| calcMean |
Calculate Mean Probabilty |
| CalcOutput |
Apply output control recommendations and calculate population dynamics |
| calcProb |
Calculate Probabilty |
| Can |
What data-limited methods can be applied to this 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 Data |
| ChkDatNA |
Check Data object is valid for a MP |
| ChkObj |
Check that a DLM object is valid |
| ChooseEffort |
Manually map the historical relative fishing effort trajectory. |
| ChooseM |
Manually map natural mortality at age or size. |
| ChooseSelect |
Manually choose the historical selectivity pattern |
| Cobia |
Cobia Data |
| compplot |
Generic comparison plot for simulation testing of Stochastic SRA method |
| 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 |
| COSEWIC_plot |
COSEWIC forward projection plot |
| cparscheck |
Internal function of runMSE for checking that the OM slot cpars slot is formatted correctly |
| 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 |
| Data-class |
Class "Data" |
| DataDescription |
DataDescription |
| Data_xl |
Read in Data object from Excel spreadsheet |
| 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 |
| derive_beta_par |
This function reduces the CV by 5 per cent until steepness values can be sampled without error |
| DFO_hist |
Deparment of Fisheries and Oceans historical plot |
| DFO_plot |
Deparment of Fisheries and Oceans trade-off plot |
| DFO_plot2 |
Deparment of Fisheries and Oceans default plot 2 |
| DFO_proj |
Deparment of Fisheries and Oceans projection plot |
| DLMDataDir |
Directory of the installed package on your computer |
| DLMextra |
Load more data from DLMextra package |
| DLMtool |
Data-Limited Methods Toolkit |
| dnormal |
Double-normal selectivity curve |
| 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-class |
Class "Fease" |
| Fease_xl |
Read in feasibility parameters from Excel spreadsheet |
| Feasibility |
Feasibility Fease |
| Feasibility2 |
Feasibility2 Fease |
| fetch.file.names |
Reads iSCAM Data, Control and Projection files |
| FlatE_Dom |
FlatE_Dom Fleet |
| FlatE_HDom |
FlatE_HDom Fleet |
| FlatE_NDom |
FlatE_NDom Fleet |
| Fleet-class |
Class "Fleet" |
| FleetDescription |
FleetDescription |
| 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) |
| ForceCor |
Forces correlation among operating model parameters for M, K, Linf and L50 |
| 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 |
| 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 |
| Generic_DecE |
Generic_DecE Fleet |
| Generic_FlatE |
Generic_FlatE Fleet |
| Generic_Fleet |
Generic_Fleet Fleet |
| Generic_IncE |
Generic_IncE Fleet |
| Generic_Obs |
Generic_Obs Obs |
| genLenComp |
Generate length composition of catch |
| getAFC |
Calculate age at first capture from length at first capture and growth |
| getBH |
Predict Beverton-Holt recruitment and return fit to S-R observations |
| getBlow |
Blow parallel optimization function |
| getclass |
get object class |
| getFMSY3 |
Calculate FMSY and related metrics using Rcpp code |
| getFref3 |
Calculate Reference Yield |
| getGpars |
Extracts growth parameters from a SS3 r4ss replist |
| getmov2 |
Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp. |
| getq3 |
optimize for catchability (q) |
| getsel |
Calculate selectivity curve |
| Gulf_blue_tilefish |
Gulf_blue_tilefish Data |
| ICI |
Index Confidence Interval (ICI) MP by Jardim et al. (2015) |
| ICI2 |
Less Precautionary Index Confidence Interval (ICI) MP by Jardim et al. (2015) |
| Imp-class |
Class "Imp" |
| ImpDescription |
ImpDescription |
| Imprecise_Biased |
Imprecise_Biased Obs |
| Imprecise_Unbiased |
Imprecise_Unbiased Obs |
| IncE_HDom |
IncE_HDom Fleet |
| IncE_NDom |
IncE_NDom Fleet |
| initialize |
~~ Methods for Function 'initialize' ~~ |
| initialize-method |
~~ Methods for Function 'initialize' ~~ |
| initialize-methods |
~~ Methods for Function 'initialize' ~~ |
| Input |
Function to run a set of input control methods |
| InputRec-class |
Class "InputRec" |
| IOTC_plot |
Indian Ocean Tuna Commission trade-off plot |
| Iratio |
Mean index ratio MP from Jardim et al. 2015 |
| iSCAM2Data |
Reads data from iSCAM file structure into a DLMtool Data object |
| iSCAM2DLM |
Reads MLE estimates from iSCAM file structure into an operating model |
| iSCAMcomps |
Combines all iSCAM age composition data across fleets |
| iSCAMinds |
Combines indices into a single index using linear modelling |
