# Management Strategy Evaluation Toolkit

## Documentation for package ‘MSEtool’ version 3.7.5

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U V W X Y

## -- A --

AAVE | Performance Metrics Methods
AAVY | Performance Metrics Methods
addMMPs | Utility functions for multiMSE objects
addMPs | Utility functions for MSE objects
Albacore | Stock class objects
Albacore_TwoFleet | MOM class objects
applyMMP | Apply multi Management Procedures (class MMP) to a hierarchical list of Data class objects
applyMP | Apply Management Procedures to an object of class Data
ASAP2Data | Convert ASAP 3 assessments into an operating model
ASAP2OM | Convert ASAP 3 assessments into an operating model
Assess2MOM | Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model.
Assess2OM | Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. 'Assess2OM' is identical to 'VPA2OM'.
Atlantic_mackerel | Data class objects
avail | What objects of this class are available
Awatea2OM | Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model

## -- B --

BAM2MOM | Import a multi-stock, multi-fleet OM from a BAM object
BAM2OM | Import a multi-stock, multi-fleet OM from a BAM object
Bluefin_tuna | Stock class objects
Bluefin_tuna_WAtl | Stock class objects
Blue_shark | Stock class objects
boxplot.Data | Boxplot of TAC recommendations
Butterfish | Stock class objects

## -- C --

calcRefYield | Calculate Reference Yield
CALsimp | Simplifies the CAL slot of data object
Can | Identify management procedures (MPs) based on data availability
Cant | Identify management procedures (MPs) based on data availability
CheckDuplicate | Check for duplicated MPs names
checkHerm | Internal Herm functions
CheckMPs | Check that specified MPs are valid and will run on MSEtool::SimulatedData
checkMSE | Utility functions for MSE objects
CheckOM | Check OM object is complete
China_rockfish | Data class objects
Choose | Manually map parameters for the historical period of operating model
ChooseEffort | Manually map parameters for the historical period of operating model
ChooseM | Manually map parameters for the historical period of operating model
ChooseSelect | Manually map parameters for the historical period of operating model
Cobia | Data class objects
CombineMMP | Create a blank MP recommendations object (class Rec) of the right dimensions
Converge | Check Convergence
COSEWIC_Blow | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_Dplot | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_Hplot | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_Pplot | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_report | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_tab | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_tab_formatted | COSEWIC MSE run using the correct MPs and projected time horizon
Cos_thresh_tab | Current default thresholds for COSEWIC satisficing
cparscheck | Internal function for checking that the 'OM@cpars' is formatted correctly
Cplot | Plot the median biomass and yield relative to last historical year
curEref | Reference management procedures

## -- D --

Data-class | Class "Data"
Data-class-objects | Data class objects
Data2csv | Converts a Data object into a .csv data file
DataDescription | DataDescription
DataDir | Directory of the data in the installed package on your computer
DataInit | Initialize Data Input Files
DataSlots | DataSlots
Data_xl | Read in Data object from Excel spreadsheet
DecE_Dom | Fleet class objects
DecE_HDom | Fleet class objects
DecE_NDom | Fleet class objects
DFO_bar | Department of Fisheries and Oceans stock status bar plot
DFO_hist | Department of Fisheries and Oceans historical plot
DFO_plot | Department of Fisheries and Oceans trade-off plot
DFO_plot2 | Department of Fisheries and Oceans default plot 2
DFO_proj | Department of Fisheries and Oceans projection plot
DFO_quant | Department of Fisheries and Oceans biomass quantile plot
DFO_report | Create a standard DFO MSE report
DFO_spider | DFO performance spider plot (top three MPs)
DFO_tab | Create a standard DFO performance table
DFO_tab_formatted | A formatted version of the standard DFO performance plot, color coded by thresholds
DLMDataDir | Directory of the installed package on your computer
DLMdiag | Identify management procedures (MPs) based on data availability
dnormal | Double-normal selectivity curve
doHCR | Hockey Stick Harvest control rule that modifies TAC.
doIfreq | Create indices that are sampled at various frequencies
Dom | Determine dominate MPs
doRec | Calculate a management recommendation given constraints

## -- E --

Emp | A flexible empirical management procedure.
Example_datafile | Data class objects
expandHerm | Internal Herm functions

## -- F --

Fease | MP feasibility diagnostic
fetch.file.names | Reads iSCAM files into a hierarchical R list object
FlatE_Dom | Fleet class objects
FlatE_HDom | Fleet class objects
FlatE_NDom | Fleet class objects
Fleet-class | Class "Fleet"
Fleet-class-objects | Fleet class objects
FleetDescription | FleetDescription
FMSYref | Reference management procedures
FMSYref50 | Reference management procedures
FMSYref75 | Reference management procedures

## -- G --

Generic_DecE | Fleet class objects
Generic_FlatE | Fleet class objects
Generic_Fleet | Fleet class objects
Generic_IncE | Fleet class objects
Generic_Obs | Obs class objects
getclass | get object class
getDataList | Get part of an MP specific data-list
getfirstlev | Extract the first dimension of a hierarchical list of recommendation objects
getmov2 | Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.
getMP | Search R session for MP
getnIVs | Count independent variables for a MICE relationship at position x in a Rel list
getsel | Calculate selectivity curve
Gulf_blue_tilefish | Data class objects

