DLMtool: Data-Limited Methods Toolkit
Version 4.1

Development, simulation testing, and implementation of management procedures for data-limited fisheries (see Carruthers et al (2014) ).

AuthorTom Carruthers [aut, cre], Adrian Hordyk [aut]
Date of publication2017-05-02 05:48:35 UTC
MaintainerTom Carruthers <t.carruthers@fisheries.ubc.ca>
LicenseGPL-2
Version4.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DLMtool")

Getting started

Package overview
README.md

Popular man pages

CC1: Constant catch management procedure of Geromont and...
CC4: Constant catch management procedure of Geromont and...
GB_CC: Geromont and Butterworth Constant Catch Harvest Control Rule
getSlopeFun: Internal function to calculate slope
Pplot: A projection by projection plot of F/FMSY and B/BMSY
SPMSY: Catch trend Surplus Production MSY MP
SRopt: Function that returns a stochastic estimate of steepness...
See all...

All man pages Function index File listing

Man pages

AJ_GOM: AJ_GOM OM
Albacore: Albacore Stock
alphaconv: Calculate alpha parameter for beta distribution from mean and...
Arrowtooth_Flounder_BC_DFO_iSCAM: Arrowtooth_Flounder_BC_DFO_iSCAM OM
Atlantic_mackerel: Atlantic_mackerel Data
avail: What objects of this class are available
AvC: Average Catch
barplot.MSE: Plot a barplot of MSE results
betaconv: Calculate beta parameter for beta distribution from mean and...
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...
BlankSelPlot: Internal function to create a blank plot for mapping...
Blow_opt: Blow internal parallel optimization function
Bluefin_tuna: Bluefin_tuna Stock
Bluefin_tuna_WAtl: Bluefin_tuna_WAtl Stock
Blue_shark: Blue_shark Stock
boxplot.Data: Boxplot of TAC recommendations
boxplot.MSE: Boxplot of MP performance from MSE object
Butterfish: Butterfish Stock
Can: What data-limited methods can be applied to this Data object?
Canary_Rockfish_BC_DFO: Canary_Rockfish_BC_DFO OM
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
checkMSE: Check that MSE object includes all slots
China_rockfish: China_rockfish Data
ChooseEffort: Manually map the historical relative fishing effort...
ChooseSelect: Manually choose the historical selectivity pattern
Cobia: Cobia Data
compplot: Generic comparison plot for simulation testing of Stochastic...
CompSRA: Age-composition-based estimate of current stock depletion...
CompSRA4010: Age-composition-based estimate of current stock depletion...
condmet: Condition met?
Converge: Check Convergence
COSEWIC_plot: COSEWIC forward projection plot
cparscheck: Internal function of runMSE for checking that the OM slot...
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
cv: Calculate CV from vector of values
DAAC: Depletion Adjusted Average Catch
Darnley_Bay_Char_DFO: Darnley_Bay_Char_DFO OM
Data-class: Class "Data"
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...
DecE_Dom: DecE_Dom Fleet
DecE_HDom: DecE_HDom Fleet
DecE_NDom: DecE_NDom Fleet
DepF: Depletion Corrected Fratio
DFO_hist: Deparment of Fisheries and Oceans historical 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
DLMtool-package: Data-Limited Methods Toolkit
DOM: How dominant is an MP?
doprojPI: Internal Projection Function
doprojPI_cpp: Rcpp version of the Projection function for calculating...
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...
Example_datafile: Example_datafile Data
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-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"
FMSYopt: Internal function FMSY and related metrics
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...
ForceCor: Forces correlation among operating model parameters for M, K,...
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
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...
getBH: Predict Beverton-Holt recruitment and return fit to S-R...
getBlow: Blow parallel optimization function
getclass: get object class
getEffhist: Calculate historical fishing mortality
getFMSY: Calculate FMSY and related metrics
getFMSY2: Calculate FMSY and related metrics using Rcpp code
getFref: Internal Get Reference F
getFref2: Internal Get Reference F using Rcpp
getGpars: Extracts growth parameters from a SS3 r4ss replist
getmov: Optimization function to find a movement model that matches...
getmov2: Optimization function to find a movement model that matches...
getq: Optimization function that find the catchability (q where...
getq2: Optimization function that find the catchability (q where...
getroot: Calculate slope from ageM and age95
getSlope1: Internal function to calculate ascending slope of selectivity...
getSlope2: Internal function to calculate slope
getSlopeFun: Internal function to calculate slope
gettempvar: Creates a time series per simulation that has gradient grad...
