Opt                   package:VGAM                   R Documentation

_M_a_x_i_m_a

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

     Generic function for the _optima_ (or optimums) of a model.

_U_s_a_g_e:

     Opt(object, ...)

_A_r_g_u_m_e_n_t_s:

  object: An object for which the computation or extraction of an
          optimum (or optima) is meaningful. 

     ...: Other arguments fed into the specific methods function of the
          model. Sometimes they are fed into the methods function for
          'Coef'. 

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

     Different models can define an optimum in different ways. Many
     models have no such notion or definition.

     Optima occur in quadratic and additive ordination, e.g., CQO or
     UQO or CAO. For these models the optimum is the value of the
     latent variable where the maximum occurs, i.e., where the fitted
     value achieves its highest value. For quadratic ordination models
     there is a formula for the optimum but for additive ordination
     models the optimum must be searched for numerically. If it occurs
     on the boundary, then the optimum is undefined.  At an optimum,
     the fitted value of the response is called the _maximum_.

_V_a_l_u_e:

     The value returned depends specifically on the methods function
     invoked.

_N_o_t_e:

     In ordination, the optimum of a species is sometimes called the
     _species score_.

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

     Thomas W. Yee

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

     Yee, T. W. (2004) A new technique for maximum-likelihood canonical
     Gaussian ordination. _Ecological Monographs_, *74*, 685-701.

     Yee, T. W. (2006) Constrained additive ordination. _Ecology_,
     *87*, 203-213.

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

     'Opt.qrrvglm', 'Max', 'Tol'.

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

     data(hspider)
     set.seed(111)  # This leads to the global solution
     hspider[,1:6] = scale(hspider[,1:6]) # Standardized environmental vars
     p1 = cqo(cbind(Alopacce, Alopcune, Alopfabr, Arctlute, Arctperi,
                    Auloalbi, Pardlugu, Pardmont, Pardnigr, Pardpull,
                    Trocterr, Zoraspin) ~
              WaterCon + BareSand + FallTwig + CoveMoss + CoveHerb + ReflLux,
              Bestof = 2,
              fam = quasipoissonff, data = hspider, Crow1positive=FALSE)
     Opt(p1)

     ## Not run: 
     index = 1:ncol(p1@y)
     persp(p1, col=index, las=1, lwd=2, main="Vertical lines at the optima")
     abline(v=Opt(p1), lty=2, col=index)
     ## End(Not run)

