FLSR                 package:FLCore                 R Documentation

_C_l_a_s_s _F_L_S_R

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

     Class for stock-recruitment models, based on 'FLModel-class'. Two
     extra 'FLQuant-class' slots are used for input data: 'rec' for the
      recruitment series, and 'ssb' for Spawning Stock Biomass or any
     other index of reproductive potential.

     All the main methods for this class are inherited from
     'FLModel-class',  although the plot method is specific to FLSR,
     and methods exist to access the specific 'FLQuant' slots, 'rec'
     and 'ssb'.

     A series of commonly-used stock-recruitment models are already
     available, including the correspodning likelihood functions and
     calculation of initial values. See  'SRModels' for more details
     and the exact formulation implemented for each of them.

_S_l_o_t_s:


     _n_a_m_e Name of the object. 'character'.

     _d_e_s_c Description of the object. 'character'.

     _r_a_n_g_e Range. 'numeric'.

     _r_e_c Recruitment series. 'FLQuant'.

     _s_s_b Index of reproductive potential. 'FLQuant'.

     _f_i_t_t_e_d Estimated values for rec. 'FLQuant'.

     _r_e_s_i_d_u_a_l_s Residuals obtained from the model fit. 'FLQuant'.

     _c_o_v_a_r Covariates for SR model. 'FLQuants'.

     _m_o_d_e_l Model formula. 'formula'.

     _g_r_a_d Function returning the gradient of the model. 'function'.

     _l_o_g_l Log-likelihood function. 'function'.

     _i_n_i_t_i_a_l Function returning initial parameter values for the
          optimizer. 'function'.

     _p_a_r_a_m_s Estimated parameter values. 'FLPar'.

     _l_o_g_L_i_k Value of the log-likelihood. 'logLik'.

     _v_c_o_v Variance-covariance matrix. 'array'.

     _d_e_t_a_i_l_s extra information on the model fit procedure. 'list'.

_E_x_t_e_n_d_s:


          FLModel FLComp

_M_e_t_h_o_d_s:


          All methods are inherited from 'FLModel-class', except for

     _p_l_o_t(_g_r_a_p_h_i_c_s) : Plot an FLSR object

      ' signature(x=FLSR,y=missing) '

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

     The FLR Team

_S_e_e _A_l_s_o:

     FLModel, FLComp

_E_x_a_m_p_l_e_s:

     # NS Herring stock-recruitment dataset
     data(nsher)

     # already fitted with a Ricker SR model
     summary(nsher)

     plot(nsher)

     # change model
     model(nsher) <- bevholt()

     # fit through MLE
     nsher <- fmle(nsher)

     plot(nsher)

