Man pages for DLMtool/DLMtool
Data-Limited Methods Toolkit

AAVYPerformance Metric: Probability AAVY < 0.2
AlbacoreAlbacore Stock
alphaconvCalculate alpha parameter for beta distribution from mean and...
applyMPApply Management Procedures to an object of class Data
Atlantic_mackerelAtlantic_mackerel Data
availWhat objects of this class are available
AvCAverage Catch
AvC_MLLAverage Catch with a size limit
barplot.MSEPlot a barplot of MSE results
betaconvCalculate beta parameter for beta distribution from mean and...
BKBeddington and Kirkwood life-history MP (simple version)
BK_CCBeddington and Kirkwood life-history method combined with...
BK_MLBeddington and Kirkwood life-history analysis with...
BlankSelPlotInternal function to create a blank plot for mapping...
Blow_optBlow internal parallel optimization function
Bluefin_tunaBluefin_tuna Stock
Bluefin_tuna_WAtlBluefin_tuna_WAtl Stock
Blue_sharkBlue_shark Stock
boxplot.DataBoxplot of TAC recommendations
ButterfishButterfish Stock
calcMeanCalculate Mean Probabilty
calcProbCalculate Probabilty
CanWhat management procedures can be applied to this Data...
CantWhat management procedures can't be applied to this DLM data...
CC1Constant catch management procedure of Geromont and...
CC4Constant catch management procedure of Geromont and...
checkMSECheck that MSE object includes all slots
China_rockfishChina_rockfish Data
ChkObjCheck that a DLM object is valid
ChooseEffortManually map the historical relative fishing effort...
ChooseMManually map natural mortality at age or size.
ChooseSelectManually choose the historical selectivity pattern
CobiaCobia Data
compplotGeneric comparison plot for simulation testing of Stochastic...
CompSRAAge-composition-based estimate of current stock depletion...
CompSRA4010Age-composition-based estimate of current stock depletion...
condmetCondition met?
ConvergeCheck Convergence
COSEWIC_plotCOSEWIC forward projection plot
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
curE75Fishing at 75 per cent of current effort levels
cvCalculate CV from vector of values
DAACDepletion Adjusted Average Catch
Data-classClass "Data"
DataInitInitialize an empty Data workbook or CSV
Data_xlRead in Data object from Excel spreadsheet
DBSRADepletion-Based Stock Reduction Analysis
DBSRA_40Depletion-Based Stock Reduction Analysis assuming 40 per cent...
DBSRA4010Depletion-Based Stock Reduction Analysis paired with 40-10...
DCACDepletion Corrected Average Catch
DCAC_40Depletion Corrected Average Catch assuming 40 per cent stock...
DCAC4010Depletion Corrected Average Catch paired with the 40-10 rule
DCAC_MLDepletion-Based Stock Reduction Analysis using mean-length...
DDDelay - Difference Stock Assessment with UMSY and MSY leading
DD4010Delay - Difference Stock Assessment with UMSY and MSY leading...
DDeEffort control version of DD - Delay - Difference Stock...
DDe75Effort control version of DD - Delay - Difference Stock...
DDesEffort searching version of DD - Delay - Difference Stock...
DecE_DomDecE_Dom Fleet
DecE_HDomDecE_HDom Fleet
DecE_NDomDecE_NDom Fleet
DepFDepletion Corrected Fratio
derive_beta_parThis function reduces the CV by 5 per cent until steepness...
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
DLMDataDirDirectory of the installed package on your computer
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 40 per cent stock depletion
DTe50Effort searching MP aiming for 50 per cent stock depletion
DynFDynamic Fratio MP
EtargetLoptEffort MP: adjust effort up/down if mean length above/below...
Example_datafileExample_datafile Data
FadaptAn adaptive MP that uses trajectory in inferred suplus...
FdemDemographic FMSY method
Fdem_CCDemographic FMSY method using catch-curve analysis to...
Fdem_MLDemographic FMSY method that uses mean length data to...
FeaseMP feasibility diagnostic
Fease-classClass "Fease"
Fease_xlRead in feasibility parameters from Excel spreadsheet
FeasibilityFeasibility Fease
Feasibility2Feasibility2 Fease
fetch.file.namesReads iSCAM Data, Control and Projection files
FlatE_DomFlatE_Dom Fleet
FlatE_HDomFlatE_HDom Fleet
FlatE_NDomFlatE_NDom Fleet
Fleet-classClass "Fleet"
FMSYrefA reference FMSY method (uses perfect information about FMSY)
FMSYref50A reference FMSY method that fishes at half of FMSY (uses...
FMSYref75A reference FMSY method that fishes at three quarters of FMSY...
ForceCorForces correlation among operating model parameters for M, K,...
