Management Strategy Evaluation Toolkit
Utility functions for multiMSE objects
Calculate parameters for beta distribution from mean and standard devi...
Apply multi Management Procedures (class MMP) to a hierarchical list o...
Apply Management Procedures to an object of class Data
Convert ASAP 3 assessments into an operating model
Reads bootstrap estimates from a stock assessment model into a multi-f...
Reads bootstrap estimates from a stock assessment model (including VPA...
What objects of this class are available
Reads MCMC estimates from Awatea (Paul Starr) processed r file structu...
Import a multi-stock, multi-fleet OM from a BAM object
Internal function to create a blank plot for mapping selectivity at le...
Blow internal parallel optimization function
Boxplot of TAC recommendations
Calculates the asymptotic distribution from an initial distribution ve...
Calculate Mean Probability
Calculate population dynamics from MP recommendation for multi-fleet o...
Calculate population dynamics from MP recommendation
Calculate Probability
Calculate Reference Yield
Optimize for catchability (q)
Simplifies the CAL slot of data object
Identify management procedures (MPs) based on data availability
Class union for isRel slot
Check for duplicated MPs names
Check that specified MPs are valid and will run on MSEtool::SimulatedD...
Utility functions for MSE objects
Check OM object is complete
Check the years to summarize performance
Manually map parameters for the historical period of operating model
Create a blank MP recommendations object (class Rec) of the right dime...
Check Convergence
Current default thresholds for COSEWIC satisficing
Internal function for checking that the OM@cpars is formatted correc...
Plot the median biomass and yield relative to last historical year
Catch at size reduction analysis
Optimization function for CSRA
Calculate CV from vector of values
Read in Data object from Excel spreadsheet
Data class objects
Class 'Data'
Converts a Data object into a .csv data file
Directory of the data in the installed package on your computer
Initialize Data Input Files
Department of Fisheries and Oceans stock status bar plot
Department of Fisheries and Oceans historical plot
Department of Fisheries and Oceans trade-off plot
Department of Fisheries and Oceans default plot 2
Department of Fisheries and Oceans projection plot
Department of Fisheries and Oceans biomass quantile plot
Create a standard DFO MSE report
DFO performance spider plot (top three MPs)
A formatted version of the standard DFO performance plot, color coded ...
Create a standard DFO performance table
Directory of the installed package on your computer
Double-normal selectivity curve
Hockey Stick Harvest control rule that modifies TAC.
Create indices that are sampled at various frequencies
Determine dominate MPs
Calculate a management recommendation given constraints
A flexible empirical management procedure.
MP feasibility diagnostic
Fleet class objects
Class 'Fleet'
Reference management procedures
Creates a time series per simulation that has a random normal walk wit...
Wrapper for C++ function to generate length composition
Calculate age at first capture from length at first capture and growth
Blow parallel optimization function
get object class
Get part of an MP specific data-list
Calculate historical fishing mortality
Extract the first dimension of a hierarchical list of recommendation o...
Optimization function to find a movement model that matches user speci...
Search R session for MP
Count independent variables for a MICE relationship at position x in a...
Optimize for catchability (q) and fishing dist for a MICE model
Calculate selectivity curve
Stock recruit parameterization
Internal Herm functions
Class 'Hist'
Wrapper for histogram function
Reconstruct historical dynamics
Derives the rate of exchange from one sex to another based on asymptot...
Imp class objects
Class 'Imp'
~~ Methods for Function initialize ~~
Function to run a set of input control methods
Reads iSCAM files into a hierarchical R list object
Reads MPD or MCMC estimates and data from iSCAM file structure into an...
Combines all iSCAM age composition data across fleets
Combines indices into a single index using linear modelling (** Deprec...
Plot several plots with a shared legend
Join Data objects present in a list
KOBE plot: a projection by projection plot of F/FMSY and B/BMSY
Length to age conversion
Label class union for performance metric objects
Lag the time-series slots in a Data object by a specified number of ...
Dimensions of a hierarchical list object
Predict missing life-history parameters
Linear interpolation of a y value at level xlev based on a vector x an...
Utility for making multi-OMs
Calculates movement matrices from user inputs for fraction in each are...
Calculates movement matrices from user inputs for fraction in each are...
