# Management Strategy Evaluation Toolkit

## Documentation for package ‘MSEtool’ version 1.7.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E F G H I L M N P R S T U V

MSEtool-package | Management Strategy Evaluation

## -- A --

Albacore_TwoFleet | A two-fleet Albacore operating model
Assessment | Class-'Assessment'
Assessment-class | Class-'Assessment'
avail | What objects of this class are available
Awatea2OM | Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model

## -- C --

calculate_TAC | Calculate MSY-based TAC from Assessment object
CASAL2OM | Reads MLE estimates from CASAL file structure into an operating model
CASALpars | Rips MLE estimates from CASAL file structure
cDD | Continuous Delay-differential assessment model
cDD_SS | Continuous Delay-differential assessment model
compare_models | Compare output from several assessment models
compare_SRA | Plot SRA scope output

## -- D --

Data-rich-MP | Model-based management procedures
DDSS_4010 | Model-based management procedures
DDSS_75MSY | Model-based management procedures
DDSS_MSY | Model-based management procedures
DD_SS | Delay - Difference Stock Assessment in TMB
DD_TMB | Delay - Difference Stock Assessment in TMB
diagnostic_AM | diagnostic_AM (diagnostic of Assessments in MSE): Did Assess models converge during MSE?

## -- E --

expandHerm | Expand the Herm list in SexPars to a matrix of fractions at age

## -- F --

fetch.file.names | Reads iSCAM Data, Control and Projection files

## -- G --

getinds | Characterize posterior predictive data
getnIVs | Count independent variables for a MICE relationship at position x in a Rel list

## -- H --

HCR40_10 | Linearly ramped harvest control rules
HCR60_20 | Linearly ramped harvest control rules
HCRlin | Generic linear harvest control rule based on biomass
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

## -- I --

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

## -- L --

ldim | Dimensions of a hierarchical list object
load.iscam.files | Reads iSCAM files into a hierarchical R list object

## -- M --

mahplot | Plot statistical power of the indicator with increasing time blocks
makemov | Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob)
make_MP | Make a custom management procedure (MP)
MMSE-class | Class "MMSE"
Model-based-MP | Model-based management procedures
MOM-class | Class "MOM"
MP | Model-based management procedures
MPCalcsNAs | Fill any NAs arising from MPCalcs (hermaphroditism mode)
MSEtool | Management Strategy Evaluation
multiData | Combine data among fleets
multiDataS | Combine data among stocks
multidebug | A basic comparison of runMSE output (MSE) and multiMSE (MMSE)
multiMSE | Run a multi-fleet multi-stock Management Strategy Evaluation

## -- N --

NIL | Item in list: get the list values from a list of lists

## -- P --

plot-method | Plot Assessment object
plot-method | Standard plot for an object of class MMSE (multi MSE)
plot-method | Standard plot for an object of class MOM
plot-method | Plot SRA scope output
plot-method | Plot profile object
plot-method | Methods for retro object
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.prof | Plot profile object
plot.retro | Methods for retro object
plot.SRA | Plot SRA scope output
plotmulti | A basic SSB plot for debugging runMSE output
plotquant | A fairly tidy time-series quantile plot
plotRel | Plot a relationship between stocks
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_mov | Calculates movement matrices from user inputs
plot_residuals | Plot residuals
plot_SR | Plot stock-recruitment function
plot_steepness | Plots probability distribution function of stock-recruit steepness
plot_timeseries | Plot time series of data
PRBcalc | Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE
prelim_AM | Preliminary Assessments in MSE
Probs | Calculates mahalanobis distance and rejection of the Null operating model
prof | Class-'prof'
prof-class | Class-'prof'
profile | Profile likelihood of assessment models
profile-method | Profile likelihood of assessment models
project | Class-'project'
project-class | Class-'project'
projection | Projections for assessment models

## -- R --

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-'retro'
retro-class | Class-'retro'
retrospective | Retrospective analysis of assessment models
retrospective-method | Retrospective analysis of assessment models
retrospective_AM | retrospective_AM (retrospective of Assessment model in MSE)

## -- S --

SCA | Statistical catch-at-age (SCA) model
SCA2 | Statistical catch-at-age (SCA) model
SCA_4010 | Model-based management procedures
SCA_75MSY | Model-based management procedures
SCA_MSY | Model-based management procedures
SCA_Pope | Statistical catch-at-age (SCA) model
SIL | Slot in list: get the slot values from a list of objects
simmov | Calculates movement matrices from user inputs
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_4010 | Model-based management procedures
SP_75MSY | Model-based management procedures
SP_Fox | Surplus production model with FMSY and MSY as leading parameters
SP_MSY | Model-based management procedures
SP_production | Find the production parameter based on depletion that produces MSY
SP_SS | Surplus production model with FMSY and MSY as leading parameters
SRA | Class-'SRA'
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
SSS_4010 | Model-based management procedures
SSS_75MSY | Model-based management procedures
SSS_MSY | Model-based management procedures
Sub_cpars | Stock-reduction analysis (SRA) for conditioning operating models
summary-method | Methods for retro object
summary-method | Summary of Assessment object
summary.Assessment | Summary of Assessment object
summary.retro | Methods for retro object
swordfish | North Atlantic Swordfish dataset

## -- T --

TAC_MSY | Calculate MSY-based TAC from Assessment object
TEG | Toms expand grid

## -- U --

userguide | Get the MSEtool vignettes

## -- V --

VPA | Virtual population analysis (VPA)