Gulf_blue_tilefish: Gulf_blue_tilefish Data
HDAAC: Hybrid Depletion Adjusted Average Catch
Herring: Herring Stock
Imp-class: Class "Imp"
Imprecise_Biased: Imprecise_Biased Obs
Imprecise_Unbiased: Imprecise_Unbiased Obs
IncE_Dom: IncE_Dom Fleet
IncE_HDom: IncE_HDom Fleet
IncE_NDom: IncE_NDom Fleet
initialize-methods: ~~ Methods for Function 'initialize' ~~
Input: Function to run a set of input control methods
iSCAM2DLM: Reads MLE estimates from iSCAM file structure into an...
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
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...
LAJ_GOM: LAJ_GOM OM
LBSPR: Apply the Length-based SPR model to DLMtool Data Object
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
LinInterp: Linear interpolation of a y value at level xlev based on a...
lmmodel-class: Class "lmmodel"
load.iscam.files: Reads iSCAM files into a hierarchical R list object
Low_Effort_Non_Target: Low_Effort_Non_Target Fleet
LS_GOM: LS_GOM OM
LSRA: Estimates R0 using SRA to match current F estimates and avoid...
LSRA2: Alternative version of LSRA that's a wrapper for LSRA_opt to...
LSRA_opt: Internal estimation function for LSRA and LSRA2 functions
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...
Mackerel: Mackerel Stock
makePerf: Convert a OM object to one without observation or process...
makeTransparent: Make colors transparent
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
mconv: Get log normal mean from transformed space mean and standard...
minlenLopt1: This input control sets the minimum length of fish caught to...
ML2D: Depletion and F estimation from mean length of catches
movdistil: Simplified a multi-area transition matrix into the best 2 x 2...
movfit: Optimization function that returns the squared difference...
movfit_Rcpp: Rcpp version of the Optimization function that returns the...
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
negcorlogspace: A function that samples multivariate normal (logspace)...
NFref: No Fishing Reference MP
NOAA_plot: National Oceanographic and Atmospheric Administration default...
Obs-class: Class "Obs"
OM-class: Class "OM"
OM_xl: Read in operating model parameters from Excel spreadsheet
OneRep: Make stochastic variables certain for only one rep
optBH: Wrapper for estimating stock recruitment parameters from...
optQ_cpp: Rcpp version of the q Optimizer
ourReefFish: Example data object
Perfect_Imp: Perfect_Imp Imp
Perfect_Info: Perfect_Info Obs
plot-Data: Plot Data object
plot-Fleet: Plot the Fleet object parameters
plotFun: Print out plotting functions
plot-Imp: Plot the Implementation object parameters
plot-MSE: Plot MSE object
plot-Obs: Plot the Observation object parameters
plotOFL: A generic OFL plot for NOAA use
plot-OM: Plot the operating model (OM) object parameters
plot-Stock: Plot the Stock object parameters
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...
Precise_Biased: Precise_Biased Obs
Precise_Unbiased: Precise_Unbiased Obs
projOpt_cpp: Rcpp version of the Projection Optimizer
qopt: Internal optimization function that find the catchability (q...
Range: Standardize values
Rcontrol: Harvest Control Rule using prior for intrinsic rate of...
Rcontrol2: MP using prior for intrinsic rate of increase with a...
RD_GOM: RD_GOM OM
read.control.file: Reads iSCAM control file
read.data.file: Reads iSCAM dat file
read.mcmc: Reads iSCAM mcmc output files
read.par.file: Reads iSCAM parameter file
read.projection.file: Reads iSCAM projection file
read.report.file: Reads iSCAM Rep file
Red_snapper: Red_snapper Data
Red_Snapper_GOM: Red_Snapper_GOM OM
Red_snapper_GOM_SS: Red_snapper_GOM_SS OM
Replace: Replace an existing Stock, Fleet, Obs, or Imp object
replic8: Enlarge (replicate) a DLM data object to create an additional...
Required: What methods need what data
Rockfish: Rockfish Stock
Rougheye_Rockfish_BC: Rougheye_Rockfish_BC OM
runInMP: Runs input control MPs on a Data object.
runMSE: Run a Management Strategy Evaluation
runMSErobust: Run a Management Strategy Evaluation
Sam: Conduct stock assessment
sampy: Sample vector
San_Francisco_Bay_herring_California: San_Francisco_Bay_herring_California OM
SBT1: SBT simple MP
SBT2: SBT complex MP
sdconv: Get log normal standard deviation from transformed space mean...
