SOSProtocol-class           package:rsbml           R Documentation

_S_O_S_P_r_o_t_o_c_o_l

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

     Holds the parameters controlling the execution of the simulation
     using the SBML ODE Solver library.

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

     Most users will probably set only the 'times' slot, either
     directly or through the 'timeStep' slot and the 'nsim' parameter
     to 'simulate'.

_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 of the form 'new("SOSProtocol",
     ...)'. Each argument in '...' should correspond to one of the
     slots described below.

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


     '_t_i_m_e_s': A '"numeric"' vector indicating the time points at which
          to evaluate the model. Defaults to 'tail(seq(0, by =
          timeStep, length.out = nsim + 1), -1)'. The model is always
          evaluated at t = 0. This slot is ignored when 'indefinite'
          (below) is 'TRUE'.

     '_t_i_m_e_S_t_e_p': A scalar '"numeric"' value, giving the length in time
          between model evaluations. This is used when calculating the
          default value of 'times', above, but is otherwise only
          relevant when the 'indefinite' slot, below, is 'TRUE'.
          Defaults to 1.

     '_i_n_d_e_f_i_n_i_t_e': A scalar '"logical"', indicating whether the
          simulation should run indefinitely, i.e. until one of the
          stopping conditions is met. See 'haltOnEvent' and
          'haltOnSteadyState' below. Defaults to 'FALSE'.

     '_a_t_o_l': Scalar '"numeric"', the absolute tolerance in integration
          error. Defaults to '1e-18'.

     '_r_t_o_l': Scalar '"numeric"', the relative tolerance in integration
          error. Defaults to '1e-10'.

     '_m_a_x_S_t_e_p': Sclar '"numeric"', the maximum number of steps for
          integration. Not to be confused with 'timeStep', etc, above,
          which control the simulation time points. Defaults to
          '10000'.

     '_o_d_e_M_e_t_h_o_d': Scalar '"character"' naming the method for solving
          ODEs. Either '"bdf"' (the default) or '"adams-moulton"'.

     '_i_t_e_r_M_e_t_h_o_d': Scalar '"character"', naming the iteration method
          used by the ODE solver, either '"newton"' (the default) or
          '"functional"'. 

     '_m_a_x_O_r_d_e_r': Scalar '"numeric"' indicating maximum order for the
          ODE solver. Defaults to '5'.

     '_s_e_n_s_M_e_t_h_o_d': Scalar '"character"' naming the method for
          sensitivity analysis. One of '"none"' (the default and
          currently the only valid option), '"simultaneous"',
          '"staggered"' or '"staggered1"'.

     '_h_a_l_t_O_n_E_v_e_n_t': Scalar '"logical"' indicating whether the
          simulation should halt when the model emits an 'Event'. This
          allows the model to stop the simulation when some state is
          reached. Defaults to 'FALSE'.

     '_h_a_l_t_O_n_S_t_e_a_d_y_S_t_a_t_e': Scalar '"logical"', indicating whether to
          halt when a steady state is detected. Defaults to 'FALSE'.

     '_u_s_e_J_a_c_o_b_i_a_n': Scalar '"logical"' indicating whether to use
          Jacobian ASTs ('TRUE', the default) or the internal
          approximation in the CVODES library.

     '_s_t_o_r_e_R_e_s_u_l_t_s': Scalar '"logical"' indicating whether to store the
          entire time course ('TRUE', the default) or just the last
          time point. Just for performance.

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

     Class '"ExperimentProtocol"', directly.

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

     No methods defined with class "SOSProtocol" in the signature.

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

     Michael Lawrence

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

     See <URL: http://www.tbi.univie.ac.at/~raim/odeSolver/> for more
     information on the SBML ODE Solver library.

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

     The 'SOSExperiment' class, which contains a 'SOSProtocol'
     instance, for setting up and running a simulation.

