Man pages for DLMtool/DLMtool
Data-Limited Methods Toolkit

alphaconvCalculate parameters for beta distribution from mean and...
applyMPApply Management Procedures to an object of class Data
availWhat objects of this class are available
AvCAverage Catch
AvC_MLLAverage Catch with a size limit
barplot.MSEPlot a barplot of MSE results
BKBeddington and Kirkwood life-history MP
BlankSelPlotInternal function to create a blank plot for mapping...
Blow_optBlow internal parallel optimization function
boxplot.DataBoxplot of TAC recommendations
calcMeanCalculate Mean Probability
calcProbCalculate Probability
CALsimpSimplifies the CAL slot of data object
CanIdentify management procedures (MPs) based on data...
CanMPWhat Data objects can be used to run this MP?
CCAge-based Catch Curve
CC1Geromont and Butterworth (2015) Constant Catch
cheatsheetsOpens the DLMtool Cheat-Sheets (requires internet connection)
checkMSEUtility functions for MSE objects
ChkObjCheck that a DLM object is valid
ChkYrsCheck the years to summarize performance
ChooseManually map parameters for the historical period of...
compplotGeneric comparison plot for simulation testing of Stochastic...
CompSRAAge-Composition Stock-Reduction Analysis
CompSRA_Internal function for CompSRA MP
condmetCondition met?
ConvergeCheck Convergence
Cos_thresh_tabCurrent default thresholds for COSEWIC satificing
cparscheckInternal function of runMSE for checking that the OM slot...
CplotPlot the median biomass and yield relative to last historical...
CSRACatch at size reduction analysis
CSRAfuncOptimization function for CSRA
curEFishing at current effort levels
cvCalculate CV from vector of values
Data2csvConverts a Data object into a .csv data file
Data-classClass "Data"
Data-class-objectsData class objects
DataDescriptionDataDescription
DataInitInitialize an empty Data workbook or CSV
Data_xlRead in Data object from Excel spreadsheet
DBSRADepletion-Based Stock Reduction Analysis
DBSRA_Depletion-based SRA internal function
DBSRAoptInternal optimization function
DCACDepletion Corrected Average Catch
DCAC_Depletion Corrected Average Catch
DDDelay - Difference Stock Assessment
DD_Delay-Difference Internal Function
DDeEffort-based Delay - Difference Stock Assessment
DD_RDelay-Difference Internal Function
demographic2Internal demographic function
DFO_barDeparment of Fisheries and Oceans stock status bar plot
DFO_histDeparment of Fisheries and Oceans historical plot
DFO_plotDeparment of Fisheries and Oceans trade-off plot
DFO_plot2Deparment of Fisheries and Oceans default plot 2
DFO_projDeparment of Fisheries and Oceans projection plot
DFO_quantDeparment of Fisheries and Oceans biomass quantile plot
DFO_reportCreate a standard DFO MSE report
DFO_spiderDFO performance spider plot (top three MPs)
DFO_tabCreate a standard DFO performance table
DFO_tab_formattedA formatted version of the standard DFO performance plot,...
DLMDataDirDirectory of the installed package on your computer
DLMenvDLMenv blank environment
DLMextraLoad more data from DLMextra package
DLMtool-packageData-Limited Methods Toolkit
dnormalDouble-normal selectivity curve
DOMHow dominant is an MP?
DTe40Effort searching MP aiming for a fixed stock depletion
DynFDynamic Fratio MP
EtargetLoptEffort Target Optimum Length
FadaptAdaptive Fratio
FdemDemographic FMSY method
Fdem_Internal function for Fdem MP
FeaseMP feasibility diagnostic
FilterSmoothKalman filter and Rauch-Tung-Striebel smoother
Fleet-classClass "Fleet"
Fleet-class-objectsFleet class objects
FleetDescriptionFleetDescription
FMSYrefReference management procedures
ForceCorForces correlation among operating model parameters for M, K,...
