Data-Limited Methods Toolkit

Documentation for package ‘DLMtool’ version 5.3

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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

DLMtool-package

Data-Limited Methods Toolkit

-- A --

AAVY	Performance Metrics Methods
Albacore	Stock class objects
applyMP	Apply Management Procedures to an object of class Data
Atlantic_mackerel	Data class objects
avail	What objects of this class are available
AvC	Average Catch
AvC_MLL	Average Catch with a size limit

-- B --

barplot.MSE	Plot a barplot of MSE results
BK	Beddington and Kirkwood life-history MP
BK_CC	Beddington and Kirkwood life-history MP
BK_ML	Beddington and Kirkwood life-history MP
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 --

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
CC	Age-based Catch Curve
CC1	Geromont and Butterworth (2015) Constant Catch
CC2	Geromont and Butterworth (2015) Constant Catch
CC3	Geromont and Butterworth (2015) Constant Catch
CC4	Geromont and Butterworth (2015) Constant Catch
CC5	Geromont and Butterworth (2015) Constant Catch
cheatsheets	Opens the DLMtool Cheat-Sheets (requires internet connection)
checkMSE	Utility functions for MSE objects
China_rockfish	Data class objects
ChkObj	Check that a DLM object is valid
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
compplot	Generic comparison plot for simulation testing of Stochastic SRA method
CompSRA	Age-Composition Stock-Reduction Analysis
CompSRA4010	Age-Composition Stock-Reduction Analysis
condmet	Condition met?
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 satificing
cparscheck	Internal function of runMSE for checking that the OM slot cpars slot is formatted correctly
Cplot	Plot the median biomass and yield relative to last historical year
curE	Fishing at current effort levels
curE75	Fishing at current effort levels

-- D --

DAAC	Depletion Corrected Average Catch
Data-class	Class "Data"
Data-class-objects	Data class objects
Data2csv	Converts a Data object into a .csv data file
DataDescription	DataDescription
DataInit	Initialize an empty Data workbook or CSV
Data_xl	Read in Data object from Excel spreadsheet
DBSRA	Depletion-Based Stock Reduction Analysis
DBSRA4010	Depletion-Based Stock Reduction Analysis
DBSRA_40	Depletion-Based Stock Reduction Analysis
DCAC	Depletion Corrected Average Catch
DCAC4010	Depletion Corrected Average Catch
DCACs	Depletion Corrected Average Catch
DCAC_40	Depletion Corrected Average Catch
DCAC_ML	Depletion Corrected Average Catch
DD	Delay - Difference Stock Assessment
DD4010	Delay - Difference Stock Assessment
DDe	Effort-based Delay - Difference Stock Assessment
DDe75	Effort-based Delay - Difference Stock Assessment
DDes	Effort-based Delay - Difference Stock Assessment
DecE_Dom	Fleet class objects
DecE_HDom	Fleet class objects
DecE_NDom	Fleet class objects
DepF	FMSY/M ratio methods
DFO_bar	Deparment of Fisheries and Oceans stock status bar plot
DFO_hist	Deparment of Fisheries and Oceans historical plot
DFO_plot	Deparment of Fisheries and Oceans trade-off plot
DFO_plot2	Deparment of Fisheries and Oceans default plot 2
DFO_proj	Deparment of Fisheries and Oceans projection plot
DFO_quant	Deparment 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
DLMenv	DLMenv blank environment
DLMextra	Load more data from DLMextra package
DLMtool	Data-Limited Methods Toolkit
dnormal	Double-normal selectivity curve
DOM	How dominant is an MP?
DTe40	Effort searching MP aiming for a fixed stock depletion
DTe50	Effort searching MP aiming for a fixed stock depletion
DynF	Dynamic Fratio MP

-- E --

EtargetLopt	Effort Target Optimum Length
Example_datafile	Data class objects

-- F --

Fadapt	Adaptive Fratio
Fdem	Demographic FMSY method
Fdem_CC	Demographic FMSY method
Fdem_ML	Demographic FMSY method
Fease	MP feasibility diagnostic
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
ForceCor	Forces correlation among operating model parameters for M, K, Linf and L50
Fratio	FMSY/M ratio methods
Fratio4010	FMSY/M ratio methods
Fratio_CC	FMSY/M ratio methods
Fratio_ML	FMSY/M ratio methods

-- G --

GB_CC	Geromont and Butterworth Constant Catch Harvest Control Rule
GB_slope	Geromont and Butterworth index slope Harvest Control Rule
GB_target	Geromont and Butterworth target CPUE and catch MP
Gcontrol	G-control MP
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
getmov2	Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.
getsel	Calculate selectivity curve
Growth2OM	Generate bootstrapped estimates of von Bertalanffy growth parameters from length-at-age data
Gulf_blue_tilefish	Data class objects

-- H --

HDAAC	Depletion Corrected Average Catch
Herring	Stock class objects
Hist-class	Class "Hist"
hist2	Wrapper for histogram function

-- I --

ICI	Index Confidence Interval
ICI2	Index Confidence Interval
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
IOTC_plot	Indian Ocean Tuna Commission trade-off plot
Iratio	Mean Index Ratio
Islope1	Index Slope Tracking MP
Islope2	Index Slope Tracking MP
Islope3	Index Slope Tracking MP
Islope4	Index Slope Tracking MP
IT10	Iterative Index Target MP
IT5	Iterative Index Target MP
Itarget1	Incremental Index Target MP
Itarget1_MPA	Itarget1 with an MPA
Itarget2	Incremental Index Target MP
Itarget3	Incremental Index Target MP
Itarget4	Incremental Index Target MP
ItargetE1	Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ItargetE2	Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ItargetE3	Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ItargetE4	Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ITe10	Index Target Effort-Based
ITe5	Index Target Effort-Based
ITM	Index Target based on natural mortality rate