## -- H --

hconv | Stock recruit parameterization
Herm-int | Internal Herm functions
Herring | Stock class objects
Hist-class | Class "Hist"
hist2 | Wrapper for histogram function
HistDescription | HistDescription

## -- I --

Imp-class | Class "Imp"
Imp-class-objects | Imp class objects
ImpDescription | ImpDescription
Imprecise_Biased | Obs class objects
Imprecise_Unbiased | Obs class objects
IncE_HDom | Fleet class objects
IncE_NDom | Fleet class objects
initialize | ~~ Methods for Function 'initialize' ~~
initialize-method | ~~ Methods for Function 'initialize' ~~
initialize-methods | ~~ Methods for Function 'initialize' ~~
Input | Function to run a set of input control methods
iSCAM | Reads iSCAM files into a hierarchical R list object
iSCAM2Data | Reads MPD or MCMC estimates and data from iSCAM file structure into an operating model
iSCAM2OM | Reads MPD or MCMC estimates and data 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 (** Deprecated **)

## -- J --

joinData | Join Data objects present in a list
joinHist | Utility functions for MSE objects
joinMSE | Utility functions for MSE objects
join_plots | Plot several plots with a shared legend

## -- K --

Kplot | KOBE plot: a projection by projection plot of F/FMSY and B/BMSY

## -- L --

Lag_Data | Lag the time-series slots in a 'Data' object by a specified number of time-steps
ldim | Dimensions of a hierarchical list object
LH2OM | Predict missing life-history parameters
LHdatabase | LHdatabase
load.iscam.files | Reads iSCAM files into a hierarchical R list object
Low_Effort_Non_Target | Fleet class objects
LTY | Performance Metrics Methods

## -- M --

Mackerel | Stock class objects
makeMOM | Utility for making multi-OMs
makemov | Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob)
makemov2 | Calculates movement matrices from user inputs for fraction in each area (fracs) the relative fraction moving to other areas, plus a mean probability of staying in any given area.
makeRel | MICE relationships for multi-OM
makeTransparent | Make colors transparent
ML2D | Depletion and F estimation from mean length of catches
MMSE-class | Class "MMSE"
MOM-class | Class "MOM"
MOM-class-objects | MOM class objects
MOM_agg_fleets | Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)
movestockCPP | Apply the movement model to the stock for one time-step
movfit_Rcpp | Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters.
MPCalcsNAs | Fill any NAs arising from MPCalcs (hermaphroditism mode)
MPtype | Management Procedure Type
MSE-class | Class "MSE"
MSEDescription | MSEDescription
MSEextra | Load more data from MSEextra package
MSYCalcs | Internal function to calculate MSY Reference Points
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 --

Needed | Identify management procedures (MPs) based on data availability
NFref | Reference management procedures
NIL | Item in list: get the list values from a list of lists
NOAA_plot | National Oceanographic and Atmospheric Administration default plot 1
NOAA_plot2 | Generic Trade-Plot Function

## -- O --

Obs-class | Class "Obs"
Obs-class-objects | Obs class objects
ObsDescription | ObsDescription
OM-class | Class "OM"
OM-class-objects | OM class objects
OMDescription | OMDescription
OMdoc | Generate OM Documentation Report
OMexample | Copy example OM XL and OM Documentation
OMinit | Initialize Operating Model
optCPU | Determine optimal number of cpus
ourReefFish | Data class objects
Overages | Imp class objects

## -- P --

P10 | Performance Metrics Methods
P100 | Performance Metrics Methods
P50 | Performance Metrics Methods
Perfect_Imp | Imp class objects
Perfect_Info | Obs class objects
PerformanceMetric | Performance Metrics Methods
PGK | Performance Metrics Methods
plot-method | Standard plot for an object of class MOM
plot.Data | Plot Data object
plot.Fleet | Plot Operating Model Object
plot.Hist | Plot Operating Model Object
plot.Imp | Plot Operating Model Object
plot.MMSE | Standard plot for an object of class MMSE (multi MSE)
plot.MOM | Standard plot for an object of class MOM
plot.MSE | Plot MSE object
plot.Obs | Plot Operating Model Object
plot.OM | Plot Operating Model Object
plot.pars | Plot Operating Model Object
plot.Stock | Plot Operating Model Object
plotFun | Print out plotting functions
plotmulti | A basic SSB plot for debugging runMSE output
plotOFL | A generic OFL plot for NOAA use
plotquant | A fairly tidy time-series quantile plot
plotRel | Plot a relationship between stocks
plot_mov | Calculates movement matrices from user inputs
plot_SS2MOM | Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)
plot_SS2OM | Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)
PMLimit | Create a table of Performance Limits and Performance Objectives
PMObj | Create a table of Performance Limits and Performance Objectives
PMobj-class | An object for storing data for analysis using data-limited methods
PNOF | Performance Metrics Methods
Porgy | Stock class objects
Pplot | A projection by projection plot of F/FMSY and B/BMSY
Pplot2 | A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield
Precise_Biased | Obs class objects
Precise_Unbiased | Obs class objects
predict.Rel | MICE relationships for multi-OM
predictLH | Predict missing life-history parameters
print.multiHist | Print method for 'multiHist' objects
print.Rel | MICE relationships for multi-OM
Project | Run a Management Strategy Evaluation
ProjectMOM | Run a multi-fleet multi-stock Management Strategy Evaluation
PWhisker | Performance Whisker Plot