SelectFun: Selectivity at length function
Sense: Sensitivity analysis
SetRecruitCycle: Function to calculate cyclic recruitment pattern given...
setup: Setup parallel processing
SG_GOM: SG_GOM OM
SH_GOM: SH_GOM OM
Simulation_1: Simulation_1 Data
SketchFun: Manually map the historical relative fishing effort...
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...
SRAcomp: Plot simulation test of Stochastic SRA method
SRAsim: Simulates catch at age and catch history data for testing SRA...
SRopt: Function that returns a stochastic estimate of steepness...
SS2DLM: Reads MLE estimates from Stock Synthesis file structure into...
StochasticSRA: Stochastic SRA construction of operating models
Stock-class: Class "Stock"
Sub: Subset MSE object by management procedure (MP) or simulation.
SubOM: Subset a Stock, Fleet, Obs, or Imp object from an OM object
summary-Data: Summary of Data object
summary-MSE: Summary of MSE object
Swordfish_OM: Swordfish_OM OM
TAC: Calculate TAC recommendations for more than one MP
TACfilter: TAC Filter
Target_All_Fish: Target_All_Fish Fleet
Targeting_Small_Fish: Targeting_Small_Fish Fleet
tdlnorm: Calculate density of log-normally distributed random numbers
testOM: testOM OM
Toothfish: Toothfish Stock
Tplot: A trade-off plot for an MSE object
Tplot2: A shorter version of the plot method for MSEs that just shows...
TradePlot: Generic Trade-off Plot
trlnorm: Generate log-normally distributed random numbers
TwoSidedFun: Internal Two sided selectivity curve
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
WM_GOM: WM_GOM OM
wormplot: Biomass wormplot
writeCSV: Internal function to write CSVs for objects
Yellowfin_Tuna_IO: Yellowfin_Tuna_IO OM
Yellowfin_tuna_IO_SS: Yellowfin_tuna_IO_SS OM
YM_GOM: YM_GOM OM
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...

Functions

AJ_GOM Man page
Albacore Man page
Arrowtooth_Flounder_BC_DFO_iSCAM Man page
Atlantic_mackerel Man page
AvC Man page Source code
BK Man page Source code
BK_CC Man page Source code
BK_ML Man page Source code
BlankSelPlot Man page Source code
Blow_opt Man page Source code
Blue_shark Man page
Bluefin_tuna Man page
Bluefin_tuna_WAtl Man page
Butterfish Man page
CC Source code
CC1 Man page Source code
CC4 Man page Source code
COSEWIC_plot Man page Source code
CSRA Man page Source code
CSRAfunc Man page Source code
Can Man page Source code
Canary_Rockfish_BC_DFO Man page
Cant Man page Source code
CheckConverg Man page Source code
CheckSelect Source code
China_rockfish Man page
ChooseEffort Man page Source code
ChooseL5 Source code
ChooseLFS Source code
ChooseSelect Man page Source code
ChooseVmaxlen Source code
Cobia Man page
CompSRA Man page Source code
CompSRA4010 Man page Source code
Converge Man page Source code
Cplot Man page Source code
DAAC Man page Source code
DBSRA Man page Source code
DBSRA4010 Man page Source code
DBSRA_40 Man page Source code
DBSRA_ML Man page Source code
DBSRAopt Source code
DCAC Man page Source code
DCAC4010 Man page Source code
DCAC_40 Man page Source code
DCAC_ML Man page Source code
DD Man page Source code
DD4010 Man page Source code
DD_R Source code
DDe Man page Source code
DDe75 Man page Source code
DDes Man page Source code
DFO_Kobe Source code
DFO_Kobe_TS Source code
