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DLMtool

DLMtool is a R package for management strategy evalaution and implementation of data-limited fishery stock assessment methods.

Find more information about DLMtool at http://datalimitedtoolkit.org/.

Installation

The released version of DLMtool can be downloaded from CRAN:

install.packages("DLMtool")

This GitHub repository contains the development version of DLMtool. The development version may be unstable, and it is not recommended for analyses.

User Guide

A User Guide for the DLMtool package are now available: https://dlmtool.github.io/DLMtool/userguide/introduction.html.

Bugs and Issues

Please report any bugs or issues through GitHub or the DLMtool website.

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Version

Install

install.packages('DLMtool')

Monthly Downloads

389

Version

5.2.3

License

GPL-2

Maintainer

Tom Carruthers

Last Published

September 11th, 2018

Functions in DLMtool (5.2.3)

Blow_opt

Blow internal parallel optimization function
CompSRA

Age-Composition Stock-Reduction Analysis
DCACs

Depletion Corrected Average Catch
CompSRA_

Internal function for CompSRA MP
DCAC_

Depletion Corrected Average Catch
DFO_proj

Deparment of Fisheries and Oceans projection plot
DFO_quant

Deparment of Fisheries and Oceans biomass quantile plot
DLMextra

Load more data from DLMextra package
DLMtool-package

Data-Limited Methods Toolkit
DecE_Dom

Fleet class objects
FilterSmooth

Kalman filter and Rauch-Tung-Striebel smoother
CSRAfunc

Optimization function for CSRA
Can

Identify management procedures (MPs) based on data availability
BK

Beddington and Kirkwood life-history MP
ForceCor

Forces correlation among operating model parameters for M, K, Linf and L50
BlankSelPlot

Internal function to create a blank plot for mapping selectivity at length
CanMP

What Data objects can be used to run this MP?
Fratio

FMSY/M ratio methods
ImpDescription

ImpDescription
ChkObj

Check that a DLM object is valid
DBSRA_

Depletion-based SRA internal function
Input

Function to run a set of input control methods
DFO_hist

Deparment of Fisheries and Oceans historical plot
DFO_bar

Deparment of Fisheries and Oceans stock status bar plot
DBSRAopt

Internal optimization function
LBSPR

Length-Based SPR Effort Control
DFO_plot

Deparment of Fisheries and Oceans trade-off plot
LBSPR_

Internal Estimation Function for LBSPR MP
DFO_report

Create a standard DFO MSE report
MRreal

Spatial closure and allocation management procedures
CC1

Geromont and Butterworth (2015) Constant Catch
DFO_spider

DFO performance spider plot (top three MPs)
DFO_plot2

Deparment of Fisheries and Oceans default plot 2
MSE-class

Class 'MSE'
CSRA

Catch at size reduction analysis
Fleet-class

Class 'Fleet'
FleetDescription

FleetDescription
Converge

Check Convergence
DataDescription

DataDescription
PWhisker

Performance Whisker Plot
DataInit

Initialize an empty Data workbook or CSV
Cos_thresh_tab

Current default thresholds for COSEWIC satificing
Iratio

Mean Index Ratio
Islope1

Index Slope Tracking MP
DD

Delay - Difference Stock Assessment
Islope_

Index Slope Internal Function
PerformanceMetric

Performance Metrics Methods
Itarget1

Incremental Index Target MP
SimulatedData

SimulatedData Data
SketchFun

Manually map the historical relative fishing effort trajectory.
Fratio_

Fratio internal function
GB_CC

Geromont and Butterworth Constant Catch Harvest Control Rule
LSRA_opt

Internal estimation function for LSRA and LSRA2 functions
StockDescription

StockDescription
Overages

Imp class objects
LtargetE1

Length Target TAE MP
LSRA_opt_cpp

Internal estimation function for LSRA and LSRA2 functions
DFO_tab_formatted

A formatted version of the standard DFO performance plot, color coded by thresholds
DFO_tab

