Data-Limited Methods Toolkit

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 Probabilty |

calcProb | Calculate Probabilty |

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 |

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 |

Data-class | Class "Data" |

Data-class-objects | Data class objects |

DataDescription | DataDescription |

DataInit | Initialize an empty Data workbook or CSV |

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 | How dominant is an MP? |

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 |

ForceCor | Forces correlation among operating model parameters for M, K,... |

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 |

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 gradient grad... |

hist2 | Wrapper for histogram function |

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 A management... |

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 Effort Control |

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 |

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" |

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 |

optQ | Optimize q for a single simulation |

PerformanceMetric | Performance Metrics |

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 |

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 |

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... |

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 |

SimulatedData | SimulatedData Data |

simYears | Simulate population dynamics for historical years |

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 - IN DEVELOPMENT |

TradePlot_old | Generic Trade-off Plot |

trlnorm | Lognormal distribution for DLMtool |

Turing | Turing Test |

userguide | Open the DLMtool User Guide |

validcpars | Valid custom parameters (cpars) |

VOI | Calculate Value Of Information |

VOI2 | Calculate Value Of Information 2 |

VOIplot | Yet another Value of Information Plot |

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 |

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