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All functions

ASAP2OM() ASAP2Data()
Convert ASAP 3 assessments into an operating model
Assess2MOM()
Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model.
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
BAM2MOM() BAM2OM()
Import a multi-stock, multi-fleet OM from a BAM object
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
CheckOM()
Check OM object is complete
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
Lag_Data()
Lag the time-series slots in a Data object by a specified number of time-steps
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() PGK() 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() MOM_agg_fleets()
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 the cpars slot in an operating model
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
Taxa_Table
Taxa_Table
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
WHAM2OM()
Takes a fitted WHAM (Wood's Hole Assessment Model) and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix.
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
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() addMPs() 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
getMP()
Search R session for MP
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.
getnIVs()
Count independent variables for a MICE relationship at position x in a Rel list
getsel()
Calculate selectivity curve
hconv() R0conv() SRalphaconv() SRbetaconv()
Stock recruit parameterization
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 initialize,Data-method initialize,Fleet-method initialize,MSE-method initialize,Obs-method initialize,OM-method initialize,Stock-method initialize initialize,Fease-method initialize,DLM_general-method
~~ 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
makeMOM()
Utility for making multi-OMs
makeRel() print(<Rel>) predict(<Rel>) simulate(<Rel>)
MICE relationships for multi-OM
makeTransparent()
Make colors transparent
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.
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(<MOM>,<missing>)
Standard plot for an object of class MOM
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
plotRel()
Plot a relationship between stocks
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(<Data>) show(<OM>) show(<Hist>) show(<MSE>) show(<MMSE>)
Show MSEtool S4 objects
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
simmov2()
Calculates movement matrices from user specified distribution among other areas
summary(<Data>)
Summary of Data object
summary(<MMSE>)
Summary of MMSE 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