runMC                package:PBSadmb                R Documentation

_R_u_n _a_n _E_x_e_c_u_t_a_b_l_e _B_i_n_a_r_y _F_i_l_e _i_n _M_C_M_C _M_o_d_e

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

     Run the executable binary file ''prefix'.exe', created by 
     'makeAD', to generate MCMC simulations.

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

     runMC(prefix, nsims=2000, nthin=20, outsuff=".mc.dat",
           logfile=FALSE, add=TRUE, verbose=TRUE)

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

  prefix: string name prefix of the ADMB project (e.g., '"vonb"').

   nsims: numeric scalar indicating number of MCMC simulations to
          perform.

   nthin: numeric scalar indicating the sampling rate or thinning of
          the  'nsims' MCMC simulations to report.

 outsuff: string name suffix of the MCMC output data file.

 logfile: logical: if 'TRUE', create a log file of the messages from
          the shell call.

     add: logical: if 'TRUE', append shell call messages to an exsiting
          log file.

 verbose: logical: if 'TRUE', report the shell call an its messages to
          the R console.

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

     This function runs ''prefix'.exe' twice, first with the arguments
     '-mcmc 'nsims' -mcsave 'nthin'' and second with the argument
     '-mceval'. By default, output goes to the file ''prefix'.mc.dat',
     although a user can specify a different output suffix.

     To see this function in action, use the PBSadmb GUI with the
     example 'vonb' or 'simpleMC'.

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

     Invisibly returns the results of the shell call.

_N_o_t_e:

     A wrapper function that can be called from a GUI exists as
     '.win.runMC'.

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

     Jon T. Schnute, Pacific Biological Station, Nanaimo BC, Canada

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

     'runAD', 'makeAD', 'cleanAD'

