enumerate.models             package:nem             R Documentation

_E_x_h_a_u_s_t_i_v_e _e_n_u_m_e_r_a_t_i_o_n _o_f _m_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'enumerate.models' is used to create the model space
     for inference by exhaustive enumeration.  It computes a list of
     all transitively closed directed graphs on a given number of
     nodes.

_U_s_a_g_e:

     enumerate.models(x,name=NULL,trans.close=TRUE,verbose=TRUE) 

_A_r_g_u_m_e_n_t_s:

       x: either the number of nodes or a vector of node names.

    name: optionally the nodenames, if they are not provided in x

trans.close: should graphs be transitively closed?

 verbose: if TRUE outputs number of (unique) models. Default: TRUE

_D_e_t_a_i_l_s:

     The model space of Nested Effects Models consists of all
     transitively closed directed graphs.  The function
     'enumerate.models' creates them in three steps: (1.) build all
     directed graphs on 'x' (or 'length(x)') nodes, (2.) transitively
     close each one of them, and (3.) remove redundant models to yield
     a unique set. So far, enumeration is limited to up to 5 nodes.

     I'm aware that this is inefficient!  It would be very desirable to
     enumerate the models directly (i.e. without creating all directed
     graphs as an intermediate step).

_V_a_l_u_e:

     a list of models. Each entry is a transitively closed adjacency
     matrix with unit main diagonal.

_A_u_t_h_o_r(_s):

     Florian Markowetz <URL: http://genomics.princeton.edu/~florian>

_S_e_e _A_l_s_o:

     'nem'

_E_x_a_m_p_l_e_s:

     enumerate.models(2)
     enumerate.models(c("Anna","Bert"))