Create a standard DFO performance table
DD_

Delay-Difference Internal Function
DOM

How dominant is an MP?
MCD

Mean Catch Depletion
Sub

Subset MSE object by management procedure (MP) or simulation.
NAor0

Is a value NA or zero.
DTe40

Effort searching MP aiming for a fixed stock depletion
EtargetLopt

Effort Target Optimum Length
NOAA_plot

National Oceanographic and Atmospheric Administration default plot 1
FMSYref

Reference management procedures
ICI

Index Confidence Interval
OneRep

Make stochastic variables certain for only one rep
PMobj-class

An object for storing data for analysis using data-limited methods
SPSRA

Surplus Production Stock Reduction Analysis
Imp-class

Class 'Imp'
LSRA

Estimates R0 using SRA to match current F estimates and avoid penalities for low stock sizes
LHdatabase

LHdatabase
SPSRA_

Surplus Production Stock Reduction Analysis Internal Function
SubCpars

Subset an OM cpars slot
SubOM

Subset a Stock, Fleet, Obs, or Imp object from an OM object
Lratio_BHI

Mean length-based indicator MP of Jardim et al. 2015
VOIplot

Yet another Value of Information Plot
VOI2

Calculate Value Of Information 2
LstepCC1

Step-wise Constant Catch
YPR_

Internal function for YPR MPs
OM-class

Class 'OM'
OMDescription

OMDescription
ReqData

ReqData
Required

What management procedures need what data
alphaconv

Calculate parameters for beta distribution from mean and standard deviation in normal space
Thresh_tab

Current default thresholds for DFO satificing
Cplot

Plot the median biomass and yield relative to last historical year
cparscheck

Internal function of runMSE for checking that the OM slot cpars slot is formatted correctly
IOTC_plot

Indian Ocean Tuna Commission trade-off plot
DBSRA

Depletion-Based Stock Reduction Analysis
DD_R

Delay-Difference Internal Function
Tplot_old

Trade-off plots for an MSE object
curE

Fishing at current effort levels
SampleStockPars

Sample Stock parameters
Sense

Sensitivity analysis
Itarget_

Incremental Index Target MP Internal Function
Itargeteff_

Incremental Index Target MP Internal Function - Effort MP
barplot.MSE

Plot a barplot of MSE results
LBSPRgen

Internal estimation function for LBSPR MP
TAC

Calculate TAC recommendations for more than one MP
LH2OM

Predict missing life-history parameters
MPtype

Management Procedure Type
boxplot.Data

Boxplot of TAC recommendations
TACfilter

TAC Filter
label.class-class

Label class union for performance metric objects
OMdoc

Generate OM Documentation Report
MPurl

Get help topic URL
makeMeanMP

Create an MP that averages the results of multiple MPs
DDe

Effort-based Delay - Difference Stock Assessment
DLMDataDir

Directory of the installed package on your computer
cheatsheets

Opens the DLMtool Cheat-Sheets (requires internet connection)
plotStock

Plot the Stock object parameters
checkMSE

Utility functions for MSE objects
popdynCPP

Population dynamics model in CPP
OMexample

Copy example OM XL and OM Documentation
AvC

Average Catch
AvC_MLL

Average Catch with a size limit
getr

Internal function to estimate r
Range

Standardize values
getsel

Calculate selectivity curve
runMSE

Run a Management Strategy Evaluation
Rcontrol

Intrinsic rate of Increase MP
DLMenv

DLMenv blank environment
Data_xl

Read in Data object from Excel spreadsheet
matlenlim

Size limit management procedures
Turing

Turing Test
VOI

Calculate Value Of Information
Choose

Manually map parameters for the historical period of operating model
ChkYrs

Check the years to summarize performance
movfit_Rcpp

Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters.
SPmod

Surplus production based catch-limit modifier
SPslope

Slope in surplus production MP
DynF

Dynamic Fratio MP
Fdem_

Internal function for Fdem MP
Atlantic_mackerel

Data class objects
applyMP

Apply Management Procedures to an object of class Data
SampleCpars

Sample custom pars
avail

What objects of this class are available
SampleFleetPars

Sample Fleet Parameters
StochasticSRA

Stochastic SRA construction of operating models
Data-class

Class 'Data'
plotObs

Plot the Observation object parameters
StochasticSRAcpp

Stochastic SRA construction of operating models
Fease

MP feasibility diagnostic
GB_slope

Geromont and Butterworth index slope Harvest Control Rule
GB_target

Geromont and Butterworth target CPUE and catch MP
compplot

Generic comparison plot for simulation testing of Stochastic SRA method
condmet

Condition met?
Fadapt

Adaptive Fratio
Fdem

Demographic FMSY method
getFref3

Calculate Reference Yield
Gcontrol

G-control MP
Growth2OM

Generate bootstrapped estimates of von Bertalanffy growth parameters from length-at-age data
sample_steepness2

