FLCore-package {FLCore} | R Documentation

## Core package of FLR, fisheries modelling in R.

### Description

FLCore contains the core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at http://flr-project.org/, including a development mailing list.

### Details

Package: | FLCore
Version: | 1.99-111
Date: | 2008
Depends: | methods, R(>= 2.8.0), graphics, stats, stats4, grid, lattice
License: | GPL 2 or above
Collate: | FLArray.R FLQuant.R FLQuantPoint.R FLAccesors.R FLComp.R FLlst-class.R FLStock.R FLCatch.R FLQuants-methods.R FLPar.R io.FLStock.R FLBiol.R FLCohort.R FLMetier.R FLFleet.R FLIndex.R FLlst-methods.R io.FLIndices.R FLModel.R FLSR.R SRmodels.R FLtest.R coerce.R zzz.R
LazyLoad: | Yes
LazyData: | Yes
Built: | R 2.8.1; i686-pc-linux-gnu; 2009-01-22 12:08:46; unix

Classes:

    FLArray                 Class FLArray
    FLBiol                  Class FLBiol
    FLBiols                 Class FLBiols
    FLCatch                 Class FLCatch
    FLCatches               Class FLCatches
    FLCohort                Class FLCohort
    FLCohorts               Class FLCohorts
    FLComp                  Class FLComp
    FLFleet                 Class FLFleet
    FLFleets                Class FLFleets
    FLIndex-class           Class FLIndex
    FLIndices               Class FLIndices
    FLMetier-class          Class FLMetier
    FLMetiers               Class FLMetiers
    FLModel                 Class FLModel for statistical models
    FLPar                   Class FLPar
    FLQuant                 FLQuant class for numerical data
    FLQuantPoint            Class FLQuantPoint
    FLQuants                Class FLQuants
    FLSR                    Class FLSR
    FLStock-class           Class FLStock
    FLStocks                Class FLStocks
    FLlst                   Class FLlst

Methods:

