# Management Strategy Evaluation Toolkit

## Documentation for package ‘MSEtool’ version 1.1.0

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

## Help Pages

MSEtool-package | Management Strategy Evaluation
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
calculate_TAC | Calculate TAC from Assessment object
Data-rich-MP | Data-rich management procedures
DDSS_4010 | Data-rich management procedures
DDSS_75MSY | Data-rich management procedures
DDSS_MSY | Data-rich 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?
fetch.file.names | Reads iSCAM Data, Control and Projection files
getGpars | Extracts growth parameters from a SS3 r4ss replist
getinds | Characterize posterior predictive data
getSR | Predict recruitment and return fit to S-R observations
HCR40_10 | Ramped harvest control rules
HCR60_20 | 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 | Ramped harvest control rules
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
LinInterp | Linear interpolation of a y value at level xlev based on a vector x and y
load.iscam.files | Reads iSCAM files into a hierarchical R list object
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)
movdistil | Simplified a multi-area transition matrix into the best 2 x 2 representation
MSEtool | Management Strategy Evaluation
negcorlogspace | A function that samples multivariate normal (logspace) variables
optSR | Wrapper for estimating stock recruitment parameters from resampled stock-recruitment data
plot-method | Plot Assessment object
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
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)
SCA | Statistical catch-at-age (SCA) model
SCA2 | Statistical catch-at-age (SCA) model
SCA_4010 | Data-rich management procedures
SCA_75MSY | Data-rich management procedures
SCA_MSY | Data-rich management procedures
simmov | Calculates movement matrices from user inputs
SP | Surplus production model with UMSY and MSY as leading parameters
SP_4010 | Data-rich management procedures
SP_75MSY | Data-rich management procedures
SP_MSY | Data-rich management procedures
SP_production | Find the production parameter based on depletion that produces MSY
SP_SS | Surplus production model with UMSY and MSY as leading parameters
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.
summary-method | Summary of Assessment object
swordfish | North Atlantic Swordfish dataset