Albacore_TwoFleet       A two-fleet Albacore operating model
Assessment-class        Class-'Assessment'
Awatea2OM               Reads MCMC estimates from Awatea (Paul Starr)
                        processed r file structure into an operating
                        model
CASAL2OM                Reads MLE estimates from CASAL file structure
                        into an operating model
CASALpars               Rips MLE estimates from CASAL file structure
DD_TMB                  Delay - Difference Stock Assessment in TMB
HCR_FB                  A Harvest Control Rule using B/BMSY and F/FMSY
                        to adjust TAC or TAE.
HCR_MSY                 Harvest control rule to fish at some fraction
                        of maximum sustainable yield
HCR_ramp                Linearly ramped harvest control rules
HCRlin                  Generic linear harvest control rule based on
                        biomass
MMSE-class              Class "MMSE"
MOM-class               Class "MOM"
MPCalcsNAs              Fill any NAs arising from MPCalcs
                        (hermaphroditism mode)
MSEtool-package         Management Strategy Evaluation
Model-based-MP          Model-based management procedures
NIL                     Item in list: get the list values from a list
                        of lists
PRBcalc                 Calculate mahalanobis distance (null and
                        alternative MSEs) and statistical power for all
                        MPs in an MSE
Probs                   Calculates mahalanobis distance and rejection
                        of the Null operating model
SCA                     Statistical catch-at-age (SCA) model
SIL                     Slot in list: get the slot values from a list
                        of objects
SOL                     Sum over list: get the list values from a list
                        of lists
SP                      Surplus production model with FMSY and MSY as
                        leading parameters
SP_production           Find the production parameter based on
                        depletion that produces MSY
SRA-class               Class-'SRA'
SRA_scope               Stock-reduction analysis (SRA) for conditioning
                        operating models
SS2Data                 Reads data Stock Synthesis file structure into
                        a Data object using package r4ss
SS2OM                   Reads MLE estimates from Stock Synthesis file
                        structure into an operating model using package
                        r4ss.
SSS                     Simple Stock Synthesis
TAC_MSY                 Calculate MSY-based TAC from Assessment object
TEG                     Toms expand grid
VPA                     Virtual population analysis (VPA)
avail                   What objects of this class are available
cDD                     Continuous Delay-differential assessment model
compare_models          Compare output from several assessment models
diagnostic_AM           diagnostic_AM (diagnostic of Assessments in
                        MSE): Did Assess models converge during MSE?
expandHerm              Expand the Herm list in SexPars to a matrix of
                        fractions at age
fetch.file.names        Reads iSCAM Data, Control and Projection files
getinds                 Characterize posterior predictive data
getnIVs                 Count independent variables for a MICE
                        relationship at position x in a Rel list
iSCAM2Data              Reads data from iSCAM file structure into a
                        DLMtool Data object
iSCAM2OM                Reads MLE estimates from iSCAM file structure
                        into an operating model
iSCAMcomps              Combines all iSCAM age composition data across
                        fleets
iSCAMinds               Combines indices into a single index using
                        linear modelling
ldim                    Dimensions of a hierarchical list object
load.iscam.files        Reads iSCAM files into a hierarchical R list
                        object
mahplot                 Plot statistical power of the indicator with
                        increasing time blocks
make_MP                 Make a custom management procedure (MP)
makemov                 Calculates movement matrices from user inputs
                        for fraction in each area (fracs) and
                        probability of staying in areas (prob)
multiData               Combine data among fleets
multiDataS              Combine data among stocks
multiMSE                Run a multi-fleet multi-stock Management
                        Strategy Evaluation
multidebug              A basic comparison of runMSE output (MSE) and
                        multiMSE (MMSE)
plot.Assessment         Plot Assessment object
plot.MMSE               Standard plot for an object of class MMSE
                        (multi MSE)
plot.MOM                Standard plot for an object of class MOM
plot.SRA                Plot SRA scope output
plot.prof               Plot profile object
plot.retro              Methods for retro object
plotRel                 Plot a relationship between stocks
plot_SR                 Plot stock-recruitment function
plot_betavar            Plots a beta variable
plot_composition        Plot composition data
plot_crosscorr          Produce a cross-correlation plot of the derived
                        data arising from getinds(MSE_object)
plot_lognormalvar       Plots a lognormal variable
plot_residuals          Plot residuals
plot_steepness          Plots probability distribution function of
                        stock-recruit steepness
plot_timeseries         Plot time series of data
plotmulti               A basic SSB plot for debugging runMSE output
plotquant               A fairly tidy time-series quantile plot
prelim_AM               Preliminary Assessments in MSE
prof-class              Class-'prof'
profile                 Profile likelihood of assessment models
project-class           Class-'project'
projection              Projections for assessment models
read.control.file       Reads iSCAM control file
read.data.file          Reads iSCAM dat file
read.mcmc               Reads iSCAM mcmc output files
read.par.file           Reads iSCAM parameter file
read.projection.file    Reads iSCAM projection file
read.report.file        Reads iSCAM Rep file
retro-class             Class-'retro'
retrospective           Retrospective analysis of assessment models
retrospective_AM        retrospective_AM (retrospective of Assessment
                        model in MSE)
simmov                  Calculates movement matrices from user inputs
summary.Assessment      Summary of Assessment object
swordfish               North Atlantic Swordfish dataset
userguide               Get the MSEtool vignettes