FratioFMSY/M ratio methods
Fratio_Fratio internal function
GB_CCGeromont and Butterworth Constant Catch Harvest Control Rule
GB_slopeGeromont and Butterworth index slope Harvest Control Rule
GB_targetGeromont and Butterworth target CPUE and catch MP
GcontrolG-control MP
getAFCCalculate age at first capture from length at first capture...
getBlowBlow parallel optimization function
getclassget object class
getEffhistCalculate historical fishing mortality
getFref3Calculate Reference Yield
getmov2Optimization function to find a movement model that matches...
getq3optimize for catchability (q)
getrInternal function to estimate r
getselCalculate selectivity curve
gettempvarCreates a time series per simulation that has gradient grad...
Growth2OMGenerate bootstrapped estimates of von Bertalanffy growth...
hist2Wrapper for histogram function
ICIIndex Confidence Interval
Imp-classClass "Imp"
Imp-class-objectsImp class objects
ImpDescriptionImpDescription
initialize-methods~~ Methods for Function 'initialize' ~~
InputFunction to run a set of input control methods
IOTC_plotIndian Ocean Tuna Commission trade-off plot
IratioMean Index Ratio
Islope_Index Slope Internal Function
Islope1Index Slope Tracking MP
IT_Index Target Internal Function
IT5Iterative Index Target MP
Itarget_Incremental Index Target MP Internal Function
Itarget1Incremental Index Target MP
Itarget1_MPAItarget1 with an MPA
ItargetE1Incremental Index Target MP - Effort-Based A management...
Itargeteff_Incremental Index Target MP Internal Function - Effort MP
ITe5Index Target Effort-Based
ITMIndex Target based on natural mortality rate
iVBInverse von Bertalanffy
joinDataJoin Data objects present in a list
join_plotsPlot several plots with a shared legend
KplotKOBE plot: a projection by projection plot of F/FMSY and...
L2ALength to age conversion
label.class-classLabel class union for performance metric objects
LBSPRLength-Based SPR Effort Control
LBSPR_Internal Estimation Function for LBSPR MP
LBSPRgenInternal estimation function for LBSPR MP
LH2OMPredict missing life-history parameters
LHdatabaseLHdatabase
LinInterpLinear interpolation of a y value at level xlev based on a...
Lratio_BHIMean length-based indicator MP of Jardim et al. 2015
LSRAEstimates R0 using SRA to match current F estimates and avoid...
LSRA2Alternative version of LSRA that's a wrapper for LSRA_opt to...
LSRA_MCMC_simInternal SRA MCMC CPP code
LSRA_optInternal estimation function for LSRA and LSRA2 functions
LSRA_opt_cppInternal estimation function for LSRA and LSRA2 functions
LstepCC1Step-wise Constant Catch
LstepCE1Step-wise Constant Effort
Ltarget1Length Target TAC MP
LtargetE1Length Target TAE MP
LW2OMEstimate length-weight parameters from data
makeMeanMPCreate an MP that averages the results of multiple MPs
makePerfConvert a OM object to one without observation or process...
makeTransparentMake colors transparent
matlenlimSize limit management procedures
MCDMean Catch Depletion
ML2DDepletion and F estimation from mean length of catches
movfit_RcppRcpp version of the Optimization function that returns the...
MPStatsCalculate Statistics for MP Performance
MPtypeManagement Procedure Type
MPurlGet help topic URL
MRrealSpatial closure and allocation management procedures
MSE-classClass "MSE"
MSEDescriptionMSEDescription
NAor0Is a value NA or zero.
NOAA_plotNational Oceanographic and Atmospheric Administration default...
