Man pages for tcarruth/MSEtool
Management Strategy Evaluation Toolkit

Albacore_TwoFleetA two-fleet Albacore operating model
availWhat objects of this class are available
Awatea2OMReads MCMC estimates from Awatea (Paul Starr) processed r...
CASAL2OMReads MLE estimates from CASAL file structure into an...
CASALparsRips MLE estimates from CASAL file structure
cDDContinuous Delay-differential assessment model
compare_modelsCompare output from several assessment models
DD_TMBDelay - Difference Stock Assessment in TMB
diagnostic_AMdiagnostic_AM (diagnostic of Assessments in MSE): Did Assess...
expandHermExpand the Herm list in SexPars to a matrix of fractions at...
fetch.file.namesReads iSCAM Data, Control and Projection files
getindsCharacterize posterior predictive data
getnIVsCount independent variables for a MICE relationship at...
getq_multioptimize for catchability (q)
getq_multi_MICEoptimize for catchability (q) and fishing dist for a MICE...
HCR_FBA Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC...
HCRlinGeneric linear harvest control rule based on biomass
HCR_MSYHarvest control rule to fish at some fraction of maximum...
HCR_rampLinearly ramped harvest control rules
HistMICEReconstruct historical dynamics
hrateDerives the rate of exchange from one sex to another based on...
iSCAM2DataReads data from iSCAM file structure into a DLMtool Data...
iSCAM2OMReads 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
ldimDimensions of a hierarchical list object
load.iscam.filesReads iSCAM files into a hierarchical R list object
mahplotPlot statistical power of the indicator with increasing time...
makemovCalculates movement matrices from user inputs for fraction in...
make_MPMake a custom management procedure (MP)
MMSE-classClass "MMSE"
Model-based-MPModel-based management procedures
MOM-classClass "MOM"
MPCalcsNAsFill any NAs arising from MPCalcs (hermaphroditism mode)
MSEtool-packageManagement Strategy Evaluation
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
NILItem in list: get the list values from a list of lists
optQ_multiOptimize q for a single simulation
plot.AssessmentPlot Assessment object
plot_betavarPlots a beta variable
plot_compositionPlot composition data
plot_crosscorrProduce a cross-correlation plot of the derived data arising...
plot_lognormalvarPlots a lognormal variable
plot.MMSEStandard plot for an object of class MMSE (multi MSE)
plot.MOMStandard plot for an object of class MOM
plotmultiA basic SSB plot for debugging runMSE output
plot.profPlot profile object
plotquantA fairly tidy time-series quantile plot
plotRelPlot a relationship between stocks
plot_residualsPlot residuals
plot.retroMethods for retro object
plot_SRPlot stock-recruitment function
plot.SRAPlot SRA scope output
plot_steepnessPlots probability distribution function of stock-recruit...
plot_timeseriesPlot time series of data
popdynMICEPopulation dynamics for a MICE model (multiyear)
popdynOneMICEPopulation dynamics for a MICE model (single year)
PRBcalcCalculate mahalanobis distance (null and alternative MSEs)...
prelim_AMPreliminary Assessments in MSE
ProbsCalculates mahalanobis distance and rejection of the Null...
profileProfile likelihood of assessment models
projectionProjections for assessment models
qestMICEInternal function for optimizing catchability (q) for a MICE...
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
ResFromRelReturns Results of a set of MICE relationships
retrospectiveRetrospective analysis of assessment models
retrospective_AMretrospective_AM (retrospective of Assessment model in MSE)
SCAStatistical catch-at-age (SCA) model
SILSlot in list: get the slot values from a list of objects
simmovCalculates movement matrices from user inputs
SOLSum over list: get the list values from a list of lists
SPSurplus production model with FMSY and MSY as leading...
SP_productionFind the production parameter based on depletion that...
SRA_scopeStock-reduction analysis (SRA) for conditioning operating...
SS2DataReads data Stock Synthesis file structure into a Data object...
SS2MOMImport Stock Synthesis to multi-fleet 2-sex MOM
SS2OMReads MLE estimates from Stock Synthesis file structure into...
SSSSimple Stock Synthesis
summary.AssessmentSummary of Assessment object
swordfishNorth Atlantic Swordfish dataset
TAC_MSYCalculate MSY-based TAC from Assessment object
TEGToms expand grid
tinyErrRemove observation error, process error, implementation error...
userguideGet the MSEtool vignettes
VPAVirtual population analysis (VPA)
VPA2OMReads bootstrap estimates from a VPA stock assessment into an...
tcarruth/MSEtool documentation built on Sept. 29, 2020, 1:57 a.m.