    AIC                     Akaike information criterion (AIC) method
    Arith                   Arithmetic methods for FLQuant objects
    BIC                     Bayesian information criterion (BIC) method
    E                       Method E
    FLBiols-methods         Method FLBiols
    FLCatch-accesors        Accesor and replacement methods for the FLCatch
                            class
    FLCatch-methods         Method FLCatch
    FLCatches-methods       Method FLCatches
    FLCohort-methods        Method FLCohort
    FLCohorts-methods       Method FLCohorts
    FLCore-package          FLCore package of the FLR system
    FLFleet-methods         Method FLFleet
    FLFleets-methods        Method FLFleets
    FLIndex                 Create FLIndex objects
    FLIndices-methods       Method FLIndices
    FLMetier-methods        Method FLMetier
    FLMetiers-methods       Method FLMetiers
    FLModel-methods         Method FLModel
    FLPar-methods           Method FLPar
    FLQuant-methods         Create FLQuant objects
    FLQuantPoint-accesors   Method lowq
    FLQuantPoint-methods    Method FLQuantPoint
    FLQuants-methods        Method FLQuants
    FLSR-methods            Method FLSR
    FLStock                 Create FLStock objects
    FLStocks-methods        Method FLStocks
    FLlst-methods           Method FLlst
    FLtest                  FLtest functions for running simple units tests
    SRModelName             Convenience function to identify an SR model by
                            its formula
    SRModels                Stock-Recruitment models
    [,FLArray,ANY,ANY-method
                            Extract or Replace Parts of an FLR Object
    ac                      FLCore-internal
    apply,ANY,missing,missing-method
                            Method apply
    as.FLBiol               Old S3 coercion methods
    as.data.frame,ANY,ANY,ANY-method
                            Method as.data.frame
    barchart,ANY,ANY-method
                            Method barchart
    bkey                    Generate key for bubbles plot
    bubbles                 Bubbles plot
    catchNames              Method catchNames
    ccplot                  Catch-curves plot
    coerce,FLlst,list-method
                            Method coerce
    computeCatch            Methods to compute total catch, landings,
                            discards and stock biomass
    createFLAccesors        Create accesor methods for a given class
    cv                      Coefficient of Variation of FLR objects with
                            multiple iterations
    dimnames<-,ANY,missing-method
                            Modify dimnames of an FLQuant
    dims                    List with information on object dimensions
    expand                  Trim FLR objects using named dimensions
    fbar                    Calculates mean harvest rate or fishing
                            mortality
    flc2flq                 Coerce FLCohort into FLQuant.
    fmle                    Method fmle
    harvest,FLBiol-method   Harvest calculations for FLBiol
    is.FLBiol               Methods to determine the class of a given
                            object
    iter                    Select or modify iterations of an FLR object
    iters                   Method iters
    jacknife                Jacknife resampling
    lapply,ANY,missing-method
                            Method lapply
    leslie                  Method for calculating Leslie matrix dynamics
                            of an FLBiol object
    lowess,FLSR,missing-method
                            Method lowess
    mcf                     Method mcf
    mean,ANY-method         Method mean
    mean.lifespan           Method for calculating mean lifespan, given the
                            natural mortality
    median,ANY,missing-method
                            Method median
    mergeFLStock            Merging FLStock objects
    metier                  Method metier
    model.frame,ANY-method
                            Method model.frame
    name                    Accesor and replacement methods for complex S4
                            classes
    names,ANY-method        Method names
    nls,ANY,ANY,missing,missing,missing,missing,missing,missing,missing,missing,missing,missing-method
                            Method nls
    ple4                    FLCore datasets
    plot,ANY,ANY-method     Method plot
    predict,ANY-method      Method predict
    print,ANY-method        Method print
    propagate               Extend an FLQuant along the iter dimension
    pv                      Population variability
    qapply                  Method qapply
    quant                   Method quant
    quantSums               Methods to compute sums, means and vars of
                            FLQuant objects
    quantTotals             Method quantTotals
    quantile,ANY-method     Method quantile
    r                       Method for calculating intrinsic rate of
                            increase from an FLBiol object
    range-methods           Method range
    readVPAFile             Input/Output of FLR objects
    revenue                 Method revenue
    rgamma,ANY,ANY,ANY,ANY-method
                            Method rgamma
    rlnorm,ANY,ANY,ANY-method
                            Method rlnorm
    rnorm,ANY,ANY,ANY-method
                            Method rnorm
    rpois,ANY,ANY,ANY-method
                            Method rpois
    sd,FLModel,missing-method
                            Standard deviation of an FLModel object
    setPlusGroup            Method setPlusGroup
    show,ANY-method         Method show
    sop                     Calculates the sum of products correction
    splom,ANY,ANY-method    Method splom
    spr0                    Method spr0
    sr                      Stock-recruitment model function
    ssb                     Method ssb
    ssbpurec                Method ssbpurec
    ssn                     Method ssn
    stripplot,ANY,ANY-method
                            Method stripplot
    summary,ANY-method      Method summary
    survprob                Method for calculating survival probabilties
                            given mortaloty in the FLBiol object
    sweep-methods           Sweep out FLQuant Summaries
    transform,ANY-method    Transform elements of a complex FLR object
    trim                    Trim FLR objects using named dimensions
    units,ANY-method        units attribute for FLQuant objects
    update,FLModel-method   Method update
    upper                   Methods upper and lower
    var,ANY,missing,missing,missing-method
                            Variance of an FLPar
    window,ANY-method       Extract time (year) windows of an FLR object

### Author(s)

FLR Team and various contributors. Initial design by Laurence T. Kell & Philippe Grosjean.

Maintainer: FLR Team <flr-team@flr-project.org>

### References

Website at http://flr-project.org/

Kell L.T., Mosqueira I., Grosjean P., Fromentin J-M., Garcia D., Hillary R., Jardim E., Pastoors M., Poos J.J., Scott F. & Scott R.D. 2007. FLR: an open-source framework for the evaluation and development of management strategies. ICES J. of Mar. Sci. 20: 289-290.

[Package FLCore version 2.2 Index]