Data-Limited Methods Toolkit


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Documentation for package ‘DLMtool’ version 1.34

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DLMtool-package Data-Limited Methods Toolkit
area1MPA An marine reserve in area 1
avail What objects of this class are available
BK Beddington and Kirkwood life-history method (simple version)
BK_CC Beddington and Kirkwood life-history method combined with catch curve analysis
BK_ML Beddington and Kirkwood life-history analysis with mean-length estimator of current abundance
Can What data-limited methods can be applied to this DLM data object?
Cant What methods can't be applied to this DLM data object
comp Comparison plots for individual simulations
CompSRA Age-composition-based estimate of current stock depletion given constant Z
DBSRA Depletion-Based Stock Reduction Analysis
DBSRA4010 Depletion-Based Stock Reduction Analysis paired with 40-10 rule
DBSRA_40 Depletion-Based Stock Reduction Analysis assuming 40 per cent stock depletion
DBSRA_ML Depletion-Based Stock Reduction Analysis using mean length estimator of stock depletion
DCAC Depletion Corrected Average Catch
DCAC4010 Depletion Corrected Average Catch paired with the 40-10 rule
DCAC_40 Depletion Corrected Average Catch assuming 40 per cent stock depletion
DCAC_ML Depletion-Based Stock Reduction Analysis using mean-length estimator of current depletion
DD Delay - Difference Stock Assessment with UMSY and MSY leading
DD4010 Delay - Difference Stock Assessment with UMSY and MSY leading coupled with a 40-10 rule
DepF Depletion Corrected Fratio
DLM-class Class '"DLM"'
DLMdat Data and Operating model objects
DLMDataDir Directory of the installed packaged on your computer
DLMtool Data-Limited Methods Toolkit
DynF Dynamic Fratio method
Fdem Demographic FMSY method
Fdem_CC Demographic FMSY method using catch-curve analysis to estimate recent Z
Fdem_ML Demographic FMSY method that uses mean length data to estimate recent Z
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 perfect information about FMSY)
FMSYref75 A reference FMSY method that fishes at three quarters of FMSY (uses perfect information about 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 catch-curve estimate of recent Z
Fratio_ML An FMSY/M ratio method that uses a mean length estimator of recent Z
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 Harvest Control Rule
Gcontrol G-control harvest control rule
getmov Optimization function to find a movement model that matches user specified movement characteristics.
getq Optimization function that find the catchability (q where F=qE) value required to get to user-specified stock depletion (current biomass / unfished biomass)
getQuota Calculate quota
initialize-method ~~ Methods for Function 'initialize' ~~
initialize-methods ~~ Methods for Function 'initialize' ~~
Kplot KOBE plot: a projection by projection plot of F/FMSY and B/BMSY
lmmodel-class Class '"lmmodel"'
matsizlim A data-limited method in which fishing vulnerability is set according to the maturity curve
MMHCR Mark Maunder's Harvest Control Rule
movfit Optimization function that returns the squared difference between user specified and calculated movement parameters.
MSE-class Class '"MSE"'
Needed Data needed to get DLM methods running
Observation-class Class '"Observation"'
OM-class Class '"OM"'
plot-method ~~ Methods for Function 'plot' ~~
plot-methods ~~ Methods for Function 'plot' ~~
Pplot A projection by projection plot of F/FMSY and B/BMSY
qopt Internal optimization function that find the catchability (q where F=qE) value required to get to user-specified stock depletion (current biomass / unfished biomass)
Rcontrol Harvest Control Rule using prior for intrinsic rate of increase
Rcontrol2 Harvest Control Rule using prior for intrinsic rate of increase with a quadratic approximation to surplus production
replic8 Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing
Required What methods need what data
runMSE Run a Management Strategy Evaluation
Sam Conduct stock assessment
SBT1 SBT simple harvest control rule
SBT2 SBT complex harvest control rule
Sense Sensitivity analysis
SPMSY Surplus Production MSY method
SPSRA Surplus Production Stock Reduction Analysis
SPSRA_ML Surplus Production Stock Reduction Analysis using a mean-length estimate of current stock depletion
Stock-class Class '"Stock"'
summary-method ~~ Methods for Function 'summary' ~~
summary-methods ~~ Methods for Function 'summary' ~~
Tplot A trade-off plot for an MSE object
YPR Yield Per Recruit analysis to get FMSY proxy F01
YPR_CC Yield Per Recruit analysis to get FMSY proxy F01 paired to a naive catch curve estimate of recent Z
YPR_ML Yield Per Recruit analysis to get FMSY proxy F01 paired with a mean-length estimate of current stock size