DFO_hist Man page Source code
DFO_plot2 Man page Source code
DFO_proj Man page Source code
DLMDataDir Man page Source code
DLMdiag Source code
DLMtool Man page
DLMtool-package Man page
DOM Man page Source code
DTe40 Man page Source code
DTe50 Man page Source code
Darnley_Bay_Char_DFO Man page
Data-class Man page
DecE_Dom Man page
DecE_HDom Man page
DecE_NDom Man page
DepF Man page Source code
DynF Man page Source code
EtargetLopt Man page Source code
Example_datafile Man page
FMSYopt Man page Source code
FMSYref Man page Source code
FMSYref50 Man page Source code
FMSYref75 Man page Source code
Fadapt Man page Source code
Fdem Man page Source code
Fdem_CC Man page Source code
Fdem_ML Man page Source code
Fease Man page Source code
Fease-class Man page
Fease_xl Man page Source code
Feasibility Man page
Feasibility2 Man page
FitSelect Source code
FlatE_Dom Man page
FlatE_HDom Man page
FlatE_NDom Man page
Fleet-class Man page
ForceCor Man page Source code
Fratio Man page Source code
Fratio4010 Man page Source code
Fratio_CC Man page Source code
Fratio_ML Man page Source code
GB_CC Man page Source code
GB_slope Man page Source code
GB_target Man page Source code
Gcontrol Man page Source code
GenLenFun Source code
Generic_DecE Man page
Generic_FlatE Man page
Generic_IncE Man page
Generic_fleet Man page
Generic_obs Man page
GetStat Source code
Gulf_blue_tilefish Man page
HDAAC Man page Source code
Herring Man page
IT10 Man page Source code
IT5 Man page Source code
ITM Man page Source code
ITe10 Man page Source code
ITe5 Man page Source code
Imp-class Man page
Imprecise_Biased Man page
Imprecise_Unbiased Man page
IncE_Dom Man page
IncE_HDom Man page
IncE_NDom Man page
Input Man page Source code
Islope1 Man page Source code
Islope4 Man page Source code
Itarget1 Man page Source code
Itarget4 Man page Source code
ItargetE1 Man page Source code
ItargetE4 Man page Source code
Jplot Man page Source code
Kplot Man page Source code
L2A Man page Source code
L95target Man page Source code
LAJ_GOM Man page
LBSPR Man page Source code
LBSPR_ItEff Man page Source code
LBSPR_ItSel Man page Source code
LBSPR_ItTAC Man page Source code
LSRA Man page Source code
LSRA2 Man page Source code
LSRA_opt Man page Source code
LS_GOM Man page
LinInterp Man page Source code
Low_Effort_Non_Target Man page
LstepCC1 Man page Source code
LstepCC4 Man page Source code
LstepCE1 Man page Source code
LstepCE2 Man page Source code
Ltarget1 Man page Source code
Ltarget4 Man page Source code
LtargetE1 Man page Source code
LtargetE4 Man page Source code
MCD Man page Source code
MCD4010 Man page Source code
ML2D Man page Source code
MLne Source code
MPStats Man page Source code
MRnoreal Man page Source code
MRreal Man page Source code
MSE-class Man page
Mackerel Man page
NAor0 Man page Source code
NFref Man page Source code
NOAA_plot Man page Source code
Needed Man page Source code
OM-class Man page
OM_xl Man page Source code
Obs-class Man page
ObsTSplot Source code
OneRep Man page Source code
Perfect_Imp Man page
Perfect_Info Man page
Porgy Man page
Pplot Man page Source code
Pplot2 Man page Source code
Precise_Biased Man page
Precise_Unbiased Man page
RD_GOM Man page
Range Man page Source code
Rcontrol Man page Source code
Rcontrol2 Man page Source code
