Man pages for MSEtool
Management Strategy Evaluation Toolkit

alphaconvCalculate parameters for beta distribution from mean and...
applyMMPApply multi Management Procedures (class MMP) to a...
applyMPApply Management Procedures to an object of class Data
ASAP2OMConvert ASAP 3 assessments into an operating model
Assess2MOMReads bootstrap estimates from a stock assessment model into...
Assess2OMReads bootstrap estimates from a stock assessment model...
availWhat objects of this class are available
Awatea2OMReads MCMC estimates from Awatea (Paul Starr) processed r...
BlankSelPlotInternal function to create a blank plot for mapping...
Blow_optBlow internal parallel optimization function
boxplot.DataBoxplot of TAC recommendations
calcMeanCalculate Mean Probability
CalcMPDynamicsCalculate population dynamics from MP recommendation
calcProbCalculate Probability
calcRefYieldCalculate Reference Yield
CalculateQOptimize for catchability (q)
CALsimpSimplifies the CAL slot of data object
CanIdentify management procedures (MPs) based on data...
char.log-classClass union for isRel slot
CheckDuplicateCheck for duplicated MPs names
CheckMPsCheck that specified MPs are valid and will run on...
checkMSEUtility functions for MSE objects
CheckOMCheck OM object is complete
ChkYrsCheck the years to summarize performance
ChooseManually map parameters for the historical period of...
CombineMMPCreate a blank MP recommendations object (class Rec) of the...
ConvergeCheck Convergence
Cos_thresh_tabCurrent default thresholds for COSEWIC satisficing
cparscheckInternal function for checking that the 'OM@cpars' is...
CplotPlot the median biomass and yield relative to last historical...
CSRACatch at size reduction analysis
CSRAfuncOptimization function for CSRA
cvCalculate CV from vector of values
Data2csvConverts a Data object into a .csv data file
Data-classClass "Data"
Data-class-objectsData class objects
DataDirDirectory of the data in the installed package on your...
DataInitInitialize Data Input Files
Data_xlRead in Data object from Excel spreadsheet
DFO_barDepartment of Fisheries and Oceans stock status bar plot
DFO_histDepartment of Fisheries and Oceans historical plot
DFO_plotDepartment of Fisheries and Oceans trade-off plot
DFO_plot2Department of Fisheries and Oceans default plot 2
DFO_projDepartment of Fisheries and Oceans projection plot
DFO_quantDepartment 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
dnormalDouble-normal selectivity curve
DomDetermine dominate MPs
expandHermExpand the Herm list in SexPars to a matrix of fractions at...
FeaseMP feasibility diagnostic
Fleet-classClass "Fleet"
Fleet-class-objectsFleet class objects
FMSYrefReference management procedures
GenerateRandomWalkCreates a time series per simulation that has a random normal...
genSizeCompWrapWrapper for C++ function to generate length composition
getAFCCalculate age at first capture from length at first capture...
getBlowBlow parallel optimization function
getclassget object class
getDataListGet part of an MP specific data-list
getEffhistCalculate historical fishing mortality
getfirstlevExtract the first dimension of a hierarchical list of...
getmov2Optimization function to find a movement model that matches...
getnIVsCount independent variables for a MICE relationship at...
getq_multi_MICEOptimize for catchability (q) and fishing dist for a MICE...
getselCalculate selectivity curve
hconvStock recruit parameterization
hist2Wrapper for histogram function
Hist-classClass "Hist"
HistMICEReconstruct historical dynamics
hrateDerives the rate of exchange from one sex to another based on...
Imp-classClass "Imp"
Imp-class-objectsImp class objects
initialize-methods~~ Methods for Function 'initialize' ~~
InputFunction to run a set of input control methods
iSCAMReads iSCAM files into a hierarchical R list object
iSCAM2OMReads MPD or MCMC estimates and data from iSCAM file...
iSCAMcompsCombines all iSCAM age composition data across fleets
iSCAMindsCombines indices into a single index using linear modelling...
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
Lag_DataLag the time-series slots in a 'Data' object by a specified...
ldimDimensions of a hierarchical list object
LH2OMPredict missing life-history parameters
LinInterpLinear interpolation of a y value at level xlev based on a...
makeMOMUtility for making multi-OMs
makemovCalculates movement matrices from user inputs for fraction in...
makeRelMICE relationships for multi-OM
makeTransparentMake colors transparent
ML2DDepletion and F estimation from mean length of catches
MMSE-classClass "MMSE"
MOM-classClass "MOM"
MOM-class-objectsMOM class objects
movestockCPPApply the movement model to the stock for one time-step
movfit_RcppRcpp version of the Optimization function that returns the...
