Albacore                Albacore Stock
Atlantic_mackerel       Atlantic_mackerel DLM_data
AvC                     Average Catch
BK                      Beddington and Kirkwood life-history MP (simple
                        version)
BK_CC                   Beddington and Kirkwood life-history method
                        combined with catch curve analysis
BK_ML                   Beddington and Kirkwood life-history analysis
                        with mean-length estimator of current abundance
Blue_shark              Blue_shark Stock
Bluefin_tuna            Bluefin_tuna Stock
Bluefin_tuna_WAtl       Bluefin_tuna_WAtl Stock
Butterfish              Butterfish Stock
CC1                     Constant catch management procedure of Geromont
                        and Butterworth (2014)
CC4                     Constant catch management procedure of Geromont
                        and Butterworth (2014)
CSRA                    Catch at size reduction analysis
CSRAfunc                Optimization function for CSRA
Can                     What data-limited methods can be applied to
                        this DLM_data object?
Cant                    What methods can't be applied to this DLM data
                        object
CheckConverg            MSE convergence diagnostic
China_rockfish          China_rockfish DLM_data
ChooseEffort            Manually map the historical relative fishing
                        effort trajectory.
ChooseSelect            Manually choose the historical selectivity
                        pattern
Cobia                   Cobia DLM_data
CompSRA                 Age-composition-based estimate of current stock
                        depletion given constant Z linked to an FMSY
                        estimate to provide OFL
CompSRA4010             Age-composition-based estimate of current stock
                        depletion given constant Z linked to an FMSY
                        estimate to provide OFL (with a 40-10 rule)
Converge                Check Convergence
Cplot                   Plot the median biomass and yield relative to
                        last historical year
DAAC                    Depletion Adjusted Average Catch
DBSRA                   Depletion-Based Stock Reduction Analysis
DBSRA4010               Depletion-Based Stock Reduction Analysis paired
                        with 40-10 harvest control rule
DBSRA_40                Depletion-Based Stock Reduction Analysis
                        assuming 40 per cent stock depletion
DBSRA_ML                Depletion-Based Stock Reduction Analysis using
                        mean length estimator of stock depletion
DCAC                    Depletion Corrected Average Catch
DCAC4010                Depletion Corrected Average Catch paired with
                        the 40-10 rule
DCAC_40                 Depletion Corrected Average Catch assuming 40
                        per cent stock depletion
DCAC_ML                 Depletion-Based Stock Reduction Analysis using
                        mean-length estimator of current depletion
DD                      Delay - Difference Stock Assessment with UMSY
                        and MSY leading
DD4010                  Delay - Difference Stock Assessment with UMSY
                        and MSY leading coupled with a 40-10 harvest
                        control rule
DDe                     Effort control version of DD - Delay -
                        Difference Stock Assessment with UMSY and MSY
                        leading
DDe75                   Effort control version of DD - Delay -
                        Difference Stock Assessment with UMSY and MSY
                        leading that fishes at 75 per cent of FMSY
DDes                    Effort searching version of DD - Delay -
                        Difference Stock Assessment with UMSY and MSY
                        leading that fishes at 75 per cent of FMSY
DLMDataDir              Directory of the installed package on your
                        computer
DLM_data-class          Class "DLM_data"
DLM_fease-class         Class "DLM_fease"
DLMtool-package         Data-Limited Methods Toolkit
DOM                     How dominant is an MP?