## -- Q --

quantile_plot | A quantile plot

## -- R --

R0conv | Stock recruit parameterization
read.control.file | Reads iSCAM files into a hierarchical R list object
read.data.file | Reads iSCAM files into a hierarchical R list object
read.mcmc | Reads iSCAM files into a hierarchical R list object
read.par.file | Reads iSCAM files into a hierarchical R list object
read.projection.file | Reads iSCAM files into a hierarchical R list object
read.report.file | Reads iSCAM files into a hierarchical R list object
RealFease | MP feasibility diagnostic using real data
Rec-class | Class "Rec"
Red_snapper | Data class objects
Replace | Replace an existing Stock, Fleet, Obs, or Imp object
replic8 | Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing
Report | Generate a Data Report
ReqData | ReqData
Required | What management procedures need what data
Rockfish | Stock class objects
runCOSEWIC | COSEWIC MSE run using the correct MPs and projected time horizon
runInMP | Runs input control MPs on a Data object.
runMP | Run a Management Procedure
runMSE | Run a Management Strategy Evaluation

## -- S --

select_MP | Select DataList for an MP from 'MMSE@PPD'
Sense | Sensitivity analysis
setup | Setup parallel processing
show | Show MSEtool S4 objects
show-method | Show the output of a PM
show-method | Show MSEtool S4 objects
show-method | Show the output of a single MP recommendation
show-MSEtool | Show MSEtool S4 objects
SIL | Slot in list: get the slot values from a list of objects
simCAA | Simulate Catch-at-Age Data
simCAL | Simulate Catch-at-Length Data
simmov | Calculates movement matrices from user inputs
simmov2 | Calculates movement matrices from user specified distribution among other areas
Simulate | Run a Management Strategy Evaluation
simulate.Rel | MICE relationships for multi-OM
SimulatedData | SimulatedData Data
SimulateMOM | Run a multi-fleet multi-stock Management Strategy Evaluation
Simulation_1 | Data class objects
SketchFun | Manually map the historical relative fishing effort trajectory.
smoothy | General purpose polynomial smoother
Snapper | Stock class objects
Sole | Stock class objects
Splot | Standard MSE projection plot
SRalphaconv | Stock recruit parameterization
SRbetaconv | Stock recruit parameterization
SS2Data | Reads data Stock Synthesis file structure into a Data object using package r4ss
SS2DataMOM | Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE
SS2MOM | Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)
SS2OM | Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)
SSBrefplot | Plot Spawning stock biomass and reference points for both historical and projected period
SSMOM2OM | Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)
Stock-class | Class "Stock"
Stock-class-objects | Stock class objects
StockDescription | StockDescription
STY | Performance Metrics Methods
Sub | Subset MSE object by management procedure (MP) or simulation.
SubCpars | Subset the cpars slot in an operating model
SubCpars-method | Subset the cpars slot in an operating model
SubOM | Subset a Stock, Fleet, Obs, or Imp object from an OM object
subsetHerm | Internal Herm functions
summary-method | Summary of Data object
summary-method | Summary of MMSE object
summary-method | Summary of MSE object

## -- T --

TAC | Calculate TAC recommendations for more than one MP
TACfilter | TAC Filter
Targeting_Small_Fish | Fleet class objects
Target_All_Fish | Fleet class objects
Taxa_Table | Taxa_Table
TEG | Tom's expand grid
testOM | OM class objects
Thresh_tab | Current default thresholds for DFO satisficing
tinyErr | Remove observation, implementation, and process error
tinyErr-method | Remove observation, implementation, and process error
Toothfish | Stock class objects
Tplot | Generic Trade-Plot Function
Tplot2 | Generic Trade-Plot Function
Tplot3 | Generic Trade-Plot Function
TradePlot | Generic Trade-Plot Function
tune_MP | Tune MP
Turing | Turing Test
TuringMOM | Turing Test

## -- U --

updateMSE | Utility functions for MSE objects
Uses | Find the Management Procedures that use a particular data slot

## -- V --

validcpars | Valid custom parameters (cpars)
VOI | Calculate Value Of Information
VOI2 | Calculate Value Of Information 2
VOIplot | Yet another Value of Information Plot
VPA2OM | Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. 'Assess2OM' is identical to 'VPA2OM'.

## -- W --

WHAM2OM | Takes a fitted SAM model and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix.
wormplot | Biomass wormplot
writeCSV | Internal function to write CSVs for objects

## -- X --

XL2Data | Import a Data object from Excel file
XL2Fleet | Import Fleet Object from Excel file
XL2OM | Load OM from Excel file
XL2Stock | Import Stock Object from Excel file

## -- Y --

Yield | Performance Metrics Methods