| 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. |
| label.class-class |
Label class union for performance metric objects |
| 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 |
| LinInterp |
Linear interpolation of a y value at level xlev based on a vector x and y |
| load.iscam.files |
Reads iSCAM files into a hierarchical R list object |
| Low_Effort_Non_Target |
Low_Effort_Non_Target Fleet |
| Lratio_BHI |
Mean length-based indicator MP of Jardim et al. 2015 using Beverton-Holt invariant M/K ratio = 1.5 and assumes FMSY = M. |
| Lratio_BHI2 |
The more general version of the mean length-based indicator MP of Jardim et al. 2015. |
| LSRA |
Estimates R0 using SRA to match current F estimates and avoid penalities for low stock sizes |
| LSRA2 |
Alternative version of LSRA that's a wrapper for LSRA_opt to return the right type of output (mode) using sapply |
| LSRA_MCMC_sim |
Internal SRA MCMC CPP code |
| LSRA_opt |
Internal estimation function for LSRA and LSRA2 functions |
| 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. |
| LTY |
Performance Metric: Probability Long-Term Yield > 0.5 Relative Yield |
| 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 retention 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 |
| movdistil |
Simplified a multi-area transition matrix into the best 2 x 2 representation |
| 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" |
| P10 |
Performance Metric: Probability B > 0.1 BMSY |
| P100 |
Performance Metric: Probability B > BMSY |
| P50 |
Performance Metric: Probability B > 0.5 BMSY |
| Perfect_Imp |
Perfect_Imp Imp |
| Perfect_Info |
Perfect_Info Obs |
| plot-method |
Plot Data object |
| plot-method |
Plot MSE object |
| plot.OM |
Plot the operating model (OM) object parameters |
| plotFleet |
Plot the Fleet object parameters |
| plotFun |
Print out plotting functions |
| plotImp |
Plot the Implementation object parameters |
| plotM |
Plot M-at-Age and Size |
| plotObs |
Plot the Observation object parameters |
| plotOFL |
A generic OFL plot for NOAA use |
| plotSelect |
Plot the vulnerability and retention curves |
| plotStock |
Plot the Stock object parameters |
| PMobj-class |
An object for storing data for analysis using data-limited methods |
| POF |
Performance Metric: Probability F < FMSY |
| popdyn |
Population dynamics model |
| Porgy |
Porgy Stock |
| Pplot |
A projection by projection plot of F/FMSY and B/BMSY |
| Pplot2 |
A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield |
| Precise_Biased |
Precise_Biased Obs |
| Precise_Unbiased |
Precise_Unbiased Obs |
| prob.class-class |
Prob class union for performance metric objects |
| PWhisker |
Performance Whisker Plot |
| Sam |
Conduct stock assessment |
| SampleCpars |
Sample custom pars |
| SampleFleetPars |
Sample Fleet Parameters |
| SampleImpPars |
Sample Implementation Error Parameters |
| SampleObsPars |
Sample Observation Parameters |
| SampleStockPars |
Sample Stock parameters |
| sample_steepness2 |
Sample steepness given mean and cv |
| 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 |
| setup |
Setup parallel processing |
| show-method |
Show the output of a PM |
| Simulation_1 |
Simulation_1 Data |
| simYears |
Simulate population dynamics for historical years |
| 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 |
| SRAcomp |
Plot simulation test of Stochastic SRA method |
| SRAsim |
Simulates catch at age and catch history data for testing SRA methods |
| SRopt |
Function that returns a stochastic estimate of steepness given observed stock recruitment data |
| SS2Data |
Reads data Stock Synthesis file structure into an data object using package r4ss |
| SS2DLM |
Reads MLE estimates from Stock Synthesis file structure into an operating model using package r4ss |
| StochasticSRA |
Stochastic SRA construction of operating models |
| StochasticSRAcpp |
Stochastic SRA construction of operating models |
| Stock-class |
Class "Stock" |
| StockDescription |
StockDescription |
| STY |
Performance Metric: Probability Short-Term Yield > 0.5 Relative Yield |
| Sub |
Subset MSE object by management procedure (MP) or simulation. |
| SubCpars |
Subset an OM cpars slot |
| SubOM |
Subset a Stock, Fleet, Obs, or Imp object from an OM object |
| summary-method |
Summary of Data object |
| summary-method |
Summary of MSE object |
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