Red_Snapper_GOM Man page
Red_snapper Man page
Red_snapper_GOM_SS Man page
Replace Man page Source code
Required Man page Source code
Rockfish Man page
Rougheye_Rockfish_BC Man page
SBT1 Man page Source code
SBT2 Man page Source code
SG_GOM Man page
SH_GOM Man page
SPMSY Man page Source code
SPSRA Man page Source code
SPSRA_ML Man page Source code
SPSRAopt Source code
SPmod Man page Source code
SPslope Man page Source code
SRAFMSY Source code
SRAcomp Man page Source code
SRAfunc Source code
SRAsim Man page Source code
SRopt Man page Source code
SS2DLM Man page Source code
Sam Man page Source code
San_Francisco_Bay_herring_California Man page
SelectFun Man page Source code
SelectFunGTG Source code
Sense Man page Source code
SetRecruitCycle Man page Source code
Simulation_1 Man page
SketchFun Man page Source code
Snapper Man page
Sole Man page
Splot Man page Source code
StatLab Source code
StochasticSRA Man page Source code
Stock-class Man page
Sub Man page Source code
SubOM Man page Source code
Swordfish_OM Man page
TAC Man page Source code
TACfilter Man page Source code
TSKplot Source code
TSplot Source code
Target_All_Fish Man page
Targeting_Small_Fish Man page
Toothfish Man page
Tplot Man page Source code
Tplot2 Man page Source code
TradePlot Man page Source code
TwoSidedFun Man page Source code
VOI Man page Source code
VOI2 Man page Source code
VOIplot Man page Source code
VPA Source code
VPAFMSY Source code
VPAopt Source code
WM_GOM Man page
YM_GOM Man page
YPR Man page Source code
YPR_CC Man page Source code
YPR_ML Man page Source code
YPRopt Source code
Yellowfin_Tuna_IO Man page
Yellowfin_tuna_IO_SS Man page
add_zones Source code
alphaconv Man page Source code
avail Man page Source code
barplot.MSE Man page Source code
betaconv Man page Source code
bheq Source code
bhnoneq Source code
bhnoneq_LL Source code
boxplot.Data Man page Source code
boxplot.MSE Man page Source code
calc.mcmc Source code
calcMSESense Source code
calcStat Source code
checkMSE Man page Source code
comp Source code
compplot Man page Source code
condmet Man page Source code
cparnamecheck Source code
cparscheck Man page Source code
curE Man page Source code
curE75 Man page Source code
cv Man page Source code
demofn Source code
demographic2 Source code
densnorm Source code
densnormasc Source code
densnormdesc Source code
doprojPI Man page Source code
doprojPI_cpp Man page Source code
encircle Source code
euc.dist Source code
extract.area.sex.matrices Source code
extract.group.matrices Source code
fetch.file.names Man page Source code
fn Source code
genLenComp Man page Source code
getAFC Man page Source code
getBH Man page Source code
getBlow Man page Source code
getDNvulnS Source code
getEffhist Man page Source code
getFMSY Man page Source code
getFMSY2 Man page Source code
getFhist Source code
getFref Man page Source code
getFref2 Man page Source code
getGpars Man page Source code
getSlope1 Man page Source code
getSlope2 Man page Source code
getSlopeFun Man page Source code
getTAC Source code
getclass Man page Source code
getdep Source code
getinitdist Source code
getmov Man page Source code
getmov2 Man page Source code
getn Source code
getq Man page Source code
getq2 Man page Source code
getr Source code
getroot Man page Source code
