Management Strategy Evaluation Toolkit

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Documentation for package ‘MSEtool’ version 3.4.0

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

-- A --

AAVE Performance Metrics Methods
AAVY Performance Metrics Methods
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
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 --

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
CheckMPs Check that specified MPs are valid and will run on MSEtool::SimulatedData
checkMSE Utility functions for MSE objects
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
Dom Determine dominate MPs

-- E --

Example_datafile Data class objects
expandHerm Expand the Herm list in SexPars to a matrix of fractions at age

-- 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.
getsel Calculate selectivity curve
Gulf_blue_tilefish Data class objects

-- H --

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 --

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)
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
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
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.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
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.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

-- R --

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 --

Sense Sensitivity analysis
setup Setup parallel processing
show-method Show the output of a PM
show-method Show the output of a single MP recommendation
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
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.
Snapper Stock class objects
Sole Stock class objects
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 an OM cpars slot
SubOM Subset a Stock, Fleet, Obs, or Imp object from an OM object
summary-method Summary of Data 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
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
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 --

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