Man pages for MSEtool
Management Strategy Evaluation Toolkit

Assessment-classClass-'Assessment'
availWhat objects of this class are available
Awatea2OMReads MCMC estimates from Awatea (Paul Starr) processed r...
calculate_TACCalculate TAC from Assessment object
Data-rich-MPData-rich management procedures
DD_TMBDelay - Difference Stock Assessment in TMB
diagnostic_AMdiagnostic_AM (diagnostic of Assessments in MSE): Did Assess...
fetch.file.namesReads iSCAM Data, Control and Projection files
getGparsExtracts growth parameters from a SS3 r4ss replist
getindsCharacterize posterior predictive data
getSRPredict recruitment and return fit to S-R observations
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_rampRamped harvest control rules
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
LinInterpLinear interpolation of a y value at level xlev based on a...
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)
movdistilSimplified a multi-area transition matrix into the best 2 x 2...
MSEtool-packageManagement Strategy Evaluation
negcorlogspaceA function that samples multivariate normal (logspace)...
optSRWrapper for estimating stock recruitment parameters from...
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_residualsPlot residuals
plot_SRPlot stock-recruitment function
plot_steepnessPlots probability distribution function of stock-recruit...
plot_timeseriesPlot time series of data
PRBcalcCalculate mahalanobis distance (null and alternative MSEs)...
prelim_AMPreliminary Assessments in MSE
ProbsCalculates mahalanobis distance and rejection of the Null...
profile_likelihoodProfile likelihood of assessment models
read.control.fileReads iSCAM control file
read.data.fileReads iSCAM dat file
read.mcmcReads iSCAM mcmc output files
read.par.fileReads iSCAM parameter file
read.projection.fileReads iSCAM projection file
read.report.fileReads iSCAM Rep file
retrospectiveRetrospective analysis of assessment models
retrospective_AMretrospective_AM (retrospective of Assessment model in MSE)
SCAStatistical catch-at-age (SCA) model
simmovCalculates movement matrices from user inputs
SPSurplus production model with UMSY and MSY as leading...
SP_productionFind the production parameter based on depletion that...
SRoptFunction that returns a stochastic estimate of steepness...
SS2DataReads data Stock Synthesis file structure into a Data object...
SS2OMReads MLE estimates from Stock Synthesis file structure into...
summary-AssessmentSummary of Assessment object
swordfishNorth Atlantic Swordfish dataset
MSEtool documentation built on Oct. 17, 2018, 9:04 a.m.