getsdasc Source code
getsddesc Source code
gettempvar Man page Source code
gety Source code
iSCAM2DLM Man page Source code
iVB Source code
identifyPch Source code
initialize,DLM_general-method Man page
initialize,Data-method Man page
initialize,Fease-method Man page
initialize,Fleet-method Man page
initialize,MSE-method Man page
initialize,OM-method Man page
initialize,Obs-method Man page
initialize,Stock-method Man page
initialize,lmmodel-method Man page
initialize-methods Man page
joinMSE Man page Source code
lmmodel-class Man page
load.iscam.files Man page Source code
makePerf Man page Source code
makeTransparent Man page Source code
matlenlim Man page Source code
matlenlim2 Man page Source code
mconv Man page Source code
minlenLopt1 Man page Source code
movdistil Man page Source code
movfit Man page Source code
movfit_Rcpp Man page Source code
needed Source code
negcorlogspace Man page Source code
optBH Man page Source code
optQ_cpp Man page Source code
ourReefFish Man page Man page
parallelMPs Source code
plot,Data,ANY-method Man page
plot,MSE,ANY-method Man page
plot.Fleet Man page Source code
plot.Imp Man page Source code
plot.OM Man page Source code
plot.Obs Man page Source code
plot.Stock Man page Source code
plotFun Man page Source code
plotOFL Man page Source code
prodPTF Source code
projOpt_cpp Man page Source code
qopt Man page Source code
range01 Man page Source code
read.control.file Man page Source code
read.data.file Man page Source code
read.mcmc Man page Source code
read.par.file Man page Source code
read.projection.file Man page Source code
read.report.file Man page Source code
replic8 Man page Source code
runInMP Man page Source code
runMSE Man page Source code
runMSErobust Man page Source code
sampy Man page Source code
sdconv Man page Source code
setup Man page Source code
slotlim Man page Source code
someplot Source code
strip.areas.groups Source code
strip.static.params Source code
summary,Data-method Man page
summary,MSE-method Man page
tdlnorm Man page Source code
testOM Man page
tradeoffplot Source code
tradeoffplot2 Source code
tradeoffplot3 Source code
tradeoffplot4 Source code
trlnorm Man page Source code
updateMSE Man page Source code
wormplot Man page Source code
writeCSV Man page Source code

Files

inst
inst/Atlantic_mackerel.csv
inst/Cobia.csv
inst/Simulation_1.csv
inst/Gulf_blue_tilefish.csv
inst/Red_snapper.csv
inst/ourReefFish.csv
inst/China_rockfish.csv
inst/Example_datafile.csv
src
src/movefit_Rcpp.cpp
src/projOpt_cpp.cpp
src/genLenComp.cpp
src/bhnoneq_Rcpp.cpp
src/DLMtool_init.c
src/doprojPI_cpp.cpp
src/RcppExports.cpp
src/optQ_cpp.cpp
NAMESPACE
NEWS.md
data
data/Canary_Rockfish_BC_DFO.RData
data/Feasibility.RData
data/Rockfish.RData
data/Simulation_1.RData
data/Perfect_Imp.RData
data/DecE_HDom.RData
data/Red_snapper_GOM_SS.RData
data/YM_GOM.RData
data/IncE_HDom.RData
data/RD_GOM.RData
data/Darnley_Bay_Char_DFO.RData
data/Example_datafile.RData
data/Sole.RData
data/IncE_Dom.RData
data/Albacore.RData
data/Snapper.RData
data/Yellowfin_tuna_IO_SS.RData
data/Low_Effort_Non_Target.RData
data/Blue_shark.RData
data/Targeting_Small_Fish.RData
data/Rougheye_Rockfish_BC.RData
data/Target_All_Fish.RData
data/Generic_DecE.RData
data/Imprecise_Unbiased.RData
data/Perfect_Info.RData