-- J --

joinData	Join Data objects present in a list
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 --

L95target	Length Target TAC MP
LBSPR	Length-Based SPR MPs
LBSPR_MLL	Length-Based SPR MPs
LH2OM	Predict missing life-history parameters
LHdatabase	LHdatabase
Low_Effort_Non_Target	Fleet class objects
Lratio_BHI	Mean length-based indicator MP of Jardim et al. 2015
Lratio_BHI2	Mean length-based indicator MP of Jardim et al. 2015
Lratio_BHI3	Mean length-based indicator MP of Jardim et al. 2015
LSRA	Estimates R0 using SRA to match current F estimates and avoid penalities for low stock sizes
LSRA2	Alternative version of LSRA that's a wrapper for LSRA_opt to return the right type of output (mode) using sapply
LSRA_MCMC_sim	Internal SRA MCMC CPP code
LSRA_opt	Internal estimation function for LSRA and LSRA2 functions
LstepCC1	Step-wise Constant Catch
LstepCC2	Step-wise Constant Catch
LstepCC3	Step-wise Constant Catch
LstepCC4	Step-wise Constant Catch
LstepCE1	Step-wise Constant Effort
LstepCE2	Step-wise Constant Effort
Ltarget1	Length Target TAC MP
Ltarget2	Length Target TAC MP
Ltarget3	Length Target TAC MP
Ltarget4	Length Target TAC MP
LtargetE1	Length Target TAE MP
LtargetE4	Length Target TAE MP
LTY	Performance Metrics Methods
LW2OM	Estimate length-weight parameters from data

-- M --

Mackerel	Stock class objects
makeMeanMP	Create an MP that averages the results of multiple MPs
makePerf	Convert a OM object to one without observation or process error
makeTransparent	Make colors transparent
matlenlim	Size limit management procedures
matlenlim2	Size limit management procedures
MCD	Mean Catch Depletion
MCD4010	Mean Catch Depletion
minlenLopt1	Size limit management procedures
ML2D	Depletion and F estimation from mean length of catches
movfit_Rcpp	Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters.
MPStats	Calculate Statistics for MP Performance
MPtype	Management Procedure Type
MRnoreal	Spatial closure and allocation management procedures
MRreal	Spatial closure and allocation management procedures
MSE-class	Class "MSE"
MSEDescription	MSEDescription

-- N --

Needed	Identify management procedures (MPs) based on data availability
NFref	Reference management procedures
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"
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.MSE	Plot MSE object
plot.OM	Plot the operating model (OM) object parameters
plotFleet	Plot the Fleet object parameters
plotFun	Print out plotting functions
plotImp	Plot the Implementation object parameters
plotM	Plot M-at-Age and Size
plotMPA	Plot the Historical Spatial Closures
plotObs	Plot the Observation object parameters
plotOFL	A generic OFL plot for NOAA use
plotSelect	Plot the vulnerability and retention curves
plotStock	Plot the Stock object parameters
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
predictLH	Predict missing life-history parameters
PWhisker	Performance Whisker Plot

-- R --

Rcontrol	Intrinsic rate of Increase MP
Rcontrol2	Intrinsic rate of Increase MP
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
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
runMSErobust	Run a Management Strategy Evaluation

-- S --

SBT1	SBT simple MP
SBT2	SBT simple MP
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
simCAA	Simulate Catch-at-Age Data
simCAL	Simulate Catch-at-Length Data
SimulatedData	SimulatedData Data
Simulation_1	Data class objects
SketchFun	Manually map the historical relative fishing effort trajectory.
slotlim	Size limit management procedures
Snapper	Stock class objects
Sole	Stock class objects
SPmod	Surplus production based catch-limit modifier
SPMSY	Catch trend Surplus Production MSY MP
SPslope	Slope in surplus production MP
SPSRA	Surplus Production Stock Reduction Analysis
SPSRA_ML	Surplus Production Stock Reduction Analysis
SRAcomp	Plot simulation test of Stochastic SRA method
SRAsim	Simulates catch at age and catch history data for testing SRA methods
StochasticSRA	Stochastic SRA construction of operating models
StochasticSRAcpp	Stochastic SRA construction of operating models
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
testOM	testOM OM
Thresh_tab	Current default thresholds for DFO satificing
tinyErr	Remove observation, implementation, and process error
Toothfish	Stock class objects
Tplot	Generic Trade-Plot Function
Tplot2	Generic Trade-Plot Function
Tplot2_old	Trade-off plots for an MSE object
Tplot3	Generic Trade-Plot Function
Tplot_old	Trade-off plots for an MSE object
TradePlot	Generic Trade-Plot Function
TradePlot_old	Generic Trade-off Plot
Turing	Turing Test

-- U --

updateMSE	Utility functions for MSE objects
userguide	Open the DLMtool User Guide
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
VOIplot2	Value of Information Plot using PM functions

-- W --

wormplot	Biomass wormplot
writeCSV	Internal function to write CSVs for objects

-- X --

XL2Data	Import a Data object from Excel file
XL2OM	Load OM from Excel file

-- Y --

Yield	Performance Metrics Methods
YPR	Yield Per Recruit analysis to get FMSY proxy F01
YPR_CC	Yield Per Recruit analysis to get FMSY proxy F01
YPR_ML	Yield Per Recruit analysis to get FMSY proxy F01