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...

Functions

avail Man page
AvC Man page
barplot.MSE Man page
BK Man page
BK_CC Man page
BK_ML Man page
boxplot.DLM_data Man page
boxplot.MSE Man page
Can Man page
Cant Man page
CC1 Man page
CC4 Man page
CheckConverg Man page
ChooseEffort Man page
comp Man page
CompSRA Man page
CompSRA4010 Man page
Cplot Man page
CSRA Man page
CSRAfunc Man page
curE Man page
curE75 Man page
DAAC Man page
DBSRA Man page
DBSRA_40 Man page
DBSRA4010 Man page
DBSRA_ML Man page
DCAC Man page
DCAC_40 Man page
DCAC4010 Man page
DCAC_ML Man page
DD Man page
DD4010 Man page
DDe Man page
DDe75 Man page
DDes Man page
DepF Man page
DLMdat Man page
DLM_data-class Man page
DLMDataDir Man page
DLM_fease-class Man page
DLM_general-class Man page
DLMtool Man page
DLMtool-package Man page
DOM Man page
DoOpt Man page
DTe40 Man page
DTe50 Man page
DynF Man page
EtargetLopt Man page
Fadapt Man page
Fdem Man page
Fdem_CC Man page
Fdem_ML Man page
Fease Man page
Fease_xl Man page
Fleet-class Man page
FMSYref Man page
FMSYref50 Man page
FMSYref75 Man page
Fratio Man page
Fratio4010 Man page
Fratio_CC Man page
Fratio_ML Man page
GB_CC Man page
GB_slope Man page
GB_target Man page
Gcontrol Man page
getAFC Man page
getmov Man page
getq Man page
HDAAC Man page
initialize,DLM_data-method Man page
initialize,DLM_fease-method Man page
initialize,DLM_general-method Man page
initialize,Fleet-method Man page
initialize,Fleet-method Man page
initialize,lmmodel-method Man page
initialize-methods Man page
initialize,MSE-method Man page
initialize,MSE-method Man page
initialize,Observation-method Man page
initialize,Observation-method Man page
initialize,OM-method Man page
initialize,OM-method Man page
initialize,Stock-method Man page
initialize,Stock-method Man page
Input Man page
Islope1 Man page
Islope4 Man page
IT10 Man page
IT5 Man page
Itarget1 Man page
Itarget4 Man page
ItargetE1 Man page
ItargetE4 Man page
ITe10 Man page
ITe5 Man page
ITM Man page
joinMSE Man page
Jplot Man page
KalmanFilter Man page
Kplot Man page
L2A Man page
L95target Man page
LBSPR Man page
LBSPR_ItEff Man page
LBSPR_ItSel Man page
LBSPR_ItTAC Man page
LBSPRSim Man page
lmmodel-class Man page
LstepCC1 Man page
LstepCC4 Man page
LstepCE1 Man page
LstepCE2 Man page
Ltarget1 Man page
Ltarget4 Man page
LtargetE1 Man page
LtargetE4 Man page
makePerf Man page
matlenlim Man page
matlenlim2 Man page
MCD Man page
MCD4010 Man page
minlenLopt1 Man page
ML2D Man page
movfit Man page
MPStats Man page
MRnoreal Man page
MRreal Man page
MSE-class Man page
NAor0 Man page
Needed Man page
NFref Man page
NOAA_plot Man page
Observation-class Man page
OM-class Man page
OM_xl Man page
OptFun Man page
ourMSE Man page
ourReefFish Man page
plot,DLM_data-method Man page
plotFun Man page
plot-methods Man page
plot,MSE-method Man page
plot,MSE-method Man page
plotOFL Man page
PorgMSE Man page
Pplot Man page
qopt Man page
Rcontrol Man page
Rcontrol2 Man page
replic8 Man page
Required Man page
runInMP Man page
runMSE Man page
runMSErobust Man page
Sam Man page
SBT1 Man page
SBT2 Man page
Sense Man page
SetRecruitCycle Man page
slotlim Man page
SnapMSE Man page
Splot Man page
SPmod Man page
SPMSY Man page
SPslope Man page
SPSRA Man page
SPSRA_ML Man page
Stock-class Man page
Sub Man page
summary,DLM_data-method Man page
summary-methods Man page
summary,MSE-method Man page
TAC Man page
Tplot Man page
Tplot2 Man page
TradePlot Man page
updateMSE Man page
VOI Man page
VOI2 Man page
VOIplot Man page
VPA Man page
wormplot Man page
writeCSV Man page
YPR Man page
YPR_CC Man page
YPR_ML Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.