FratioAn FMSY/M ratio method
Fratio4010An FMSY/M ratio method paired with the 40-10 rule
Fratio_CCA data-limited method that uses FMSY/M ratio and a naive...
Fratio_MLAn FMSY/M ratio MP that uses a mean length estimator of...
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
Generic_DecEGeneric_DecE Fleet
Generic_FlatEGeneric_FlatE Fleet
Generic_FleetGeneric_Fleet Fleet
Generic_IncEGeneric_IncE Fleet
Generic_ObsGeneric_Obs Obs
getAFCCalculate age at first capture from length at first capture...
getBHPredict Beverton-Holt recruitment and return fit to S-R...
getBlowBlow parallel optimization function
getclassget object class
getEffhistCalculate historical fishing mortality
getFref3Calculate Reference Yield
getGparsExtracts growth parameters from a SS3 r4ss replist
getmov2Optimization function to find a movement model that matches...
getq3optimize for catchability (q)
getselCalculate selectivity curve
gettempvarCreates a time series per simulation that has gradient grad...
Gulf_blue_tilefishGulf_blue_tilefish Data
HDAACHybrid Depletion Adjusted Average Catch
HerringHerring Stock
hist2Wrapper for histogram function
ICIIndex Confidence Interval (ICI) MP by Jardim et al. (2015)
ICI2Less Precautionary Index Confidence Interval (ICI) MP by...
Imp-classClass "Imp"
Imprecise_BiasedImprecise_Biased Obs
Imprecise_UnbiasedImprecise_Unbiased Obs
IncE_HDomIncE_HDom Fleet
IncE_NDomIncE_NDom Fleet
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 MP from Jardim et al. 2015
iSCAM2DataReads data from iSCAM file structure into a DLMtool Data...
iSCAM2DLMReads MLE estimates from iSCAM file structure into an...
iSCAMcompsCombines all iSCAM age composition data across fleets
iSCAMindsCombines indices into a single index using linear modelling
Islope1A management procedure that incrementally adjusts the TAC to...
Islope4A management procedure that incrementally adjusts the TAC to...
IT10Index Target 10
IT5Index Target 5
Itarget1A management procedure that incrementally adjusts the TAC...
Itarget1_MPAA example mixed control MP that uses the Itarget1 output...
Itarget4A management procedure that incrementally adjusts the TAC...
ItargetE1A management procedure that incrementally adjusts the effort...
ItargetE4A management procedure that incrementally adjusts the Effort...
ITe10Index Target Effort-Based 10
ITe5Index Target Effort-Based 5
ITMIndex Target based on natural mortality rate
joinMSEJoin multiple MSE objects together
KplotKOBE plot: a projection by projection plot of F/FMSY and...
L2ALength to age conversion
L95targetA management procedure that adjusts the TAC up/down from...
label.class-classLabel class union for performance metric objects
LinInterpLinear interpolation of a y value at level xlev based on a...
load.iscam.filesReads iSCAM files into a hierarchical R list object
Low_Effort_Non_TargetLow_Effort_Non_Target Fleet
Lratio_BHIMean length-based indicator MP of Jardim et al. 2015 using...
Lratio_BHI2The more general version of the mean length-based indicator...
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
LstepCC1A management procedure that incrementally adjusts the TAC...
LstepCC4A management procedure that incrementally adjusts the TAC...
LstepCE1A management procedure that incrementally adjusts the TAC...
LstepCE2A management procedure that incrementally adjusts the Effort...
Ltarget1A management procedure that incrementally adjusts the TAC to...
Ltarget4A management procedure that incrementally adjusts the TAC to...
LtargetE1A management procedure that incrementally adjusts the Effort...
LtargetE4A management procedure that incrementally adjusts the Effort...
LTYPerformance Metric: Probability Long-Term Yield > 0.5...
MackerelMackerel Stock
makePerfConvert a OM object to one without observation or process...
makeTransparentMake colors transparent
matlenlimA data-limited method in which fishing retention is set...
matlenlim2A data-limited method in which fishing vulnerability is set...
MCDMean Catch Depletion
MCD4010Mean Catch Depletion
mconvGet log normal mean from transformed space mean and standard...
minlenLopt1This input control sets the minimum length of fish caught to...
ML2DDepletion and F estimation from mean length of catches
movdistilSimplified a multi-area transition matrix into the best 2 x 2...
movfit_RcppRcpp version of the Optimization function that returns the...
MPStatsCalculate Statistics for MP Performance
MPtypeManagement Procedure Type
MRnorealAn marine reserve in area 1 with no spatial reallocation of...
MRrealA marine reserve in area 1 with full reallocation of fishing...
MSE-classClass "MSE"
NAor0Is a value NA or zero.
NeededData needed to get MPs running
negcorlogspaceA function that samples multivariate normal (logspace)...
NFrefNo Fishing Reference MP
NOAA_plotNational Oceanographic and Atmospheric Administration default...
