FLCore-package            package:FLCore            R Documentation

_C_o_r_e _p_a_c_k_a_g_e _o_f _F_L_R, _f_i_s_h_e_r_i_e_s _m_o_d_e_l_l_i_n_g _i_n _R.

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_D_e_t_a_i_l_s:


       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


_A_u_t_h_o_r(_s):

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

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

_R_e_f_e_r_e_n_c_e_s:

     Website at <URL: 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.

