DLMtool: Data-Limited Methods Toolkit

Simulation testing and implementation of data-limited fishery stock assessment methods.

AuthorTom Carruthers and Adrian Hordyk
Date of publication2016-12-27 15:28:19
MaintainerTom Carruthers <t.carruthers@fisheries.ubc.ca>
LicenseGPL-2
Version3.2.2

View on CRAN

Man pages

avail: What objects of this class are available

AvC: An MP where the TAC is average historical catch

barplot.MSE: Plot a barplot of MSE results

BK: Beddington and Kirkwood life-history MP (simple version)

BK_CC: Beddington and Kirkwood life-history method combined with...

BK_ML: Beddington and Kirkwood life-history analysis with...

boxplot.DLM_data: Boxplot of TAC recommendations

boxplot.MSE: Boxplot of MP performance from MSE object

Can: What data-limited methods can be applied to this DLM_data...

Cant: What methods can't be applied to this DLM data object

CC1: Constant catch management procedure of Geromont and...

CC4: Constant catch management procedure of Geromont and...

CheckConverg: MSE convergence diagnostic

ChooseEffort: Manually choose the historical relative fishing effort...

comp: Comparison plots for individual simulations

CompSRA: Age-composition-based estimate of current stock depletion...

CompSRA4010: Age-composition-based estimate of current stock depletion...

Cplot: Plot the median biomass and yield relative to last historical...

CSRA: Catch at size reduction analysis

CSRAfunc: Optimization function for CSRA

curE: Fishing at current effort levels

curE75: Fishing at 75 per cent of current effort levels

DAAC: Depletion Adjusted Average Catch

DBSRA: Depletion-Based Stock Reduction Analysis

DBSRA_40: Depletion-Based Stock Reduction Analysis assuming 40 per cent...

DBSRA4010: Depletion-Based Stock Reduction Analysis paired with 40-10...

DBSRA_ML: Depletion-Based Stock Reduction Analysis using mean length...

DCAC: Depletion Corrected Average Catch

DCAC_40: Depletion Corrected Average Catch assuming 40 per cent stock...

DCAC4010: Depletion Corrected Average Catch paired with the 40-10 rule

DCAC_ML: Depletion-Based Stock Reduction Analysis using mean-length...

DD: Delay - Difference Stock Assessment with UMSY and MSY leading

DD4010: Delay - Difference Stock Assessment with UMSY and MSY leading...

DDe: Effort control version of DD - Delay - Difference Stock...

DDe75: Effort control version of DD - Delay - Difference Stock...

DDes: Effort searching version of DD - Delay - Difference Stock...

DepF: Depletion Corrected Fratio

DLMdat: Data and Operating model objects

DLM_data-class: Class '"DLM_data"'

DLMDataDir: Directory of the installed package on your computer

DLM_fease-class: Class '"DLM_fease"'

DLM_general-class: Class '"DLM_general"'

DLMtool-package: Data-Limited Methods Toolkit

DOM: How dominant is an MP?

DoOpt: Optimization routine for LBSPR methods

DTe40: Effort searching MP aiming for 40 per cent stock depletion.

DTe50: Effort searching MP aiming for 50 per cent stock depletion.

DynF: Dynamic Fratio MP

EtargetLopt: Effort MP: adjust effort up/down if mean length above/below...

Fadapt: An adaptive MP that uses trajectory in inferred suplus...

Fdem: Demographic FMSY method

Fdem_CC: Demographic FMSY method using catch-curve analysis to...

Fdem_ML: Demographic FMSY method that uses mean length data to...

Fease: MP feasibility diagnostic

Fease_xl: Read in feasibility parameters from Excel spreadsheet

Fleet-class: Class '"Fleet"'

FMSYref: A reference FMSY method (uses perfect information about FMSY)

FMSYref50: A reference FMSY method that fishes at half of FMSY (uses...

FMSYref75: A reference FMSY method that fishes at three quarters of FMSY...

Fratio: An FMSY/M ratio method

Fratio4010: An FMSY/M ratio method paired with the 40-10 rule

Fratio_CC: A data-limited method that uses FMSY/M ratio and a naive...

Fratio_ML: An FMSY/M ratio MP that uses a mean length estimator of...

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

getAFC: Calculate age at first capture from length at first capture...

getmov: Optimization function to find a movement model that matches...

getq: Optimization function that find the catchability (q where...

HDAAC: Hybrid Depletion Adjusted Average Catch

initialize-methods: ~~ Methods for Function 'initialize' ~~

Input: Function to run a set of input control methods

Islope1: A management procedure that incrementally adjusts the TAC to...

Islope4: A management procedure that incrementally adjusts the TAC to...

