| 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 |
| CC1 |
Constant catch management procedure of Geromont and Butterworth (2014) |
| CC4 |
Constant catch management procedure of Geromont and Butterworth (2014) |
| CheckConverg |
MSE convergence diagnostic |
| checkMSE |
Check that MSE object includes all slots |
| China_rockfish |
China_rockfish DLM_data |
| ChooseEffort |
Manually map the historical relative fishing effort trajectory. |
| ChooseSelect |
Manually choose the historical selectivity pattern |
| Cobia |
Cobia DLM_data |
| CompSRA |
Age-composition-based estimate of current stock depletion given constant Z linked to an FMSY estimate to provide OFL |
| CompSRA4010 |
Age-composition-based estimate of current stock depletion given constant Z linked to an FMSY estimate to provide OFL (with a 40-10 rule) |
| condmet |
Condition met? |
| Converge |
Check Convergence |
| Cplot |
Plot the median biomass and yield relative to last historical year |
| 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 |
| cv |
Calculate CV from vector of values |
| DAAC |
Depletion Adjusted Average Catch |
| DBSRA |
Depletion-Based Stock Reduction Analysis |
| DBSRA4010 |
Depletion-Based Stock Reduction Analysis paired with 40-10 harvest control 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 harvest control rule |
| DDe |
Effort control version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading |
| DDe75 |
Effort control version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading that fishes at 75 per cent of FMSY |
| DDes |
Effort searching version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading that fishes at 75 per cent of FMSY |
| DecE_Dom |
DecE_Dom Fleet |
| DecE_HDom |
DecE_HDom Fleet |
| DecE_NDom |
DecE_NDom Fleet |
| DepF |
Depletion Corrected Fratio |
| DLMDataDir |
Directory of the installed package on your computer |
| DLMtool |
Data-Limited Methods Toolkit |
| DLM_data-class |
Class "DLM_data" |
| DLM_fease-class |
Class "DLM_fease" |
| DOM |
How dominant is an MP? |
| 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 |
| Fadapt |
An adaptive MP that uses trajectory in inferred suplus production and fishing mortality rate to update a TAC |
| 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 |
| Fease |
MP feasibility diagnostic |
| Fease_xl |
Read in feasibility parameters from Excel spreadsheet |
| Feasibility |
Feasibility DLM_fease |
| Feasibility2 |
Feasibility2 DLM_fease |
| FlatE_Dom |
FlatE_Dom Fleet |
| FlatE_HDom |
FlatE_HDom Fleet |
| FlatE_NDom |
FlatE_NDom Fleet |
| 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 MP that uses a mean length estimator of recent Z |
| Imprecise_Biased |
Imprecise_Biased Observation |
| Imprecise_Unbiased |
Imprecise_Unbiased Observation |
| IncE_Dom |
IncE_Dom Fleet |
| IncE_HDom |
IncE_HDom Fleet |
| IncE_NDom |
IncE_NDom Fleet |
| initialize-method |
~~ Methods for Function 'initialize' ~~ |
| 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 maintain a constant CPUE or relative abundance index |
| Islope4 |
A management procedure that incrementally adjusts the TAC to maintain a constant CPUE or relative abundance index |
| IT10 |
Index Target 10 |
| IT5 |
Index Target 5 |
| Itarget1 |
A management procedure that incrementally adjusts the TAC (starting from reference level that is a fraction of mean recent catches) to reach a target CPUE / relative abundance index |
| Itarget4 |
A management procedure that incrementally adjusts the TAC (starting from reference level that is a fraction of mean recent catches) to reach a target CPUE / relative abundance index |
| ItargetE1 |
A management procedure that incrementally adjusts the effort to reach a target CPUE / relative abundance index |
| ItargetE4 |
A management procedure that incrementally adjusts the Effort to reach a target CPUE / relative abundance index |
| ITe10 |
Index Target Effort-Based 10 |
| ITe5 |
Index Target Effort-Based 5 |
