DLMtool: Data-Limited Methods Toolkit

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

Author
Tom Carruthers and Adrian Hordyk
Date of publication
2016-10-18 00:15:11
Maintainer
Tom Carruthers <t.carruthers@fisheries.ubc.ca>
License
GPL-2
Version
3.2.2

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