data/ourReefFish.RData
data/Toothfish.RData
data/LAJ_GOM.RData
data/Butterfish.RData
data/Precise_Biased.RData
data/Mackerel.RData
data/DecE_NDom.RData
data/Red_Snapper_GOM.RData
data/Bluefin_tuna.RData
data/testOM.RData
data/SG_GOM.RData
data/Yellowfin_Tuna_IO.RData
data/Cobia.RData
data/Generic_obs.RData
data/Precise_Unbiased.RData
data/Generic_FlatE.RData
data/FlatE_NDom.RData
data/Gulf_blue_tilefish.RData
data/SH_GOM.RData
data/Feasibility2.RData
data/Swordfish_OM.RData
data/datalist
data/DecE_Dom.RData
data/Red_snapper.RData
data/WM_GOM.RData
data/Generic_IncE.RData
data/Arrowtooth_Flounder_BC_DFO_iSCAM.RData
data/Generic_fleet.RData
data/FlatE_Dom.RData
data/Imprecise_Biased.RData
data/San_Francisco_Bay_herring_California.RData
data/China_rockfish.RData
data/Bluefin_tuna_WAtl.RData
data/Porgy.RData
data/LS_GOM.RData
data/Herring.RData
data/AJ_GOM.RData
data/IncE_NDom.RData
data/Atlantic_mackerel.RData
data/FlatE_HDom.RData
R
R/plotOM.R
R/Replace.r
R/SubOM.r
R/plotStock.r
R/Output.r
R/plotFleet.r
R/MiscInt.r
R/MSEObj.r
R/DFO.R
R/XLloadfuns.r
R/LBSPR_MPs.r
R/MiscFuns.r
R/dataObjects.r
R/DefineClasses.r
R/Input.r
R/runMSE.r
R/iSCAM2DLM.R
R/RcppExports.R
R/DataObj.r
R/SS2DLM.R
R/DLMtool-package.R
R/Blow_funcs.R
R/StochasticSRA.R
R/ChooseEffort.r
R/ChooseSelect.r
R/plotObsImp.R
R/runMSErobust.r
R/cpars.R
README.md
MD5
DESCRIPTION
man
man/Feasibility2.Rd
man/SRAsim.Rd
man/Gcontrol.Rd
man/movdistil.Rd
man/plot-OM.Rd
man/getSlopeFun.Rd
man/DynF.Rd
man/SelectFun.Rd
man/Imp-class.Rd
man/SRAcomp.Rd
man/Generic_FlatE.Rd
man/plot-Stock.Rd
man/Rcontrol2.Rd
man/GB_CC.Rd
man/testOM.Rd
man/VOI.Rd
man/SPslope.Rd
man/Required.Rd
man/Splot.Rd
man/FMSYref50.Rd
man/DTe50.Rd
man/SG_GOM.Rd
man/Cobia.Rd
man/summary-Data.Rd
man/ITM.Rd
man/getFref2.Rd
man/ItargetE4.Rd
man/lmmodel-class.Rd
man/DBSRA.Rd
man/Sub.Rd
man/getGpars.Rd
man/Generic_obs.Rd
man/Perfect_Imp.Rd
man/Atlantic_mackerel.Rd
man/SetRecruitCycle.Rd
man/WM_GOM.Rd
man/CompSRA.Rd
man/cv.Rd
man/alphaconv.Rd
man/matlenlim2.Rd
man/Fdem_CC.Rd
man/Ltarget4.Rd
man/OM_xl.Rd
man/BK_CC.Rd
man/Porgy.Rd
man/SBT1.Rd
man/getclass.Rd
man/Tplot.Rd
man/tdlnorm.Rd
man/Fdem.Rd
man/Sole.Rd
man/Fdem_ML.Rd
man/read.control.file.Rd
man/YPR_CC.Rd
man/plot-MSE.Rd
man/Albacore.Rd
man/avail.Rd
man/Sense.Rd
man/Rockfish.Rd
man/StochasticSRA.Rd
man/GB_target.Rd
man/IncE_HDom.Rd
man/curE.Rd
man/LBSPR_ItSel.Rd
man/COSEWIC_plot.Rd
man/Blow_opt.Rd
man/Data-class.Rd
man/getAFC.Rd
man/DFO_plot2.Rd
man/optQ_cpp.Rd
man/LBSPR_ItEff.Rd
man/Butterfish.Rd
man/Snapper.Rd
man/DLMtool-package.Rd
man/getq2.Rd
man/Herring.Rd
man/Needed.Rd
man/AJ_GOM.Rd
man/Mackerel.Rd
man/getFref.Rd
man/FMSYref.Rd
man/DCAC_ML.Rd
man/plot-Fleet.Rd
man/YPR_ML.Rd
man/makePerf.Rd
man/Toothfish.Rd
man/read.data.file.Rd
man/Itarget4.Rd
man/plot-Imp.Rd
man/movfit_Rcpp.Rd
man/LSRA_opt.Rd
man/wormplot.Rd
man/read.report.file.Rd
man/mconv.Rd
man/Red_snapper.Rd
man/Pplot2.Rd
man/SBT2.Rd
man/updateMSE.Rd
man/getFMSY.Rd
man/DDe75.Rd
man/Precise_Unbiased.Rd
man/SketchFun.Rd
man/Stock-class.Rd
man/slotlim.Rd
man/SPMSY.Rd
man/getmov.Rd
man/matlenlim.Rd
man/IT5.Rd
man/MPStats.Rd
man/EtargetLopt.Rd
man/Rcontrol.Rd
man/SS2DLM.Rd
man/Target_All_Fish.Rd
man/Perfect_Info.Rd
man/YM_GOM.Rd
man/Darnley_Bay_Char_DFO.Rd
man/Fratio_ML.Rd
