average Catch |
| AvC_MLL | Average Catch with a size limit |
| barplot.MSE | Plot a barplot of MSE results |
| BK | Beddington and Kirkwood life-history MP |
| BlankSelPlot | Internal function to create a blank plot for mapping... |
| Blow_opt | Blow internal parallel optimization function |
| boxplot.Data | Boxplot of TAC recommendations |
| calcMean | Calculate Mean Probability |
| CalcMPDynamics | Calculate population dynamics from MP recommendation |
| calcProb | Calculate Probability |
| CALsimp | Simplifies the CAL slot of data object |
| Can | Identify management procedures (MPs) based on data... |
| CanMP | What Data objects can be used to run this MP? |
| CC | Age-based Catch Curve |
| CC1 | Geromont and Butterworth (2015) Constant Catch |
| char.log-class | Class union for isRel slot |
| cheatsheets | Opens the DLMtool Cheat-Sheets (requires internet connection) |
| checkMSE | Utility functions for MSE objects |
| ChkObj | Check that a DLM object is valid |
| ChkYrs | Check the years to summarize performance |
| Choose | Manually map parameters for the historical period of... |
| compplot | Generic comparison plot for simulation testing of Stochastic... |
| CompSRA | Age-Composition Stock-Reduction Analysis |
| CompSRA_ | Internal function for CompSRA MP |
| condmet | Condition met? |
| Converge | Check Convergence |
| Cos_thresh_tab | Current default thresholds for COSEWIC satificing |
| cparscheck | Internal function of runMSE for checking that the OM slot... |
| Cplot | Plot the median biomass and yield relative to last historical... |
| CSRA | Catch at size reduction analysis |
| CSRAfunc | Optimization function for CSRA |
| curE | Fishing at current effort levels |
| cv | Calculate CV from vector of values |
| Data2csv | Converts a Data object into a .csv data file |
| Data-class | Class "Data" |
| Data-class-objects | Data class objects |
| DataDescription | DataDescription |
| DataInit | Initialize Data Input Files |
| Data_xl | Read in Data object from Excel spreadsheet |
| DBSRA | Depletion-Based Stock Reduction Analysis |
| DBSRA_ | Depletion-based SRA internal function |
| DBSRAopt | Internal optimization function |
| DCAC | Depletion Corrected Average Catch |
| DCAC_ | Depletion Corrected Average Catch |
| DD | Delay - Difference Stock Assessment |
| DD_ | Delay-Difference Internal Function |
| DDe | Effort-based Delay - Difference Stock Assessment |
| DD_R | Delay-Difference Internal Function |
| demographic2 | Internal demographic function |
| DFO_bar | Deparment of Fisheries and Oceans stock status bar plot |
| DFO_hist | Deparment of Fisheries and Oceans historical plot |
| DFO_plot | Deparment of Fisheries and Oceans trade-off plot |
| DFO_plot2 | Deparment of Fisheries and Oceans default plot 2 |
| DFO_proj | Deparment of Fisheries and Oceans projection plot |
| DFO_quant | Deparment 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,... |
| DLMDataDir | Directory of the installed package on your computer |
| DLMenv | DLMenv blank environment |
| DLMextra | Load more data from DLMextra package |
| DLMtool-package | Data-Limited Methods Toolkit |
| dnormal | Double-normal selectivity curve |
| Dom | Determine dominate MPs |
| DTe40 | Effort searching MP aiming for a fixed stock depletion |
| DynF | Dynamic Fratio MP |
| EtargetLopt | Effort Target Optimum Length |
| Fadapt | Adaptive Fratio |
| Fdem | Demographic FMSY method |
| Fdem_ | Internal function for Fdem MP |
| Fease | MP feasibility diagnostic |
| FilterSmooth | Kalman filter and Rauch-Tung-Striebel smoother |
| Fleet-class | Class "Fleet" |
| Fleet-class-objects | Fleet class objects |
| FleetDescription | FleetDescription |
| FMSYref | Reference management procedures |
| Fratio | FMSY/M ratio methods |
| Fratio_ | Fratio internal function |
| GB_CC | Geromont and Butterworth Constant Catch Harvest Control Rule |
| GB_slope | Geromont and Butterworth index slope Harvest Control Rule |
| GB_target | Geromont and Butterworth target CPUE and catch MP |
| Gcontrol | G-control MP |
| genSizeCompWrap | Wrapper for C++ function to generate length composition |
| getAFC | Calculate age at first capture from length at first capture... |
| getBlow | Blow parallel optimization function |
| getclass | get object class |
| getEffhist | Calculate historical fishing mortality |