IT10: Index Target 10

IT5: Index Target 5

Itarget1: A management procedure that incrementally adjusts the TAC...

Itarget4: A management procedure that incrementally adjusts the TAC...

ItargetE1: A management procedure that incrementally adjusts the effort...

ItargetE4: A management procedure that incrementally adjusts the Effort...

ITe10: Index Target Effort-Based 10

ITe5: Index Target Effort-Based 5

ITM: Index Target based on natural mortality rate

joinMSE: Join multiple MSE objects together

Jplot: Joint probability plot

KalmanFilter: Kalman filter and Rauch-Tung-Striebel smoother

Kplot: KOBE plot: a projection by projection plot of F/FMSY and...

L2A: Length to age conversion

L95target: A management procedure that adjusts the TAC up/down from...

LBSPR: Apply LBSPR model to time-series of catch-at-length

LBSPR_ItEff: Length-based SPR model with HCR that iteratively adjusts...

LBSPR_ItSel: Length-based SPR model with HCR that iteratively adjusts...

LBSPR_ItTAC: Length-based SPR model with HCR that iteratively adjusts TAC

LBSPRSim: Per-Recruit Length-Based Spawning Potential Ratio Simulation...

lmmodel-class: Class '"lmmodel"'

LstepCC1: A management procedure that incrementally adjusts the TAC...

LstepCC4: A management procedure that incrementally adjusts the TAC...

LstepCE1: A management procedure that incrementally adjusts the TAC...

LstepCE2: A management procedure that incrementally adjusts the Effort...

Ltarget1: A management procedure that incrementally adjusts the TAC to...

Ltarget4: A management procedure that incrementally adjusts the TAC to...

LtargetE1: A management procedure that incrementally adjusts the Effort...

LtargetE4: A management procedure that incrementally adjusts the Effort...

makePerf: Convert a OM object to one without observation or process...

matlenlim: A data-limited method in which fishing vulnerability is set...

matlenlim2: A data-limited method in which fishing vulnerability is set...

MCD: Mean Catch Depletion

MCD4010: Mean Catch Depletion

minlenLopt1: This input control sets the minimum length of fish caught to...

ML2D: Depletion and F estimation from mean length of catches

movfit: Optimization function that returns the squared difference...

MPStats: Calculate Statistics for MP Performance

MRnoreal: An marine reserve in area 1 with no spatial reallocation of...

MRreal: An marine reserve in area 1 with full reallocation of fishing...

MSE-class: Class '"MSE"'

NAor0: Is a value NA or zero.

Needed: Data needed to get MPs running

NFref: No Fishing Reference MP

NOAA_plot: National Oceanographic and Atmospheric Administration default...

Observation-class: Class '"Observation"'

OM-class: Class '"OM"'

OM_xl: Read in operating model parameters from Excel spreadsheet

OptFun: Objective function for LBSPR methods

ourMSE: Example MSE object used in the vignette

ourReefFish: Example data object

plotFun: Print out plotting functions

plot-methods: ~~ Methods for Function 'plot' ~~

plotOFL: A generic OFL plot for NOAA use

PorgMSE: Example MSE object used in the vignette

Pplot: A projection by projection plot of F/FMSY and B/BMSY

qopt: Internal optimization function that find the catchability (q...

Rcontrol: Harvest Control Rule using prior for intrinsic rate of...

Rcontrol2: MP using prior for intrinsic rate of increase with a...

replic8: Enlarge (replicate) a DLM data object to create an additional...

Required: What methods need what data

runInMP: Runs input control MPs on a DLM_data object.

runMSE: Run a Management Strategy Evaluation

runMSErobust: Run a Management Strategy Evaluation

Sam: Conduct stock assessment

SBT1: SBT simple MP

SBT2: SBT complex MP

Sense: Sensitivity analysis

SetRecruitCycle: Function to calculate cyclic recruitment pattern given...

slotlim: An data-limited method which sets a slot limit

SnapMSE: Example MSE object used in the vignette

Splot: Scatter plot of B/BMSY or B/B0 and F/FMSY

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 using a...

Stock-class: Class '"Stock"'

Sub: Subset MSE object by management procedure (MP) or simulation.

summary-methods: ~~ Methods for Function 'summary' ~~

TAC: Calculate TAC recommendations for more than one MP

Tplot: A trade-off plot for an MSE object

Tplot2: A trade-off plot for an MSE object that compares long-term...

