FLAssess              package:FLAssess              R Documentation

_F_L_A_s_s_e_s_s _c_l_a_s_s _a_n_d _m_e_t_h_o_d_s

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

     FLAssess is the basic structure for age-based stock assessment. It
     provides  a standard class for data input, diagnostic inspection
     and stock status estimation;  either for use within a working
     group setting or as part of a formal Management Strategy
     Evaluation (MSE). 

     The FLAssess class can be extended to create specific
     implementations of assessment methods e.g. FLICA, FLSURBA, FLXSA,
     providing a common interface for all assessmnet methods. For
     example, within ICES there are two main stock assessment methods,
     ICA for pelagic and XSA for demersal  stocks. However, differences
     between the methods are mainly artefacts of how they were 
     independently developed rather than methodological. By
     incorporating such methods in a common  class this problem will
     hopefully be avoided in the future. 

     FLAssess also incorporates methods for performing virtual
     population analysis (VPA) and stock  projection.

     In common with other FLR classes, all of the slots of the FLAssess
     class have accessor and replacement methods. Users are encouraged
     to use these instead of the @ slot accessor.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls to the methods VPA or SepVPA. They
     also can be created by calls of the form 'new("FLAssess", ...)'.

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


     '_n_a_m_e': A character string give name of stock.

     '_d_e_s_c': Whatever you want.

     '_h_a_r_v_e_s_t': An FLQuant that contains estimated fishing
          mortlaity-at-age.

     '_c_a_t_c_h._n': An FLQuant that contains estimated catch
          numbers-at-age.

     '_s_t_o_c_k._n': An FLQuant that contains estimated stock
          numbers-at-age.

     '_h_a_r_v_e_s_t': An FLQuant that contains estimated fishing
          mortlaity-at-age.

     '_i_n_d_e_x._n_a_m_e': A vector containing names for the FLIndexs

     '_i_n_d_e_x._r_a_n_g_e': A list containing ranges for the FLIndexs

     '_i_n_d_e_x': A list of FLQuants, corresponding to the index values
          used when fitting.

     '_i_n_d_e_x._h_a_t': A list of FLQuants, corresponding to the fitted index
          values.

     '_i_n_d_e_x._r_e_s': A list of FLQuants, corresponding to the index
          residuals.

     '_i_n_d_e_x._v_a_r': A list of FLQuants, corresponding to the variances of
          index values in fitting.    

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

     Summarise contents:

_s_u_m_m_a_r_y: Returns a list with a vector for each dimension in the object,
     which contains the levels of each dimension.

_s_h_o_w: Prints the given object. Plots:

_p_l_o_t: Plots stock.n against index Update FLstock:

+: Updates a FLStock with stock.n and harvest estimates from an
     FLAssess object

_m_e_r_g_e: Updates a FLStock with stock.n and harvest estimates from an
     FLAssess object

_u_p_d_a_t_e: Updates a FLStock with stock.n, catch.n & harvest estimates
     Stock Assessment methods:

_S_e_p_V_P_A: Separable VPA

_V_P_A: Virtual Population Analysis

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

     Laurence Kell

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

     'FLIndices-class', 'FLStock-class'

