Plot all scores and the temperature at each iteration during the simulated annealing process.
1  plotAllScores(plot.obj,fileName=NULL)

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 $$ now.score)/ now.score. startTemp:starting temperature of the simulated annealing process. temperature:final temperature that the simulated annealing reaches. temperatureStep:temperature decreasing step in the simulated annealing (SA) process. nIterations:number of iterations in the simulated annealing method. optimality:type of optimality, i.e. "A" (Aoptimality) or "D" (Doptimality). Aoptimality minimizes $Trace((X'X)^1)$, which corresponds to minimum average variance of the parameter estimates. Doptimality minimizes $det(X'X)^1$, which corresponds to minimum generalized variance of the parameter estimates. 
fileName 
the final optimal design table(s) in 
Draw a plot that visualizeds the scores (yaxis) at each iteration during the simulated annealing process (xaxis is time of moving)
The calculation of score is dependent on the choice of optimality.
Cooling is defined as (newScore $$ nowScore)/nowScore.
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>
Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical
genomics: the added value from environmental perturbation, Trends Genet
(2008) 24:518524.
Y. Li, M. Swertz, G. Vera, J. Fu, R. Breitling, and R.C. Jansen. designGG:
An Rpackage and Web tool for the optimal design of genetical genomics
experiments. BMC Bioinformatics 10:188(2009)
http://gbic.biol.rug.nl/designGG
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