| getFref3 | Calculate Reference Yield |
| getmov2 | Optimization function to find a movement model that matches... |
| getq3 | optimize for catchability (q) |
| getr | Internal function to estimate r |
| getsel | Calculate selectivity curve |
| gettempvar | Creates a time series per simulation that has a random normal... |
| Growth2OM | Generate bootstrapped estimates of von Bertalanffy growth... |
| hist2 | Wrapper for histogram function |
| Hist-class | Class "Hist" |
| ICI | Index Confidence Interval |
| Imp-class | Class "Imp" |
| Imp-class-objects | Imp class objects |
| ImpDescription | ImpDescription |
| initialize-methods | ~~ Methods for Function 'initialize' ~~ |
| Input | Function to run a set of input control methods |
| IOTC_plot | Indian Ocean Tuna Commission trade-off plot |
| Iratio | Mean Index Ratio |
| Islope_ | Index Slope Internal Function |
| Islope1 | Index Slope Tracking MP |
| IT_ | Index Target Internal Function |
| IT5 | Iterative Index Target MP |
| Itarget_ | Incremental Index Target MP Internal Function |
| Itarget1 | Incremental Index Target MP |
| Itarget1_MPA | Itarget1 with an MPA |
| ItargetE1 | Incremental Index Target MP - Effort-Based |
| Itargeteff_ | Incremental Index Target MP Internal Function - Effort MP |
| ITe5 | Index Target Effort-Based |
| ITM | Index Target based on natural mortality rate |
| iVB | Inverse von Bertalanffy |
| joinData | Join Data objects present in a list |
| join_plots | Plot several plots with a shared legend |
| Kplot | KOBE plot: a projection by projection plot of F/FMSY and... |
| L2A | Length to age conversion |
| label.class-class | Label class union for performance metric objects |
| LBSPR | Length-Based SPR MPs |
| LBSPR_ | Internal Estimation Function for LBSPR MP |
| LBSPRgen | Internal estimation function for LBSPR MP |
| LH2OM | Predict missing life-history parameters |
| LHdatabase | LHdatabase |
| LinInterp | Linear interpolation of a y value at level xlev based on a... |
| Lratio_BHI | Mean length-based indicator MP of Jardim et al. 2015 |
| LSRA | Estimates R0 using SRA to match current F estimates and avoid... |
| LSRA2 | Alternative version of LSRA that's a wrapper for LSRA_opt to... |
| LSRA_MCMC_sim | Internal SRA MCMC CPP code |
| LSRA_opt | Internal estimation function for LSRA and LSRA2 functions |
| LSRA_opt_cpp | Internal estimation function for LSRA and LSRA2 functions |
| LstepCC1 | Step-wise Constant Catch |
| LstepCE1 | Step-wise Constant Effort |
| Ltarget1 | Length Target TAC MP |
| LtargetE1 | Length Target TAE MP |
| LW2OM | Estimate length-weight parameters from data |
| makeMeanMP | Create an MP that averages the results of multiple MPs |
| makePerf | Convert a OM object to one without observation or process... |
| makeTransparent | Make colors transparent |
| matlenlim | Size limit management procedures |
| MCD | Mean Catch Depletion |
| ML2D | Depletion and F estimation from mean length of catches |
| movfit_Rcpp | Rcpp version of the Optimization function that returns the... |
| MPStats | Calculate Statistics for MP Performance |
| MPtype | Management Procedure Type |
| MPurl | Get help topic URL |
| MRreal | Spatial closure and allocation management procedures |
| MSE-class | Class "MSE" |
| MSEDescription | MSEDescription |
| MSYCalcs | Internal function to calculate MSY Reference Points |
| NAor0 | Is a value NA or zero. |
| NOAA_plot | National Oceanographic and Atmospheric Administration default... |
| Obs-class | Class "Obs" |
| Obs-class-objects | Obs class objects |
| ObsDescription | ObsDescription |
| OM-class | Class "OM" |
| OMDescription | OMDescription |
| OMdoc | Generate OM Documentation Report |
| OMexample | Copy example OM XL and OM Documentation |
| OMinit | Initialize Operating Model |
| OneRep | Make stochastic variables certain for only one rep |
| optCPU | Determine optimal number of cpus |
| optMSY | Optimize yield for a single simulation |
| optMSY_eq | Internal wrapper function to calculate MSY reference points |
| optQ | Optimize q for a single simulation |
| PerformanceMetric | Performance Metrics Methods |
| plot.Data | Plot Data object |
| plot-Fleet | Plot the Fleet object parameters |
| plotFun | Print out plotting functions |
| plot-Imp | Plot the Implementation object parameters |
| plotM | Plot M-at-Age and Size |
