All functions

Assess2OM() VPA2OM()

Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. Assess2OM is identical to VPA2OM.

Awatea2OM()

Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model

CALsimp()

Simplifies the CAL slot of data object

Can() Cant() DLMdiag() Needed()

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

ChooseEffort() ChooseM() ChooseSelect()

Manually map parameters for the historical period of operating model

CombineMMP()

Create a blank MP recommendations object (class Rec) of the right dimensions

Converge()

Check Convergence

Cos_thresh_tab()

Current default thresholds for COSEWIC satisficing

Cplot()

Plot the median biomass and yield relative to last historical year

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

Atlantic_mackerel China_rockfish Cobia Example_datafile Gulf_blue_tilefish ourReefFish Red_snapper Simulation_1

Data class objects

Data-class

Class 'Data'

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

Dom()

Determine dominate MPs

FMSYref() FMSYref50() FMSYref75() NFref() curEref()

Reference management procedures

Fease()

MP feasibility diagnostic

DecE_Dom DecE_HDom DecE_NDom FlatE_Dom FlatE_HDom FlatE_NDom Generic_DecE Generic_FlatE Generic_Fleet Generic_IncE IncE_HDom IncE_NDom Low_Effort_Non_Target Target_All_Fish Targeting_Small_Fish

Fleet class objects

Fleet-class

Class 'Fleet'

FleetDescription

FleetDescription

Hist-class

Class 'Hist'

HistDescription

HistDescription

Overages Perfect_Imp

Imp class objects

Imp-class

Class 'Imp'

ImpDescription

ImpDescription

Input()

Function to run a set of input control methods

Kplot()

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

LH2OM() predictLH()

Predict missing life-history parameters

LHdatabase

LHdatabase

ML2D()

Depletion and F estimation from mean length of catches

MMSE-class

Class 'MMSE'

Albacore_TwoFleet

MOM class objects

MOM-class

Class 'MOM'

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

NIL()

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

NOAA_plot()

National Oceanographic and Atmospheric Administration default plot 1

testOM

OM class objects

OM-class

Class 'OM'

OMDescription

OMDescription

OMdoc()

Generate OM Documentation Report

OMexample()

Copy example OM XL and OM Documentation

OMinit()

Initialize Operating Model

Generic_Obs Imprecise_Biased Imprecise_Unbiased Perfect_Info Precise_Biased Precise_Unbiased

Obs class objects

Obs-class

Class 'Obs'

ObsDescription

ObsDescription

PMLimit() PMObj()

Create a table of Performance Limits and Performance Objectives

PMobj-class

An object for storing data for analysis using data-limited methods

PWhisker()

Performance Whisker Plot

P10() P50() P100() PNOF() LTY() STY() Yield() AAVY() AAVE()

Performance Metrics Methods

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

RealFease()

MP feasibility diagnostic using real data

Rec-class

Class 'Rec'

Replace()

Replace an existing Stock, Fleet, Obs, or Imp object

Report()

Generate a Data Report

ReqData

ReqData

Required()

What management procedures need what data

SIL()

Slot in list: get the slot values from a list of 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() plot_SS2MOM() SS2OM() SSMOM2OM() plot_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

Sense()

Sensitivity analysis

SimulatedData

SimulatedData Data

SketchFun()

Manually map the historical relative fishing effort trajectory.

Albacore Blue_shark Bluefin_tuna Bluefin_tuna_WAtl Butterfish Herring Mackerel Porgy Rockfish Snapper Sole Toothfish

Stock class objects

Stock-class

Class 'Stock'

StockDescription

StockDescription

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

TAC()

Calculate TAC recommendations for more than one MP

TACfilter()

TAC Filter

TEG()

Tom's expand grid

Thresh_tab()

Current default thresholds for DFO satisficing

TradePlot() Tplot() Tplot2() Tplot3() NOAA_plot2()

Generic Trade-Plot Function

Turing() TuringMOM()

Turing Test

Uses()

Find the Management Procedures that use a particular data slot

VOI()

Calculate Value Of Information

VOI2()

Calculate Value Of Information 2

VOIplot()

Yet another Value of Information Plot

XL2Data()

Import a Data object from Excel file

XL2Fleet()

Import Fleet Object from Excel file

XL2OM() XL2OM()

Load OM from Excel file

XL2Stock()

Import Stock Object from Excel file

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

avail()

What objects of this class are available

boxplot(<Data>)

Boxplot of TAC recommendations

calcRefYield()

Calculate Reference Yield

checkMSE() joinMSE() joinHist() updateMSE()

Utility functions for MSE objects

cparscheck()

Internal function for checking that the OM@cpars is formatted correctly

dnormal()

Double-normal selectivity curve

expandHerm()

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

getDataList()

Get part of an MP specific data-list

getclass()

get object class

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

hist2()

Wrapper for histogram function

load.iscam.files() fetch.file.names() read.report.file() read.data.file() read.control.file() read.projection.file() read.par.file() read.mcmc()

Reads iSCAM files into a hierarchical R list object

iSCAM2OM() iSCAM2Data()

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 **)

initialize-methods

~~ Methods for Function initialize ~~

joinData()

Join Data objects present in a list

join_plots()

Plot several plots with a shared legend

ldim()

Dimensions of a hierarchical list object

makeTransparent()

Make colors transparent

makemov()

Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob)

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.

multiData()

Combine data among fleets

multiDataS()

Combine data among stocks

SimulateMOM() ProjectMOM() multiMSE()

Run a multi-fleet multi-stock Management Strategy Evaluation

multidebug()

A basic comparison of runMSE output (MSE) and multiMSE (MMSE)

optCPU()

Determine optimal number of cpus

plot(<Data>)

Plot Data object

plot(<MMSE>)

Standard plot for an object of class MMSE (multi MSE)

plot(<MSE>)

Plot MSE object

plot(<pars>) plot(<Stock>) plot(<Fleet>) plot(<Obs>) plot(<Imp>) plot(<Hist>) plot(<OM>)

Plot Operating Model Object

plotFun()

Print out plotting functions

plotOFL()

A generic OFL plot for NOAA use

plotmulti()

A basic SSB plot for debugging runMSE output

plotquant()

A fairly tidy time-series quantile plot

replic8()

Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing

runCOSEWIC() COSEWIC_Pplot() COSEWIC_Dplot() COSEWIC_Blow() COSEWIC_Hplot() COSEWIC_report() COSEWIC_tab() COSEWIC_tab_formatted()

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

Simulate() Project() runMSE()

Run a Management Strategy Evaluation

setup()

Setup parallel processing

show(<PMobj>)

Show the output of a PM

show(<Rec>)

Show the output of a single MP recommendation

simCAA()

Simulate Catch-at-Age Data

simCAL()

Simulate Catch-at-Length Data

simmov() plot_mov()

Calculates movement matrices from user inputs

summary(<Data>)

Summary of Data object

summary(<MSE>)

Summary of MSE object

tinyErr()

Remove observation, implementation, and process error

validcpars()

Valid custom parameters (cpars)

wormplot()

Biomass wormplot

writeCSV()

Internal function to write CSVs for objects