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**DLMtool**: Data-Limited Methods Toolkit**Sub**: Subset MSE object by management procedure (MP) or simulation.

# Subset MSE object by management procedure (MP) or simulation.

### Description

Subset the MSE object by particular MPs (either MP number or name), or particular simulations, or a subset of the projection years (e.g., 1: < projection years).

### Usage

1 |

### Arguments

`MSEobj` |
A MSE object. |

`MPs` |
A vector MPs names or MP numbers to subset the MSE object. Defaults to all MPs. |

`sims` |
A vector of simulation numbers to subset the MSE object. Can also be a logical vector. Defaults to all simulations. |

`years` |
A numeric vector of projection years. Should start at 1 and increase by one to some value equal or less than the total number of projection years. |

### Author(s)

A. Hordyk

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- 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...