All functions |
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Convert ASAP 3 assessments into an operating model |
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Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model. |
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Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. |
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Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model |
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Simplifies the CAL slot of data object |
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Identify management procedures (MPs) based on data availability |
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Check for duplicated MPs names |
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Check that specified MPs are valid and will run on MSEtool::SimulatedData |
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Check OM object is complete |
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Manually map parameters for the historical period of operating model |
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Create a blank MP recommendations object (class Rec) of the right dimensions |
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Check Convergence |
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Current default thresholds for COSEWIC satisficing |
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Plot the median biomass and yield relative to last historical year |
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Department of Fisheries and Oceans stock status bar plot |
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Department of Fisheries and Oceans historical plot |
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Department of Fisheries and Oceans trade-off plot |
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Department of Fisheries and Oceans default plot 2 |
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Department of Fisheries and Oceans projection plot |
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Department of Fisheries and Oceans biomass quantile plot |
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Create a standard DFO MSE report |
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DFO performance spider plot (top three MPs) |
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Create a standard DFO performance table |
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A formatted version of the standard DFO performance plot, color coded by thresholds |
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Directory of the installed package on your computer |
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Data class objects |
Class |
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Converts a Data object into a .csv data file |
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DataDescription |
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Directory of the data in the installed package on your computer |
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Initialize Data Input Files |
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DataSlots |
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Read in Data object from Excel spreadsheet |
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Determine dominate MPs |
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Reference management procedures |
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MP feasibility diagnostic |
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Fleet class objects |
Class |
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FleetDescription |
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Class |
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HistDescription |
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Imp class objects |
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Class |
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ImpDescription |
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Function to run a set of input control methods |
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KOBE plot: a projection by projection plot of F/FMSY and B/BMSY |
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Predict missing life-history parameters |
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LHdatabase |
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Lag the time-series slots in a |
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Depletion and F estimation from mean length of catches |
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Class |
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MOM class objects |
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Class |
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Fill any NAs arising from MPCalcs (hermaphroditism mode) |
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Management Procedure Type |
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Class |
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MSEDescription |
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Load more data from MSEextra package |
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Item in list: get the list values from a list of lists |
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National Oceanographic and Atmospheric Administration default plot 1 |
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OM class objects |
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Class |
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OMDescription |
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Generate OM Documentation Report |
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Copy example OM XL and OM Documentation |
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Initialize Operating Model |
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Obs class objects |
Class |
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ObsDescription |
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Create a table of Performance Limits and Performance Objectives |
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An object for storing data for analysis using data-limited methods |
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Performance Whisker Plot |
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Performance Metrics Methods |
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A projection by projection plot of F/FMSY and B/BMSY |
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A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield |
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MP feasibility diagnostic using real data |
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Class |
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Replace an existing Stock, Fleet, Obs, or Imp object |
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Generate a Data Report |
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ReqData |
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What management procedures need what data |
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Slot in list: get the slot values from a list of objects |
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Reads data Stock Synthesis file structure into a Data object using package r4ss |
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Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE |
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Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) |
Plot Spawning stock biomass and reference points for both historical and projected period |
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Sensitivity analysis |
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SimulatedData Data |
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Manually map the historical relative fishing effort trajectory. |
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Stock class objects |
Class |
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StockDescription |
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Subset MSE object by management procedure (MP) or simulation. |
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Subset the cpars slot in an operating model |
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Subset a Stock, Fleet, Obs, or Imp object from an OM object |
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Calculate TAC recommendations for more than one MP |
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TAC Filter |
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Tom's expand grid |
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Taxa_Table |
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Current default thresholds for DFO satisficing |
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Generic Trade-Plot Function |
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Turing Test |
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Find the Management Procedures that use a particular data slot |
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Calculate Value Of Information |
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Calculate Value Of Information 2 |
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Yet another Value of Information Plot |
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Takes a fitted WHAM (Wood's Hole Assessment Model) and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix. |
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Import a Data object from Excel file |
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Import Fleet Object from Excel file |
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Load OM from Excel file |
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Import Stock Object from Excel file |
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Apply multi Management Procedures (class MMP) to a hierarchical list of Data class objects |
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Apply Management Procedures to an object of class Data |
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What objects of this class are available |
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Boxplot of TAC recommendations |
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Calculate Reference Yield |
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Utility functions for MSE objects |
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Internal function for checking that the |
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Double-normal selectivity curve |
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Expand the Herm list in SexPars to a matrix of fractions at age |
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Get part of an MP specific data-list |
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get object class |
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Extract the first dimension of a hierarchical list of recommendation objects |
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Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp. |
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Count independent variables for a MICE relationship at position x in a Rel list |
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Calculate selectivity curve |
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Stock recruit parameterization |
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Wrapper for histogram function |
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Reads iSCAM files into a hierarchical R list object |
Reads MPD or MCMC estimates and data from iSCAM file structure into an operating model |
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Combines all iSCAM age composition data across fleets |
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Combines indices into a single index using linear modelling (** Deprecated **) |
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~~ Methods for Function |
Join Data objects present in a list |
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Plot several plots with a shared legend |
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Dimensions of a hierarchical list object |
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Utility for making multi-OMs |
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MICE relationships for multi-OM |
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Make colors transparent |
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Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob) |
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Apply the movement model to the stock for one time-step |
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Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters. |
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Combine data among fleets |
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Combine data among stocks |
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Run a multi-fleet multi-stock Management Strategy Evaluation |
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A basic comparison of runMSE output (MSE) and multiMSE (MMSE) |
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Determine optimal number of cpus |
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Plot Data object |
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Standard plot for an object of class MMSE (multi MSE) |
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Standard plot for an object of class MOM |
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Plot MSE object |
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Plot Operating Model Object |
Print out plotting functions |
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A generic OFL plot for NOAA use |
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Plot a relationship between stocks |
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A basic SSB plot for debugging runMSE output |
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A fairly tidy time-series quantile plot |
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Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing |
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COSEWIC MSE run using the correct MPs and projected time horizon |
Runs input control MPs on a Data object. |
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Run a Management Procedure |
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Run a Management Strategy Evaluation |
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Setup parallel processing |
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Show the output of a PM |
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Show the output of a single MP recommendation |
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Simulate Catch-at-Age Data |
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Simulate Catch-at-Length Data |
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Calculates movement matrices from user inputs |
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Summary of Data object |
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Summary of MMSE object |
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Summary of MSE object |
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Remove observation, implementation, and process error |
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Valid custom parameters (cpars) |
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Biomass wormplot |
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Internal function to write CSVs for objects |