pomp-methods              package:pomp              R Documentation

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

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

     Methods of the 'pomp' class.

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

     ## S4 method for signature 'pomp':
     coef(object, pars, ...)
     ## S4 replacement method for signature 'pomp':
     coef(object, pars, ...) <- value
     ## S4 method for signature 'pomp':
     data.array(object, vars, ...)
     ## S4 method for signature 'pomp':
     states(object, vars, ...)
     ## S4 method for signature 'pomp':
     time(x, t0 = FALSE, ...)
     ## S4 replacement method for signature 'pomp':
     time(object, include.t0 = FALSE, ...) <- value
     ## S4 method for signature 'pomp':
     show(object)
     ## S4 method for signature 'pomp':
     as(object, class)
     ## S4 method for signature 'pomp, data.frame':
     coerce(from, to = "data.frame", strict = TRUE)
     ## S4 method for signature 'pomp':
     print(x, ...)
     ## S4 method for signature 'pomp':
     plot(x, y, variables, panel = lines,
           nc = NULL, yax.flip = FALSE,
           mar = c(0, 5.1, 0, if (yax.flip) 5.1 else 2.1),
           oma = c(6, 0, 5, 0), axes = TRUE, ...)

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

object, x: The 'pomp' object.

    pars: optional character; names of parameters to be retrieved or
          set. 

    vars: optional character; names of observed variables to be
          retrieved. 

   value: numeric; values to be assigned to the parameters. 

      t0: logical; if TRUE, the zero time is prepended to the time
          vector. 

include.t0: logical; if TRUE, the first element in 'value' is taken to
          be the initial time. 

   class: character; name of the class to which 'object' should be
          coerced. 

from, to: the classes between which coercion should be performed. 

  strict: ignored. 

       y: ignored.

variables: optional character; names of variables to plot. 

   panel: a function of prototype 'panel(x, col, bg, pch, type, ...)'
          which gives the action to be carried out in each panel of the
          display. 

      nc: the number of columns to use. Defaults to 1 for up to 4
          series, otherwise to 2. 

yax.flip: logical; if TRUE, the y-axis (ticks and numbering) should
          flip from side 2 (left) to 4 (right) from series to series. 

mar, oma: the 'par' settings for 'mar' and 'oma' to use. Modify with
          care! 

    axes: logical; indicates if x- and y- axes should be drawn. 

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

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


     _c_o_e_f 'coef(object)' returns the contents of the 'params' slot of
          'object'. 'coef(object,pars)' returns only those parameters
          named in 'pars'.

     _c_o_e_f<- Assigns values to the 'params' slot of the 'pomp' object.
          If 'coef(object)' exists, then 'coef(object) <- value' has
          the effect of replacing the parameters of 'object' with
          'value'; the names of 'value' will be ignored and the names
          of 'coef(object)' will be unchanged. If 'coef(object)' does
          not exist, then 'coef(object) <- value' assigns 'value' to
          the parameters of 'object'; the names of 'coef(object)' will
          be those of 'value' and an error will be generated if 'value'
          does not have names. If 'coef(object)' exists, then
          'coef(object,pars) <- value' replaces those parameters of
          'object' named in 'pars' with the elements of 'value'; the
          names of 'value' are ignored. If 'coef(object)' does not
          exist, then 'coef(object,pars) <- value' assigns 'value' to
          the parameters of 'object'; in this case, the names of
          'object' will be 'pars' and the names of 'value' will be
          ignored.

     _d_a_t_a._a_r_r_a_y 'data.array(object)' returns the array of observations.
          'data.array(object,vars)' gives just the observations of
          variables named 'vars'. 'vars' may specify the variables by
          position or by name.

     _s_t_a_t_e_s 'states(object)' returns the array of states.
          'states(object,vars)' gives just the state variables named in
          'vars'. 'vars' may specify the variables by position or by
          name.

     _t_i_m_e 'time(object)' returns the vector of observation times.
          'time(object,t0=TRUE)' returns the vector of observation
          times with the zero-time 't0' prepended.

     _t_i_m_e<- 'time(object) <- value' replaces the observation times slot
          ('times') of 'object' with 'value'. 'time(object,include.t0 =
          TRUE) <- value' has the same effect, but the first element in
          'value' is taken to be the initial time. The second and
          subsequent elements of 'value' are taken to be the
          observation times. Those data and states (if they exist)
          corresponding to the new times are retained.

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

     _p_l_o_t Plots the data and state trajectories (if the latter exist).
          Additional arguments are passed to the low-level plotting
          routine.

     _p_r_i_n_t Prints the 'pomp' object in a nice way.

     _a_s, _c_o_e_r_c_e The 'coerce' method should typically not be used
          directly. It is defined by 'setAs' as a method to be used by
          'as'. A 'pomp' object can be coerced to a data frame via
          'as(object,"data.frame")'. The data frame contains the times,
          the data, and the state trajectories, if they exist.

     _r_p_r_o_c_e_s_s simulates the process model. See 'rprocess-pomp'.

     _d_p_r_o_c_e_s_s evaluates the process model density. See 'dprocess-pomp'.

     _r_m_e_a_s_u_r_e simulates the measurement model. See 'rmeasure-pomp'.

     _d_m_e_a_s_u_r_e evaluates the measurement-model density. See
          'dmeasure-pomp'.

     _s_k_e_l_e_t_o_n evaluates the deterministic skeleton (be it a vector
          field or a map). See 'skeleton-pomp'.

     _i_n_i_t._s_t_a_t_e returns a vector of initialial conditions. See
          'init.state-pomp'.

     _s_i_m_u_l_a_t_e 'simulate' can be used to simulate state and observation
          trajectories. See documentation under 'simulate-pomp'.


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

     Aaron A. King kingaa at umich dot edu

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

     'pomp', pomp-class, 'rprocess', 'dprocess', 'rmeasure',
     'dmeasure', 'init.state', simulate-pomp