| ITM |
Index Target based on natural mortality rate |
| L2A |
Length to age conversion |
| L95target |
A management procedure that adjusts the TAC up/down from reference (target) level (that is a fraction of mean recent premanagement catches) to reach a target mean length of fish caught. |
| LBSPR |
Apply the Length-based SPR model to DLMtool Data Object |
| LBSPR_ItEff |
Length-based SPR model with HCR that iteratively adjusts Effort |
| LBSPR_ItSel |
Length-based SPR model with HCR that iteratively adjusts Selectivity |
| LBSPR_ItTAC |
Length-based SPR model with HCR that iteratively adjusts TAC |
| lmmodel-class |
Class "lmmodel" |
| Low_Effort_Non_Target |
Low_Effort_Non_Target Fleet |
| LstepCC1 |
A management procedure that incrementally adjusts the TAC according to the mean length of recent catches. |
| LstepCC4 |
A management procedure that incrementally adjusts the TAC according to the mean length of recent catches. |
| LstepCE1 |
A management procedure that incrementally adjusts the TAC according to the mean length of recent catches. |
| LstepCE2 |
A management procedure that incrementally adjusts the Effort according to the mean length of recent catches. |
| Ltarget1 |
A management procedure that incrementally adjusts the TAC to reach a target mean length in catches. |
| Ltarget4 |
A management procedure that incrementally adjusts the TAC to reach a target mean length in catches. |
| LtargetE1 |
A management procedure that incrementally adjusts the Effort to reach a target mean length in catches. |
| LtargetE4 |
A management procedure that incrementally adjusts the Effort to reach a target mean length in catches. |
| Mackerel |
Mackerel Stock |
| makePerf |
Convert a OM object to one without observation or process error |
| makeTransparent |
Make colors transparent |
| matlenlim |
A data-limited method in which fishing vulnerability is set according to the maturity curve |
| matlenlim2 |
A data-limited method in which fishing vulnerability is set slightly higher than the maturity curve |
| MCD |
Mean Catch Depletion |
| MCD4010 |
Mean Catch Depletion |
| mconv |
Get log normal mean from transformed space mean and standard deviation |
| minlenLopt1 |
This input control sets the minimum length of fish caught to a fraction of the length that maximises the biomass, Lopt. |
| ML2D |
Depletion and F estimation from mean length of catches |
| movfit |
Optimization function that returns the squared difference between user specified and calculated movement parameters. (deprecated: now in Rcpp) |
| movfit_Rcpp |
Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters. |
| MPStats |
Calculate Statistics for MP Performance |
| MRnoreal |
An marine reserve in area 1 with no spatial reallocation of fishing effort |
| MRreal |
An marine reserve in area 1 with full reallocation of fishing effort |
| MSE-class |
Class "MSE" |
| mypars |
mypars DLM_general |
| Sam |
Conduct stock assessment |
| sampy |
Sample vector |
| SBT1 |
SBT simple MP |
| SBT2 |
SBT complex MP |
| sdconv |
Get log normal standard deviation from transformed space mean and standard deviation |
| Sense |
Sensitivity analysis |
| SetRecruitCycle |
Function to calculate cyclic recruitment pattern given user-specified values of period and amplitude. |
| setup |
Setup parallel processing |
| Simulation_1 |
Simulation_1 DLM_data |
| SketchFun |
Manually map the historical relative fishing effort trajectory. |
| slotlim |
An data-limited method which sets a slot limit |
| Snapper |
Snapper Stock |
| Sole |
Sole Stock |
| Splot |
Scatter plot of B/BMSY or B/B0 and F/FMSY for lastYrs |
| 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 mean-length estimate of current stock depletion |
| Stock-class |
Class "Stock" |
| Sub |
Subset MSE object by management procedure (MP) or simulation. |
| summary-method |
Summary of DLM_data object |
| summary-method |
Summary of MSE object |
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