Obs-classClass "Obs"
OM-classClass "OM"
OMdocGenerate OM Documentation Report
OMexampleCopy example OM XL and OM Documentation
OMinitInitialize Operating Model
OneRepMake stochastic variables certain for only one rep
optBHWrapper for estimating stock recruitment parameters from...
optCPUDetermine optimal number of cpus
optMSYOptimize yield for a single simulation
optQOptimize q for a single simulation
ourReefFishExample data object
OveragesOverages Imp
P10Performance Metric: Probability B > 0.1 BMSY
P100Performance Metric: Probability B > BMSY
P50Performance Metric: Probability B > 0.5 BMSY
Perfect_ImpPerfect_Imp Imp
Perfect_InfoPerfect_Info Obs
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...
POFPerformance Metric: Probability F < FMSY
popdynCPPPopulation dynamics model in CPP
popdynOneTScppPopulation dynamics model for one annual time-step
PorgyPorgy Stock
PplotA projection by projection plot of F/FMSY and B/BMSY
Pplot2A projection by projection plot of F/FMSY, B/BMSY, B/B0, and...
Precise_BiasedPrecise_Biased Obs
Precise_UnbiasedPrecise_Unbiased Obs
prob.class-classProb class union for performance metric objects
PWhiskerPerformance Whisker Plot
RangeStandardize values
RcontrolHarvest Control Rule using prior for intrinsic rate of...
Rcontrol2MP using prior for intrinsic rate of increase with a...
read.control.fileReads iSCAM control file iSCAM dat file
read.mcmcReads iSCAM mcmc output files
read.par.fileReads iSCAM parameter file
read.projection.fileReads iSCAM projection file iSCAM Rep file
Rec-classClass "Rec"
Red_snapperRed_snapper Data
ReplaceReplace an existing Stock, Fleet, Obs, or Imp object
replic8Enlarge (replicate) a DLM data object to create an additional...
RequiredWhat management procedures need what data
RockfishRockfish Stock
runInMPRuns input control MPs on a Data object.
runMPRun a Management Procedure
runMSERun a Management Strategy Evaluation
runMSEnomsgrunMSE with no messages - for testing
runMSErobustRun 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
SBT2SBT complex MP
sdconvGet log normal standard deviation from transformed space mean...
SenseSensitivity analysis
setupSetup parallel processing
show-MSEShow the output of a PM
show-RecShow the output of a single MP recommendation
SimulatedDataSimulatedData Data
Simulation_1Simulation_1 Data
simYearsSimulate population dynamics for historical years
SketchFunManually map the historical relative fishing effort...
slotlimAn data-limited method which sets a slot limit
SnapperSnapper Stock
SoleSole Stock
SPmodSurplus production based catch-limit modifier
SPMSYCatch trend Surplus Production MSY MP
SPslopeSlope in surplus production MP
SPSRASurplus Production Stock Reduction Analysis
SPSRA_MLSurplus Production Stock Reduction Analysis using a...
SRAcompPlot simulation test of Stochastic SRA method
SRAsimSimulates catch at age and catch history data for testing SRA...
SRoptFunction that returns a stochastic estimate of steepness...
SS2DataReads data Stock Synthesis file structure into an data object...
SS2DLMReads MLE estimates from Stock Synthesis file structure into...
StochasticSRAStochastic SRA construction of operating models
StochasticSRAcppStochastic SRA construction of operating models
Stock-classClass "Stock"
STYPerformance Metric: Probability Short-Term Yield > 0.5...
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
Target_All_FishTarget_All_Fish Fleet
Targeting_Small_FishTargeting_Small_Fish Fleet
tdlnormCalculate density of log-normally distributed random numbers
testOMtestOM OM
ToothfishToothfish Stock
TplotA trade-off plot for an MSE object
Tplot2A shorter version of the plot method for MSEs that just shows...
Tplot3Test Trade-Off Plot
TradePlotGeneric Trade-off Plot
trlnormGenerate log-normally distributed random numbers
updateMSEUpdate an MSE object with new slots
userguideOpen the DLMtool User Guide
validcparsValid custom parameters (cpars)
VOICalculate Value Of Information
VOI2Calculate Value Of Information 2
VOIplotYet another Value of Information Plot
wormplotBiomass wormplot
writeCSVInternal function to write CSVs for objects
XL2DataImport a Data object from Excel file
XL2OMLoad OM from Excel file
YieldPerformance Metric: Average Yield
YPRYield Per Recruit analysis to get FMSY proxy F01
YPR_CCYield Per Recruit analysis to get FMSY proxy F01 paired to a...
YPR_MLYield Per Recruit analysis to get FMSY proxy F01 paired with...
DLMtool/DLMtool documentation built on March 21, 2018, 7:48 p.m.