TradePlot: Generic Trade-off Plot

updateMSE: Update an MSE object with new slots

VOI: Calculate Value Of Information

VOI2: Calculate Value Of Information 2

VOIplot: Yet another Value of Information Plot

VPA: Robust Virtual Population Analysis

wormplot: Biomass wormplot.

writeCSV: Internal function to write CSVs for objects

YPR: Yield Per Recruit analysis to get FMSY proxy F01

YPR_CC: Yield Per Recruit analysis to get FMSY proxy F01 paired to a...

YPR_ML: Yield Per Recruit analysis to get FMSY proxy F01 paired with...

Files in this package

DLMtool
DLMtool/inst
DLMtool/inst/Atlantic_mackerel.csv
DLMtool/inst/Cobia.csv
DLMtool/inst/Simulation_1.csv
DLMtool/inst/Gulf_blue_tilefish.csv
DLMtool/inst/Red_snapper.csv
DLMtool/inst/ourReefFish.csv
DLMtool/inst/doc
DLMtool/inst/doc/DLMtool.html
DLMtool/inst/doc/DLMtool.Rmd
DLMtool/inst/doc/DLMtool.R
DLMtool/inst/China_rockfish.csv
DLMtool/inst/Example_datafile.csv
DLMtool/src
DLMtool/src/bhnoneq_Rcpp.cpp
DLMtool/src/RcppExports.cpp
DLMtool/NAMESPACE
DLMtool/data
DLMtool/data/DLMdat.RData
DLMtool/data/ourMSE.rda
DLMtool/data/datalist
DLMtool/data/ourReefFish.rda
DLMtool/data/PorgMSE.rda
DLMtool/data/SnapMSE.rda
DLMtool/R
DLMtool/R/ClassMeths.r
DLMtool/R/MiscInt.r
DLMtool/R/MSEObj.r
DLMtool/R/XLloadfuns.r
DLMtool/R/MiscFuns.r
DLMtool/R/DLM_output.R
DLMtool/R/runMSE.r
DLMtool/R/RcppExports.R
DLMtool/R/DataObj.r
DLMtool/R/DLM_input.R
DLMtool/vignettes
DLMtool/vignettes/DLMtool.Rmd
DLMtool/MD5
DLMtool/build
DLMtool/build/vignette.rds
DLMtool/DESCRIPTION
DLMtool/man
DLMtool/man/summary-methods.Rd DLMtool/man/Gcontrol.Rd DLMtool/man/DynF.Rd DLMtool/man/Rcontrol2.Rd DLMtool/man/GB_CC.Rd DLMtool/man/VOI.Rd DLMtool/man/SPslope.Rd DLMtool/man/Required.Rd DLMtool/man/Splot.Rd DLMtool/man/FMSYref50.Rd DLMtool/man/DTe50.Rd DLMtool/man/ITM.Rd DLMtool/man/ItargetE4.Rd DLMtool/man/lmmodel-class.Rd DLMtool/man/DBSRA.Rd DLMtool/man/Sub.Rd DLMtool/man/SnapMSE.Rd DLMtool/man/SetRecruitCycle.Rd DLMtool/man/CompSRA.Rd DLMtool/man/matlenlim2.Rd DLMtool/man/Fdem_CC.Rd DLMtool/man/plot-methods.Rd DLMtool/man/Ltarget4.Rd DLMtool/man/OM_xl.Rd DLMtool/man/BK_CC.Rd DLMtool/man/SBT1.Rd DLMtool/man/Tplot.Rd DLMtool/man/Fdem.Rd DLMtool/man/Fdem_ML.Rd DLMtool/man/YPR_CC.Rd DLMtool/man/avail.Rd DLMtool/man/Sense.Rd DLMtool/man/GB_target.Rd DLMtool/man/curE.Rd DLMtool/man/LBSPR_ItSel.Rd DLMtool/man/PorgMSE.Rd DLMtool/man/getAFC.Rd DLMtool/man/LBSPR_ItEff.Rd DLMtool/man/DLMtool-package.Rd DLMtool/man/DoOpt.Rd DLMtool/man/Needed.Rd DLMtool/man/FMSYref.Rd DLMtool/man/DCAC_ML.Rd DLMtool/man/YPR_ML.Rd DLMtool/man/makePerf.Rd DLMtool/man/DLM_general-class.Rd DLMtool/man/Itarget4.Rd DLMtool/man/DLM_data-class.Rd DLMtool/man/wormplot.Rd DLMtool/man/SBT2.Rd DLMtool/man/updateMSE.Rd DLMtool/man/DDe75.Rd DLMtool/man/Stock-class.Rd