mif-methods               package:pomp               R Documentation

_M_e_t_h_o_d_s _o_f _t_h_e "_m_i_f" _c_l_a_s_s

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

     Methods of the "mif" class.

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

     ## S4 method for signature 'mif':
     logLik(object, ...)
     conv.rec(object, ...)
     ## S4 method for signature 'mif':
     conv.rec(object, pars, ...)
     pred.mean(object, ...)
     ## S4 method for signature 'mif':
     pred.mean(object, pars, ...)
     pred.var(object, ...)
     ## S4 method for signature 'mif':
     pred.var(object, pars, ...)
     filter.mean(object, ...)
     ## S4 method for signature 'mif':
     filter.mean(object, pars, ...)
     ## S4 method for signature 'mif':
     plot(x, y = NULL, ...)
     compare.mif(z)

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

  object: The 'mif' object.

    pars: Names of parameters.

       x: The 'mif' object.

       y: Ignored.

       z: A 'mif' object or list of 'mif' objects.

     ...: Further arguments (either ignored or passed to underlying
          functions). 

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


     _c_o_n_v._r_e_c 'conv.rec(object, pars = NULL)' returns the columns of
          the convergence-record matrix corresponding to the names in
          'pars'. By default, all rows are returned.

     _l_o_g_L_i_k Returns the value in the 'loglik' slot.

     _m_i_f Re-runs the MIF iterations. See the documentation for 'mif'.

     _c_o_m_p_a_r_e._m_i_f Given a 'mif' object or a list of 'mif' objects,
          'compare.mif' produces a set of diagnostic plots.

     _p_l_o_t Plots a series of diagnostic plots. When 'x' is a 'mif'
          object, 'plot(x)' is equivalent to 'compare.mif(list(x))'.

     _p_r_e_d._m_e_a_n 'pred.mean(object, pars = NULL)' returns the rows of the
          prediction-mean matrix corresponding to the names in 'pars'.
          By default, all rows are returned.

     _p_r_e_d._v_a_r 'pred.var(object, pars = NULL)' returns the rows of the
          prediction-variance matrix corresponding to the names in
          'pars'. By default, all rows are returned.

     _f_i_l_t_e_r._m_e_a_n 'filter.mean(object, pars = NULL)' returns the rows of
          the filtering-mean matrix corresponding to the names in
          'pars'. By default, all rows are returned.

     _p_r_e_d_v_a_r_p_l_o_t 'predvarplot(object, pars = NULL, mean = FALSE, ...)'
          produces a plot of the scaled prediction variances for each
          parameter. This can be used to diagnose a good value of the
          'mif' parameters 'var.factor' and 'ic.lag'. If used in this
          way, one should run 'mif' with 'Nmif=1' first. Additional
          arguments in '...' will be passed to the actual plotting
          function.

     _p_r_i_n_t Prints a summary of the 'mif' object.

     _s_h_o_w Displays the 'mif' object.

     _p_f_i_l_t_e_r See 'pfilter-mif'.


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

     Aaron A. King kingaa at umich dot edu

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

     E. L. Ionides, C. Bret\'o, & A. A. King, Inference for nonlinear
     dynamical systems, Proc. Natl. Acad. Sci. U.S.A., 103:18438-18443,
     2006.

     A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma, Inapparent
     infections and cholera dynamics, Nature, 454:877-880, 2008.

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

     'mif', 'pomp', 'pomp-class', 'pfilter'

