FLBiol                package:FLCore                R Documentation

_C_l_a_s_s _F_L_B_i_o_l

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

     This is a class for the modelling of age/length or biomass
     structured populations. It is  in its structure a subset of the
     'FLStock-class' class, but lacks the  harvesting information of
     that class. The slots are for mortality (natural or otherwise),
     fecundity/maturity/per capita birth rates, numbers, weight and
     mortality components  before spawning/birthing period. 

     The non-accessor methods for this class calculate mature stock
     biomass/numbers of eggs/etc. and many life-history methods are
     available that calculate natural mortality  (given certain
     information), the intrinsic rate of increase _r_ (using various
     methods), or to apply a Leslie-transition matrix model for
     estimating the population  dynamics.

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


     _n for the numbers in the population. 'FLQuant'.

     _m for the mortality rate of the population. 'FLQuant'.

     _w_t for the weight of the population. 'FLQuant'.

     _f_e_c for the fecundity/maturity/per capita birth rate. 'FLQuant'.

     _s_p_w_n for the proportion of mortality before spawning/birth.
          'FLQuant'.

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

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

     _r_a_n_g_e range of the dimensions. 'numeric'.

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


          FLComp

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


     _a_s._F_L_B_i_o_l(_F_L_C_o_r_e) : Coerces object ino an 'FLBiol' object.

      ' signature(object=missing) '

     _a_s._F_L_S_R(_F_L_C_o_r_e) : Coerces an 'FLBiol' into an 'FLSR' object.

      ' signature(object=missing) '

     _c_o_e_r_c_e(_m_e_t_h_o_d_s) : Describe method

      ' signature(from=NULL,to=FLBiol,strict=missing) '

     _c_o_e_r_c_e(_m_e_t_h_o_d_s) : Describe method

      ' signature(from=FLBiol,to=FLStock,strict=missing) '

     _c_o_e_r_c_e(_m_e_t_h_o_d_s) : Describe method

      ' signature(from=FLStock,to=FLBiol,strict=missing) '

     _f_e_c(_F_L_C_o_r_e) : accesses the 'fec' slot.

      ' signature(object=missing) '

     _f_e_c<-(_F_L_C_o_r_e) : replacement method for this slot.

      ' signature(object=FLBiol,value=FLQuant) '

     _l_e_s_l_i_e(_F_L_C_o_r_e) : applies a Leslie-transition matrix model for the
          'FLBiol' object.

      ' signature(object=FLBiol,value=FLBiol) '

     _m(_F_L_C_o_r_e) : accesses the mortality slot.

      ' signature(object=missing) '

     _m<-(_F_L_C_o_r_e) : replacement method for this slot.

      ' signature(object=FLBiol,value=FLQuant) '

     _n(_F_L_C_o_r_e) : accesses the numbers slot.

      ' signature(object=missing) '

     _n<-(_F_L_C_o_r_e) : replacement method for this slot.

      ' signature(object=FLBiol,value=FLQuant) '

     _p_l_o_t(_g_r_a_p_h_i_c_s) : default plot method for 'FLBiol'.

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

     _s_p_w_n(_F_L_C_o_r_e) : accesses the 'spwn' slot.

      ' signature(object=missing) '

     _s_p_w_n<-(_F_L_C_o_r_e) : replacement method for this slot.

      ' signature(object=FLBiol,value=FLQuant) '

     _s_s_b(_F_L_C_o_r_e) : calculates the spawning stock biomass.

      ' signature(object=missing) '

     _w_t(_F_L_C_o_r_e) : accesses the weight slot.

      ' signature(object=missing) '

     _w_t<-(_F_L_C_o_r_e) : replacement method for this slot.

      ' signature(object=FLBiol,value=FLQuant) '

     _f_b_a_r(_F_L_C_o_r_e) : calculates fbar

      ' signature(object=FLBiol) '

     _f_b_a_r(_F_L_C_o_r_e) : calculates harvest, as fishing mortality. The ratio
          of F between the plusgroup, if specified, and the previous
          age, 'fratio', defaults to 1.

      ' signature(object=FLBiol) '

     _c_a_t_c_h._n(_F_L_C_o_r_e) : calculates catch by quant

      ' signature(object=FLBiol) '

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

     The FLR Team

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

     as.FLBiol, as.FLSR, coerce, fec, fec<-, m, m<-, n, n<-, plot,
     spwn, spwn<-, ssb, wt, wt<-, FLComp

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

     # An FLBiol example dataser
     data(ple4.biol)

     summary(ple4.biol)

