Assessment-class        Class-'Assessment'
Awatea2OM               Reads MCMC estimates from Awatea (Paul Starr)
                        processed r file structure into an operating
                        model
DD_TMB                  Delay - Difference Stock Assessment in TMB
Data-rich-MP            Data-rich management procedures
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                Ramped harvest control rules
HCRlin                  Generic linear harvest control rule based on
                        biomass
LinInterp               Linear interpolation of a y value at level xlev
                        based on a vector x and y
MSEtool-package         Management Strategy Evaluation
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
SP                      Surplus production model with UMSY and MSY as
                        leading parameters
SP_production           Find the production parameter based on
                        depletion that produces MSY
SRopt                   Function that returns a stochastic estimate of
                        steepness given observed stock recruitment data
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.
avail                   What objects of this class are available
calculate_TAC           Calculate TAC from Assessment object
diagnostic_AM           diagnostic_AM (diagnostic of Assessments in
                        MSE): Did Assess models converge during MSE?
fetch.file.names        Reads iSCAM Data, Control and Projection files
getGpars                Extracts growth parameters from a SS3 r4ss
                        replist
getSR                   Predict recruitment and return fit to S-R
                        observations
getinds                 Characterize posterior predictive data
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
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)
movdistil               Simplified a multi-area transition matrix into
                        the best 2 x 2 representation
negcorlogspace          A function that samples multivariate normal
                        (logspace) variables
optSR                   Wrapper for estimating stock recruitment
                        parameters from resampled stock-recruitment
                        data
plot,Assessment,ANY-method
                        Plot Assessment object
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
prelim_AM               Preliminary Assessments in MSE
profile_likelihood      Profile likelihood of 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
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-method
                        Summary of Assessment object
swordfish               North Atlantic Swordfish dataset