man/Yellowfin_tuna_IO_SS.Rd
man/initialize-methods.Rd
man/LAJ_GOM.Rd
man/TwoSidedFun.Rd
man/DecE_Dom.Rd
man/Fratio4010.Rd
man/Converge.Rd
man/IT10.Rd
man/Itarget1.Rd
man/VOI2.Rd
man/summary-MSE.Rd
man/iSCAM2DLM.Rd
man/DCAC.Rd
man/ChooseEffort.Rd
man/LstepCE2.Rd
man/DD.Rd
man/LBSPR.Rd
man/Fratio_CC.Rd
man/LSRA.Rd
man/SubOM.Rd
man/CSRA.Rd
man/getmov2.Rd
man/Fease_xl.Rd
man/load.iscam.files.Rd
man/TACfilter.Rd
man/CC1.Rd
man/Feasibility.Rd
man/runMSErobust.Rd
man/AvC.Rd
man/Ltarget1.Rd
man/TradePlot.Rd
man/getEffhist.Rd
man/curE75.Rd
man/DFO_proj.Rd
man/China_rockfish.Rd
man/MRnoreal.Rd
man/compplot.Rd
man/Canary_Rockfish_BC_DFO.Rd
man/DFO_hist.Rd
man/FlatE_NDom.Rd
man/DBSRA_ML.Rd
man/IncE_NDom.Rd
man/HDAAC.Rd
man/MCD.Rd
man/runMSE.Rd
man/ML2D.Rd
man/MSE-class.Rd
man/DDes.Rd
man/plotFun.Rd
man/ITe10.Rd
man/doprojPI_cpp.Rd
man/BK_ML.Rd
man/Fease.Rd
man/DepF.Rd
man/GB_slope.Rd
man/Blue_shark.Rd
man/fetch.file.names.Rd
man/read.mcmc.Rd
man/DDe.Rd
man/DTe40.Rd
man/trlnorm.Rd
man/betaconv.Rd
man/MCD4010.Rd
man/DCAC4010.Rd
man/DAAC.Rd
man/getFMSY2.Rd
man/Generic_IncE.Rd
man/VOIplot.Rd
man/Fadapt.Rd
man/LstepCE1.Rd
man/gettempvar.Rd
man/Generic_DecE.Rd
man/LstepCC4.Rd
man/Bluefin_tuna_WAtl.Rd
man/CSRAfunc.Rd
man/DLMDataDir.Rd
man/Arrowtooth_Flounder_BC_DFO_iSCAM.Rd
man/DD4010.Rd
man/Input.Rd
man/CompSRA4010.Rd
man/Imprecise_Unbiased.Rd
man/MRreal.Rd
man/LinInterp.Rd
man/ItargetE1.Rd
man/Red_Snapper_GOM.Rd
man/Generic_fleet.Rd
man/Obs-class.Rd
man/DOM.Rd
man/writeCSV.Rd
man/LtargetE1.Rd
man/NAor0.Rd
man/barplot.MSE.Rd
man/SPmod.Rd
man/Red_snapper_GOM_SS.Rd
man/FlatE_Dom.Rd
man/TAC.Rd
man/Can.Rd
man/getSlope1.Rd
man/BK.Rd
man/Low_Effort_Non_Target.Rd
man/Swordfish_OM.Rd
man/NOAA_plot.Rd
man/RD_GOM.Rd
man/Tplot2.Rd
man/getBlow.Rd
man/SH_GOM.Rd
man/FMSYopt.Rd
man/Fratio.Rd
man/sampy.Rd
man/plot-Obs.Rd
man/joinMSE.Rd
man/Bluefin_tuna.Rd
man/SPSRA_ML.Rd
man/getBH.Rd
man/getroot.Rd
man/L95target.Rd
man/checkMSE.Rd
man/SPSRA.Rd
man/BlankSelPlot.Rd
man/makeTransparent.Rd
man/Jplot.Rd
man/read.par.file.Rd
man/Islope4.Rd
man/DBSRA_40.Rd
man/minlenLopt1.Rd
man/Yellowfin_Tuna_IO.Rd
man/Fleet-class.Rd
man/Pplot.Rd
man/Range.Rd
man/getSlope2.Rd
man/LSRA2.Rd
man/Precise_Biased.Rd
man/Targeting_Small_Fish.Rd
man/LstepCC1.Rd
man/DecE_NDom.Rd
man/CC4.Rd
man/LtargetE4.Rd
man/ForceCor.Rd
man/plotOFL.Rd
man/boxplot.Data.Rd
man/LS_GOM.Rd
man/cparscheck.Rd
man/getq.Rd
man/San_Francisco_Bay_herring_California.Rd
man/Kplot.Rd
man/projOpt_cpp.Rd
man/plot-Data.Rd
man/Replace.Rd
man/boxplot.MSE.Rd
man/CheckConverg.Rd
man/FlatE_HDom.Rd
man/runInMP.Rd
man/Islope1.Rd
man/DecE_HDom.Rd
man/ChooseSelect.Rd
man/qopt.Rd
man/Rougheye_Rockfish_BC.Rd
man/condmet.Rd
man/setup.Rd
man/genLenComp.Rd
man/L2A.Rd
man/optBH.Rd
man/negcorlogspace.Rd
man/YPR.Rd
man/DBSRA4010.Rd
man/Fease-class.Rd
man/ITe5.Rd
man/Gulf_blue_tilefish.Rd
man/Simulation_1.Rd
man/sdconv.Rd
man/Cant.Rd
man/Example_datafile.Rd
man/FMSYref75.Rd
man/ourReefFish.Rd
man/doprojPI.Rd
man/Imprecise_Biased.Rd
man/replic8.Rd
man/OM-class.Rd
man/Cplot.Rd
man/LBSPR_ItTAC.Rd
man/NFref.Rd
man/read.projection.file.Rd
man/IncE_Dom.Rd
man/movfit.Rd
man/OneRep.Rd
man/SRopt.Rd
man/DCAC_40.Rd
man/Sam.Rd
DLMtool documentation built on May 19, 2017, 10:51 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.