Obs-classClass "Obs"
Obs-class-objectsObs class objects
ObsDescriptionObsDescription
OM-classClass "OM"
OMDescriptionOMDescription
OMdocGenerate OM Documentation Report
OMexampleCopy example OM XL and OM Documentation
OMinitInitialize Operating Model
OneRepMake stochastic variables certain for only one rep
optCPUDetermine optimal number of cpus
optMSYOptimize yield for a single simulation
optQOptimize q for a single simulation
PerformanceMetricPerformance Metrics Methods
plot.DataPlot Data object
plot-FleetPlot the Fleet object parameters
plotFunPrint out plotting functions
plot-ImpPlot the Implementation object parameters
plotMPlot M-at-Age and Size
plotMPAPlot the Historical Spatial Closures
plot.MSEPlot MSE object
plot-ObsPlot the Observation object parameters
plotOFLA generic OFL plot for NOAA use
plot-OMPlot the operating model (OM) object parameters
plotSelectPlot the vulnerability and retention curves
plotStockPlot the Stock object parameters
PMobj-classAn object for storing data for analysis using data-limited...
popdynCPPPopulation dynamics model in CPP
popdynOneTScppPopulation dynamics model for one annual time-step
PplotA projection by projection plot of F/FMSY and B/BMSY
Pplot2A projection by projection plot of F/FMSY, B/BMSY, B/B0, and...
prob.class-classProb class union for performance metric objects
PWhiskerPerformance Whisker Plot
RangeStandardize values
RcontrolIntrinsic rate of Increase MP
Rec-classClass "Rec"
ReplaceReplace an existing Stock, Fleet, Obs, or Imp object
replic8Enlarge (replicate) a DLM data object to create an additional...
ReqDataReqData
RequiredWhat management procedures need what data
runCOSEWICCOSEWIC MSE run using the correct MPs and projected time...
runInMPRuns input control MPs on a Data object.
runMPRun a Management Procedure
runMSERun a Management Strategy Evaluation
SampleCparsSample custom pars
SampleFleetParsSample Fleet Parameters
SampleImpParsSample Implementation Error Parameters
SampleObsParsSample Observation Parameters
sample_steepness2Sample steepness given mean and cv
SampleStockParsSample Stock parameters
sampySample vector
SBT1SBT simple MP
sdconvGet parameters of lognormal distribution from mean and...
SenseSensitivity analysis
setupSetup parallel processing
show-MSEShow the output of a PM
show-RecShow the output of a single MP recommendation
SimulatedDataSimulatedData Data
SketchFunManually map the historical relative fishing effort...
SPmodSurplus production based catch-limit modifier
SPMSYCatch trend Surplus Production MSY MP
SPslopeSlope in surplus production MP
SPSRASurplus Production Stock Reduction Analysis
SPSRA_Surplus Production Stock Reduction Analysis Internal Function
SRAcompPlot simulation test of Stochastic SRA method
SRAsimSimulates catch at age and catch history data for testing SRA...
StochasticSRAStochastic SRA construction of operating models
StochasticSRAcppStochastic SRA construction of operating models
Stock-classClass "Stock"
Stock-class-objectsStock class objects
StockDescriptionStockDescription
SubSubset MSE object by management procedure (MP) or simulation.
SubCparsSubset an OM cpars slot
SubOMSubset a Stock, Fleet, Obs, or Imp object from an OM object
summary-DataSummary of Data object
summary-MSESummary of MSE object
TACCalculate TAC recommendations for more than one MP
TACfilterTAC Filter
testOMtestOM OM
Thresh_tabCurrent default thresholds for DFO satificing
tinytiny
tinyErrRemove observation, implementation, and process error
TplotTrade-off plots for an MSE object
TradePlotGeneric Trade-Plot Function
TradePlot_oldGeneric Trade-off Plot
trlnormLognormal distribution for DLMtool
TuringTuring Test
userguideOpen the DLMtool User Guide
validcparsValid custom parameters (cpars)
VOICalculate Value Of Information
VOI2Calculate Value Of Information 2
VOIplotYet another Value of Information Plot
VOIplot2Value of Information Plot using PM functions
wormplotBiomass wormplot
writeCSVInternal function to write CSVs for objects
XL2DataImport a Data object from Excel file
XL2OMLoad OM from Excel file
YPRYield Per Recruit analysis to get FMSY proxy F01
YPR_Internal function for YPR MPs
DLMtool/DLMtool documentation built on Dec. 11, 2018, 8:08 a.m.