DTe40                   Effort searching MP aiming for 40 per cent
                        stock depletion
DTe50                   Effort searching MP aiming for 50 per cent
                        stock depletion
DecE_Dom                DecE_Dom Fleet
DecE_HDom               DecE_HDom Fleet
DecE_NDom               DecE_NDom Fleet
DepF                    Depletion Corrected Fratio
DynF                    Dynamic Fratio MP
EtargetLopt             Effort MP: adjust effort up/down if mean length
                        above/below Ltarget
Example_datafile        Example_datafile DLM_data
FMSYref                 A reference FMSY method (uses perfect
                        information about FMSY)
FMSYref50               A reference FMSY method that fishes at half of
                        FMSY (uses perfect information about FMSY)
FMSYref75               A reference FMSY method that fishes at three
                        quarters of FMSY (uses perfect information
                        about FMSY)
Fadapt                  An adaptive MP that uses trajectory in inferred
                        suplus production and fishing mortality rate to
                        update a TAC
Fdem                    Demographic FMSY method
Fdem_CC                 Demographic FMSY method using catch-curve
                        analysis to estimate recent Z
Fdem_ML                 Demographic FMSY method that uses mean length
                        data to estimate recent Z
Fease                   MP feasibility diagnostic
Fease_xl                Read in feasibility parameters from Excel
                        spreadsheet
Feasibility             Feasibility DLM_fease
Feasibility2            Feasibility2 DLM_fease
FlatE_Dom               FlatE_Dom Fleet
FlatE_HDom              FlatE_HDom Fleet
FlatE_NDom              FlatE_NDom Fleet
Fleet-class             Class "Fleet"
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 catch-curve estimate of recent Z
Fratio_ML               An FMSY/M ratio MP that uses a mean length
                        estimator of recent Z
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_IncE            Generic_IncE Fleet
Generic_fleet           Generic_fleet Fleet
Generic_obs             Generic_obs Observation
Gulf_blue_tilefish      Gulf_blue_tilefish DLM_data
HDAAC                   Hybrid Depletion Adjusted Average Catch
Herring                 Herring Stock
IT10                    Index Target 10
IT5                     Index Target 5
ITM                     Index Target based on natural mortality rate
ITe10                   Index Target Effort-Based 10
ITe5                    Index Target Effort-Based 5
Imprecise_Biased        Imprecise_Biased Observation
Imprecise_Unbiased      Imprecise_Unbiased Observation
IncE_Dom                IncE_Dom Fleet
IncE_HDom               IncE_HDom Fleet
IncE_NDom               IncE_NDom Fleet
Input                   Function to run a set of input control methods
Islope1                 A management procedure that incrementally
                        adjusts the TAC to maintain a constant CPUE or
                        relative abundance index
Islope4                 A management procedure that incrementally
                        adjusts the TAC to maintain a constant CPUE or
                        relative abundance index
Itarget1                A management procedure that incrementally
                        adjusts the TAC (starting from reference level
                        that is a fraction of mean recent catches) to
                        reach a target CPUE / relative abundance index
Itarget4                A management procedure that incrementally
                        adjusts the TAC (starting from reference level
                        that is a fraction of mean recent catches) to
                        reach a target CPUE / relative abundance index
ItargetE1               A management procedure that incrementally
                        adjusts the effort to reach a target CPUE /
                        relative abundance index
ItargetE4               A management procedure that incrementally
                        adjusts the Effort to reach a target CPUE /
                        relative abundance index
Jplot                   Joint probability plot
Kplot                   KOBE plot: a projection by projection plot of
                        F/FMSY and B/BMSY
L2A                     Length to age conversion
L95target               A management procedure that adjusts the TAC
                        up/down from reference (target) level (that is
                        a fraction of mean recent premanagement
                        catches) to reach a target mean length of fish
                        caught.
LBSPR                   Apply the Length-based SPR model to DLMtool
                        Data Object
LBSPR_ItEff             Length-based SPR model with HCR that
                        iteratively adjusts Effort
LBSPR_ItSel             Length-based SPR model with HCR that
                        iteratively adjusts Selectivity
LBSPR_ItTAC             Length-based SPR model with HCR that
                        iteratively adjusts TAC
Low_Effort_Non_Target   Low_Effort_Non_Target Fleet
LstepCC1                A management procedure that incrementally
                        adjusts the TAC according to the mean length of
                        recent catches.
LstepCC4                A management procedure that incrementally
                        adjusts the TAC according to the mean length of
                        recent catches.
LstepCE1                A management procedure that incrementally
                        adjusts the TAC according to the mean length of
                        recent catches.
LstepCE2                A management procedure that incrementally
                        adjusts the Effort according to the mean length
                        of recent catches.
Ltarget1                A management procedure that incrementally
                        adjusts the TAC to reach a target mean length
                        in catches.
Ltarget4                A management procedure that incrementally
                        adjusts the TAC to reach a target mean length
                        in catches.
LtargetE1               A management procedure that incrementally
                        adjusts the Effort to reach a target mean
                        length in catches.
LtargetE4               A management procedure that incrementally
                        adjusts the Effort to reach a target mean
                        length in catches.
MCD                     Mean Catch Depletion
MCD4010                 Mean Catch Depletion
ML2D                    Depletion and F estimation from mean length of
                        catches
MPStats                 Calculate Statistics for MP Performance
MRnoreal                An marine reserve in area 1 with no spatial
                        reallocation of fishing effort
MRreal                  An marine reserve in area 1 with full
                        reallocation of fishing effort
MSE-class               Class "MSE"
Mackerel                Mackerel Stock
NAor0                   Is a value NA or zero.
