plotAllScores            package:designGG            R Documentation

_P_l_o_t _s_c_o_r_e_s _p_r_o_f_i_l_e_s

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

     Plot all scores and the temperature at each iteration during the
     simulated annealing  process.

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

      plotAllScores(plot.obj,fileName=NULL) 

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

plot.obj: a list containing: scores, cooling, startTemp, temperature, 
          temperature.step, nIterations and optimality.  Details can be
          found below.  

  scores: A- or D- optimality score of all accepted designs during
          optimization process. 

 cooling: describes the cooling step in the Simulated Annealing,
          defined as (new.score $-$ now.score)/ now.score. 

startTemp: starting temperature of the simulated annealing process. 

temperature: final temperature that the simulated annealing reaches. 

temperatureStep: temperature decreasing step in the simulated annealing
          (SA) process. 

nIterations: number of iterations in the simulated annealing method. 

optimality: type of optimality, i.e. "A" (A-optimality) or "D"
          (D-optimality). A-optimality minimizes $Trace((X'X)^{-1})$,
          which corresponds to minimum average variance of the
          parameter estimates. D-optimality minimizes $det(X'X)^{-1}$,
          which corresponds to minimum generalized variance of the
          parameter estimates. 

fileName: the final optimal design table(s) in 'csv' format and a plot
          (in 'png'  format) of the all scores during SA process (if
          'plotScores' = T) will be  produced. The users can specify
          the table and plot name by setting  'fileName'. If 'NULL'
          (default) it produces files starting with '"myDesignGG"'. 

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

     Draw a plot that visualizeds the scores (y-axis) at each iteration
     during  the simulated annealing process (x-axis is time of moving)

_N_o_t_e:

     The calculation of score is dependent on the choice of optimality.
      Cooling is defined as (newScore $-$ nowScore)/nowScore.

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

     Yang Li <yang.li@rug.nl>, Gonzalo Vera
     <gonzalo.vera.rodriguez@gmail.com> 
      Rainer Breitling <r.breitling@rug.nl>, Ritsert Jansen
     <r.c.jansen@rug.nl>

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

     Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical
     genomics: the added value from environmental perturbation, Trends
     Genet (2008) 24:518-524. 
      Y. Li, M. Swertz, G. Vera, J. Fu, R. Breitling, and R.C. Jansen.
     designGG: An R-package and Web tool for the optimal design of
     genetical genomics experiments. (submitted) 
      http://gbic.biol.rug.nl/designGG

