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 |