DLMtool/man/slotlim.Rd DLMtool/man/SPMSY.Rd DLMtool/man/getmov.Rd DLMtool/man/matlenlim.Rd DLMtool/man/IT5.Rd DLMtool/man/MPStats.Rd DLMtool/man/EtargetLopt.Rd DLMtool/man/Rcontrol.Rd DLMtool/man/Fratio_ML.Rd DLMtool/man/KalmanFilter.Rd DLMtool/man/initialize-methods.Rd DLMtool/man/DLM_fease-class.Rd DLMtool/man/comp.Rd DLMtool/man/Fratio4010.Rd DLMtool/man/IT10.Rd DLMtool/man/Itarget1.Rd DLMtool/man/VOI2.Rd DLMtool/man/DCAC.Rd DLMtool/man/ChooseEffort.Rd DLMtool/man/LstepCE2.Rd DLMtool/man/DD.Rd DLMtool/man/LBSPR.Rd DLMtool/man/Fratio_CC.Rd DLMtool/man/CSRA.Rd DLMtool/man/Fease_xl.Rd DLMtool/man/CC1.Rd DLMtool/man/runMSErobust.Rd DLMtool/man/AvC.Rd DLMtool/man/Ltarget1.Rd DLMtool/man/TradePlot.Rd DLMtool/man/curE75.Rd DLMtool/man/MRnoreal.Rd DLMtool/man/DBSRA_ML.Rd DLMtool/man/HDAAC.Rd DLMtool/man/MCD.Rd DLMtool/man/runMSE.Rd DLMtool/man/ML2D.Rd DLMtool/man/MSE-class.Rd DLMtool/man/DDes.Rd DLMtool/man/plotFun.Rd DLMtool/man/ourMSE.Rd DLMtool/man/ITe10.Rd DLMtool/man/BK_ML.Rd DLMtool/man/Fease.Rd DLMtool/man/DepF.Rd DLMtool/man/GB_slope.Rd DLMtool/man/DDe.Rd DLMtool/man/DTe40.Rd DLMtool/man/boxplot.DLM_data.Rd DLMtool/man/MCD4010.Rd DLMtool/man/DCAC4010.Rd DLMtool/man/DAAC.Rd DLMtool/man/VOIplot.Rd DLMtool/man/Fadapt.Rd DLMtool/man/LstepCE1.Rd DLMtool/man/LstepCC4.Rd DLMtool/man/CSRAfunc.Rd DLMtool/man/DLMDataDir.Rd DLMtool/man/DD4010.Rd DLMtool/man/Input.Rd DLMtool/man/CompSRA4010.Rd DLMtool/man/MRreal.Rd DLMtool/man/ItargetE1.Rd DLMtool/man/DOM.Rd DLMtool/man/writeCSV.Rd DLMtool/man/LtargetE1.Rd DLMtool/man/NAor0.Rd DLMtool/man/barplot.MSE.Rd DLMtool/man/SPmod.Rd DLMtool/man/TAC.Rd DLMtool/man/Can.Rd DLMtool/man/BK.Rd DLMtool/man/NOAA_plot.Rd DLMtool/man/Tplot2.Rd DLMtool/man/OptFun.Rd DLMtool/man/Fratio.Rd DLMtool/man/Observation-class.Rd DLMtool/man/joinMSE.Rd DLMtool/man/SPSRA_ML.Rd DLMtool/man/L95target.Rd DLMtool/man/SPSRA.Rd DLMtool/man/Jplot.Rd DLMtool/man/Islope4.Rd DLMtool/man/DBSRA_40.Rd DLMtool/man/minlenLopt1.Rd DLMtool/man/Fleet-class.Rd DLMtool/man/Pplot.Rd DLMtool/man/LstepCC1.Rd DLMtool/man/LBSPRSim.Rd DLMtool/man/CC4.Rd DLMtool/man/LtargetE4.Rd DLMtool/man/plotOFL.Rd DLMtool/man/getq.Rd DLMtool/man/Kplot.Rd DLMtool/man/boxplot.MSE.Rd DLMtool/man/CheckConverg.Rd DLMtool/man/runInMP.Rd DLMtool/man/Islope1.Rd DLMtool/man/qopt.Rd DLMtool/man/DLMdat.Rd DLMtool/man/VPA.Rd
DLMtool/man/ChooseSelect.rd
DLMtool/man/L2A.Rd DLMtool/man/YPR.Rd DLMtool/man/DBSRA4010.Rd DLMtool/man/ITe5.Rd DLMtool/man/Cant.Rd DLMtool/man/FMSYref75.Rd DLMtool/man/ourReefFish.Rd DLMtool/man/replic8.Rd DLMtool/man/OM-class.Rd DLMtool/man/Cplot.Rd DLMtool/man/LBSPR_ItTAC.Rd DLMtool/man/NFref.Rd DLMtool/man/movfit.Rd DLMtool/man/DCAC_40.Rd DLMtool/man/Sam.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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