Sample steepness given mean and cv
summary,Data-method

Summary of Data object
summary,MSE-method

Summary of MSE object
IT_

Index Target Internal Function
ITe5

Index Target Effort-Based
IT5

Iterative Index Target MP
VOIplot2

Value of Information Plot using PM functions
plot.Data

Plot Data object
getclass

get object class
joinData

Join Data objects present in a list
XL2OM

Load OM from Excel file
XL2Data

Import a Data object from Excel file
Kplot

KOBE plot: a projection by projection plot of F/FMSY and B/BMSY
YPR

Yield Per Recruit analysis to get FMSY proxy F01
L2A

Length to age conversion
LW2OM

Estimate length-weight parameters from data
join_plots

Plot several plots with a shared legend
ITM

Index Target based on natural mortality rate
cv

Calculate CV from vector of values
Itarget1_MPA

Itarget1 with an MPA
demographic2

Internal demographic function
ItargetE1

Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
setup

Setup parallel processing
show,PMobj-method

Show the output of a PM
optQ

Optimize q for a single simulation
LinInterp

Linear interpolation of a y value at level xlev based on a vector x and y
userguide

Open the DLMtool User Guide
LstepCE1

Step-wise Constant Effort
plotFleet

Plot the Fleet object parameters
validcpars

Valid custom parameters (cpars)
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
getBlow

Blow parallel optimization function
Ltarget1

Length Target TAC MP
ML2D

Depletion and F estimation from mean length of catches
getEffhist

Calculate historical fishing mortality
Obs-class

Class 'Obs'
iVB

Inverse von Bertalanffy
MPStats

Calculate Statistics for MP Performance
initialize-methods

~~ Methods for Function initialize ~~
ObsDescription

ObsDescription
plot.MSE

Plot MSE object
plotFun

Print out plotting functions
OMinit

Initialize Operating Model
Generic_Obs

Obs class objects
replic8

Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing
runCOSEWIC

COSEWIC MSE run using the correct MPs and projected time horizon
runInMP

Runs input control MPs on a Data object.
SBT1

SBT simple MP
wormplot

Biomass wormplot
runMP

Run a Management Procedure
Pplot

A projection by projection plot of F/FMSY and B/BMSY
writeCSV

Internal function to write CSVs for objects
SPMSY

Catch trend Surplus Production MSY MP
SRAcomp

Plot simulation test of Stochastic SRA method
SRAsim

Simulates catch at age and catch history data for testing SRA methods
Pplot2

A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield
Rec-class

Class 'Rec'
Replace

Replace an existing Stock, Fleet, Obs, or Imp object
SampleImpPars

Sample Implementation Error Parameters
SampleObsPars

Sample Observation Parameters
Albacore

Stock class objects
plotSelect

Plot the vulnerability and retention curves
plotOFL

A generic OFL plot for NOAA use
Stock-class

Class 'Stock'
sampy

Sample vector
sdconv

Get parameters of lognormal distribution from mean and standard deviation in normal space
getAFC

Calculate age at first capture from length at first capture and growth
dnormal

Double-normal selectivity curve
testOM

testOM OM
tiny

tiny
TradePlot

Generic Trade-Plot Function
gettempvar

Creates a time series per simulation that has gradient grad and random normal walk with sigma
TradePlot_old

Generic Trade-off Plot
hist2

Wrapper for histogram function
plotImp

Plot the Implementation object parameters
plot.OM

Plot the operating model (OM) object parameters
popdynOneTScpp

Population dynamics model for one annual time-step
calcMean

Calculate Mean Probability
prob.class-class

Prob class union for performance metric objects
calcProb

Calculate Probability
getmov2

Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.
makePerf

Convert a OM object to one without observation or process error
getq3

optimize for catchability (q)
makeTransparent

Make colors transparent
optCPU

Determine optimal number of cpus
optMSY

Optimize yield for a single simulation
plotM

Plot M-at-Age and Size
plotMPA

Plot the Historical Spatial Closures
show,Rec-method

Show the output of a single MP recommendation
simYears

Simulate population dynamics for historical years
tinyErr

Remove observation, implementation, and process error
trlnorm

Lognormal distribution for DLMtool
CC

Age-based Catch Curve