MPCalcsNAsFill any NAs arising from MPCalcs (hermaphroditism mode)
MPtypeManagement Procedure Type
MPurlGet help topic URL
MSE-classClass "MSE"
MSEextraLoad more data from MSEextra package
MSYCalcsInternal function to calculate MSY Reference Points
multiDataCombine data among fleets
multiDataSCombine data among stocks
multidebugA basic comparison of runMSE output (MSE) and multiMSE (MMSE)
multiMSERun a multi-fleet multi-stock Management Strategy Evaluation
NAor0Is a value NA or zero.
NILItem in list: get the list values from a list of lists
NOAA_plotNational Oceanographic and Atmospheric Administration default...
Obs-classClass "Obs"
Obs-class-objectsObs class objects
OM-classClass "OM"
OM-class-objectsOM class objects
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
optMSY_eqInternal wrapper function to calculate MSY reference points...
optQOptimize q for a single simulation
optYieldOptimize yield for a single simulation
PerformanceMetricPerformance Metrics Methods
plot.DataPlot Data object
plotFunPrint out plotting functions
plot.MMSEStandard plot for an object of class MMSE (multi MSE)
plot.MOMStandard plot for an object of class MOM
plot.MSEPlot MSE object
plotmultiA basic SSB plot for debugging runMSE output
plotOFLA generic OFL plot for NOAA use
plotquantA fairly tidy time-series quantile plot
plotRelPlot a relationship between stocks
plot.StockPlot Operating Model Object
PMLimitCreate a table of Performance Limits and Performance...
PMobj-classAn object for storing data for analysis using data-limited...
popdynCPPPopulation dynamics model in CPP
popdynMICEPopulation dynamics for a MICE model (multiyear)
popdynOneMICEPopulation dynamics for a MICE model (single year)
popdynOneTScppAging and Mortality for one 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
qestMICEInternal function for optimizing catchability (q) for a MICE...
RangeStandardize values
RealFeaseMP feasibility diagnostic using real data
Rec-classClass "Rec"
ReplaceReplace an existing Stock, Fleet, Obs, or Imp object
replic8Enlarge (replicate) a DLM data object to create an additional...
ReportGenerate a Data Report
RequiredWhat management procedures need what data
ResFromRelReturns Results of a set of MICE relationships
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
sdconvGet parameters of lognormal distribution from mean and...
SenseSensitivity analysis
setupSetup parallel processing
show-MSEShow the output of a PM
show-MSEtoolShow MSEtool S4 objects
show-RecShow the output of a single MP recommendation
SILSlot in list: get the slot values from a list of objects
simCAASimulate Catch-at-Age Data
simCALSimulate Catch-at-Length Data
simmovCalculates movement matrices from user inputs
SimulatedDataSimulatedData Data
SketchFunManually map the historical relative fishing effort...
SS2DataReads data Stock Synthesis file structure into a Data object...
SS2DataMOMReads data Stock Synthesis file structure into a nested Data...
SS2MOMImport Stock Synthesis to MOM (2-sex multi-fleet) or OM...
SSBrefplotPlot Spawning stock biomass and reference points for both...
Stock-classClass "Stock"
Stock-class-objectsStock class objects
SubSubset MSE object by management procedure (MP) or simulation.
SubCparsSubset the cpars slot in an operating model
SubOMSubset a Stock, Fleet, Obs, or Imp object from an OM object
summary-DataSummary of Data object
summary-MMSESummary of MMSE object
summary-MSESummary of MSE object
TACCalculate TAC recommendations for more than one MP
TACfilterTAC Filter
TEGTom's expand grid
Thresh_tabCurrent default thresholds for DFO satisficing
tinyErrRemove observation, implementation, and process error
TradePlotGeneric Trade-Plot Function
trlnormLognormal distribution
TuringTuring Test
UsesFind the Management Procedures that use a particular data...
validcparsValid custom parameters (cpars)
VOICalculate Value Of Information
VOI2Calculate Value Of Information 2
VOIplotYet another Value of Information Plot
WHAM2OMTakes a fitted WHAM (Wood's Hole Assessment Model) and...
wormplotBiomass wormplot
writeCSVInternal function to write CSVs for objects
XL2DataImport a Data object from Excel file
XL2FleetImport Fleet Object from Excel file
XL2OMLoad OM from Excel file
XL2StockImport Stock Object from Excel file
MSEtool documentation built on July 26, 2023, 5:21 p.m.