| plotMPA | Plot the Historical Spatial Closures |
| plot.MSE | Plot MSE object |
| plot-Obs | Plot the Observation object parameters |
| plotOFL | A generic OFL plot for NOAA use |
| plot-OM | Plot the operating model (OM) object parameters |
| plotSelect | Plot the vulnerability and retention curves |
| plotStock | Plot the Stock object parameters |
| plot.Stock | Plot Operating Model Object |
| PMLimit | Create a table of Performance Limits and Performance... |
| PMobj-class | An object for storing data for analysis using data-limited... |
| popdynCPP | Population dynamics model in CPP |
| popdynOneTScpp | Population dynamics model for one annual time-step |
| 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... |
| prob.class-class | Prob class union for performance metric objects |
| PWhisker | Performance Whisker Plot |
| Range | Standardize values |
| Rcontrol | Intrinsic rate of Increase MP |
| RealFease | MP feasibility diagnostic using real data |
| Rec-class | Class "Rec" |
| Replace | Replace an existing Stock, Fleet, Obs, or Imp object |
| replic8 | Enlarge (replicate) a DLM data object to create an additional... |
| Report | Generate a Data Report |
| ReqData | ReqData |
| Required | What management procedures need what data |
| runCOSEWIC | COSEWIC MSE run using the correct MPs and projected time... |
| runInMP | Runs input control MPs on a Data object. |
| runMP | Run a Management Procedure |
| runMSE | Run a Management Strategy Evaluation |
| SampleCpars | Sample custom pars |
| SampleFleetPars | Sample Fleet Parameters |
| SampleImpPars | Sample Implementation Error Parameters |
| SampleObsPars | Sample Observation Parameters |
| sample_steepness2 | Sample steepness given mean and cv |
| SampleStockPars | Sample Stock parameters |
| sampy | Sample vector |
| SBT1 | SBT simple MP |
| sdconv | Get parameters of lognormal distribution from mean and... |
| Sense | Sensitivity analysis |
| setup | Setup parallel processing |
| show-MSE | Show the output of a PM |
| show-Rec | Show the output of a single MP recommendation |
| simCAA | Simulate Catch-at-Age Data |
| simCAL | Simulate Catch-at-Length Data |
| SimulatedData | SimulatedData Data |
| SketchFun | Manually map the historical relative fishing effort... |
| SPmod | Surplus production based catch-limit modifier |
| SPMSY | Catch trend Surplus Production MSY MP |
| SPslope | Slope in surplus production MP |
| SPSRA | Surplus Production Stock Reduction Analysis |
| SPSRA_ | Surplus Production Stock Reduction Analysis Internal Function |
| SRAcomp | Plot simulation test of Stochastic SRA method |
| SRAsim | Simulates catch at age and catch history data for testing SRA... |
| StochasticSRA | Stochastic SRA construction of operating models |
| StochasticSRAcpp | Stochastic SRA construction of operating models |
| Stock-class | Class "Stock" |
| Stock-class-objects | Stock class objects |
| StockDescription | StockDescription |
| Sub | Subset MSE object by management procedure (MP) or simulation. |
| SubCpars | Subset an OM cpars slot |
| SubOM | Subset a Stock, Fleet, Obs, or Imp object from an OM object |
| summary-Data | Summary of Data object |
| summary-MSE | Summary of MSE object |
| TAC | Calculate TAC recommendations for more than one MP |
| TACfilter | TAC Filter |
| testOM | testOM OM |
| Thresh_tab | Current default thresholds for DFO satificing |
| tiny | tiny |
| tinyErr | Remove observation, implementation, and process error |
| Tplot | Trade-off plots for an MSE object |
| TradePlot | Generic Trade-Plot Function |
| TradePlot_old | Generic Trade-off Plot |
| trlnorm | Lognormal distribution for DLMtool |
| Turing | Turing Test |
| userguide | Open the DLMtool User Guide |
| Uses | Find the Management Procedures that use a particular data... |
| validcpars | Valid custom parameters (cpars) |
| VOI | Calculate Value Of Information |
| VOI2 | Calculate Value Of Information 2 |
| VOIplot | Yet another Value of Information Plot |
| VOIplot2 | Value of Information Plot using PM functions |
| wormplot | Biomass wormplot |
| writeCSV | Internal function to write CSVs for objects |
| XL2Data | Import a Data object from Excel file |
| XL2OM | Load OM from Excel file |
| YPR | Yield Per Recruit analysis to get FMSY proxy F01 |
| YPR_ | Internal function for YPR MPs |