NFref                   No Fishing Reference MP
NOAA_plot               National Oceanographic and Atmospheric
                        Administration default plot 1
Needed                  Data needed to get MPs running
OM-class                Class "OM"
OM_xl                   Read in operating model parameters from Excel
                        spreadsheet
Observation-class       Class "Observation"
Perfect_Info            Perfect_Info Observation
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 yield
Precise_Biased          Precise_Biased Observation
Precise_Unbiased        Precise_Unbiased Observation
Range                   Standardize values
Rcontrol                Harvest Control Rule using prior for intrinsic
                        rate of increase
Rcontrol2               MP using prior for intrinsic rate of increase
                        with a quadratic approximation to surplus
                        production
Red_snapper             Red_snapper DLM_data
Required                What methods need what data
Rockfish                Rockfish Stock
SBT1                    SBT simple MP
SBT2                    SBT complex MP
SPMSY                   Catch trend Surplus Production MSY MP
SPSRA                   Surplus Production Stock Reduction Analysis
SPSRA_ML                Surplus Production Stock Reduction Analysis
                        using a mean-length estimate of current stock
                        depletion
SPmod                   Surplus production based catch-limit modifier
SPslope                 Slope in surplus production MP
Sam                     Conduct stock assessment
Sense                   Sensitivity analysis
SetRecruitCycle         Function to calculate cyclic recruitment
                        pattern given user-specified values of period
                        and amplitude.
Simulation_1            Simulation_1 DLM_data
SketchFun               Manually map the historical relative fishing
                        effort trajectory.
Snapper                 Snapper Stock
Sole                    Sole Stock
Splot                   Scatter plot of B/BMSY or B/B0 and F/FMSY for
                        lastYrs
Stock-class             Class "Stock"
Sub                     Subset MSE object by management procedure (MP)
                        or simulation.
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
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 the overall trade-offs
TradePlot               Generic Trade-off Plot
VOI                     Calculate Value Of Information
VOI2                    Calculate Value Of Information 2
VOIplot                 Yet another Value of Information Plot
YPR                     Yield Per Recruit analysis to get FMSY proxy
                        F01
YPR_CC                  Yield Per Recruit analysis to get FMSY proxy
                        F01 paired to a naive catch curve estimate of
                        recent Z
YPR_ML                  Yield Per Recruit analysis to get FMSY proxy
                        F01 paired with a mean-length estimate of
                        current stock size
alphaconv               Calculate alpha parameter for beta distribution
                        from mean and standard deviation
avail                   What objects of this class are available
barplot.MSE             Plot a barplot of MSE results
betaconv                Calculate beta parameter for beta distribution
                        from mean and standard deviation
boxplot.DLM_data        Boxplot of TAC recommendations
boxplot.MSE             Boxplot of MP performance from MSE object
checkMSE                Check that MSE object includes all slots
condmet                 Condition met?
curE                    Fishing at current effort levels
curE75                  Fishing at 75 per cent of current effort levels
cv                      Calculate CV from vector of values
genLenComp              Generate length composition of catch
getAFC                  Calculate age at first capture from length at
                        first capture and growth
getclass                get object class
getmov                  Optimization function to find a movement model
                        that matches user specified movement
                        characteristics.
getmov2                 Optimization function to find a movement model
                        that matches user specified movement
                        characteristics modified for Rcpp.
initialize-methods      ~~ Methods for Function 'initialize' ~~
joinMSE                 Join multiple MSE objects together
lmmodel-class           Class "lmmodel"
makePerf                Convert a OM object to one without observation
                        or process error
makeTransparent         Make colors transparent
matlenlim               A data-limited method in which fishing
                        vulnerability is set according to the maturity
                        curve
matlenlim2              A data-limited method in which fishing
                        vulnerability is set slightly higher than the
                        maturity curve
mconv                   Get log normal mean from transformed space mean
                        and standard deviation
minlenLopt1             This input control sets the minimum length of
                        fish caught to a fraction of the length that
                        maximises the biomass, Lopt.
movfit                  Optimization function that returns the squared
                        difference between user specified and
                        calculated movement parameters. (deprecated:
                        now in Rcpp)
movfit_Rcpp             Rcpp version of the Optimization function that
                        returns the squared difference between user
                        specified and calculated movement parameters.
mypars                  mypars DLM_general
ourReefFish             Example data object
plot,DLM_data-method    Plot DLM_data object
plot,MSE-method         Plot MSE object
plotFun                 Print out plotting functions
plotOFL                 A generic OFL plot for NOAA use
replic8                 Enlarge (replicate) a DLM data object to create
                        an additional dimension for simulation /
                        sensitivity testing
runInMP                 Runs input control MPs on a DLM_data object.
runMSE                  Run a Management Strategy Evaluation
runMSErobust            Run a Management Strategy Evaluation
sampy                   Sample vector
sdconv                  Get log normal standard deviation from
                        transformed space mean and standard deviation
setup                   Setup parallel processing
slotlim                 An data-limited method which sets a slot limit
summary,DLM_data-method
                        Summary of DLM_data object
summary,MSE-method      Summary of MSE object
tdlnorm                 Calculate density of log-normally distributed
                        random numbers
trlnorm                 Generate log-normally distributed random
                        numbers
updateMSE               Update an MSE object with new slots
wormplot                Biomass wormplot
writeCSV                Internal function to write CSVs for objects