MICE relationships for multi-OM
Make colors transparent
Depletion and F estimation from mean length of catches
Class 'MMSE'
MOM class objects
Class 'MOM'
Apply the movement model to the stock for one time-step
Rcpp version of the Optimization function that returns the squared dif...
Fill any NAs arising from MPCalcs (hermaphroditism mode)
Management Procedure Type
Get help topic URL
Class 'MSE'
Load more data from MSEextra package
Internal function to calculate MSY Reference Points
Combine data among fleets
Combine data among stocks
A basic comparison of runMSE output (MSE) and multiMSE (MMSE)
Run a multi-fleet multi-stock Management Strategy Evaluation
Is a value NA or zero.
Item in list: get the list values from a list of lists
National Oceanographic and Atmospheric Administration default plot 1
Obs class objects
Class 'Obs'
OM class objects
Class 'OM'
Generate OM Documentation Report
Copy example OM XL and OM Documentation
Initialize Operating Model
Make stochastic variables certain for only one rep
Determine optimal number of cpus
Internal wrapper function to calculate MSY reference points (now using...
Optimize q for a single simulation
Optimize yield for a single simulation
Performance Metrics Methods
Plot Data object
Standard plot for an object of class MMSE (multi MSE)
Standard plot for an object of class MOM
Plot MSE object
Plot Operating Model Object
Print out plotting functions
A basic SSB plot for debugging runMSE output
A generic OFL plot for NOAA use
A fairly tidy time-series quantile plot
Plot a relationship between stocks
Create a table of Performance Limits and Performance Objectives
An object for storing data for analysis using data-limited methods
Population dynamics model in CPP
Population dynamics for a MICE model (multiyear)
Population dynamics for a MICE model (single year)
Aging and Mortality for one time-step
A projection by projection plot of F/FMSY and B/BMSY
A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield
Prob class union for performance metric objects
Performance Whisker Plot
Internal function for optimizing catchability (q) for a MICE model
A quantile plot
Standardize values
MP feasibility diagnostic using real data
Class 'Rec'
Replace an existing Stock, Fleet, Obs, or Imp object
Enlarge (replicate) a DLM data object to create an additional dimensio...
Generate a Data Report
What management procedures need what data
Returns Results of a set of MICE relationships
COSEWIC MSE run using the correct MPs and projected time horizon
Runs input control MPs on a Data object.
Run a Management Procedure
Run a Management Strategy Evaluation
Sample steepness given mean and cv
Sample custom pars
Sample Fleet Parameters
Sample Implementation Error Parameters
Sample Observation Parameters
Sample Stock parameters
Get parameters of lognormal distribution from mean and standard deviat...
Select DataList for an MP from MMSE@PPD
Sensitivity analysis
Setup parallel processing
Show the output of a PM
Show MSEtool S4 objects
Show the output of a single MP recommendation
Slot in list: get the slot values from a list of objects
Simulate Catch-at-Age Data
Simulate Catch-at-Length Data
Calculates movement matrices from user inputs
Calculates movement matrices from user specified distribution among ot...
Manually map the historical relative fishing effort trajectory.
General purpose polynomial smoother
Standard MSE projection plot
Reads data Stock Synthesis file structure into a Data object using pac...
Reads data Stock Synthesis file structure into a nested Data object an...
Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, s...
Plot Spawning stock biomass and reference points for both historical a...
Stock class objects
Class 'Stock'
Subset MSE object by management procedure (MP) or simulation.
Subset the cpars slot in an operating model
Subset a Stock, Fleet, Obs, or Imp object from an OM object
Summary of Data object
Summary of MMSE object
Summary of MSE object
Calculate TAC recommendations for more than one MP
TAC Filter
Tom's expand grid
Current default thresholds for DFO satisficing
Remove observation, implementation, and process error
Generic Trade-Plot Function
Lognormal distribution
Tune MP
Turing Test
Find the Management Procedures that use a particular data slot
Valid custom parameters (cpars)
Calculate Value Of Information
Calculate Value Of Information 2
Yet another Value of Information Plot
Takes a fitted SAM model and samples historical population and fishing...
Biomass wormplot
Internal function to write CSVs for objects
Import a Data object from Excel file
Import Fleet Object from Excel file
Load OM from Excel file
Import Stock Object from Excel file
Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).