| plotAllScores {designGG} | R Documentation |
Plot all scores and the temperature at each iteration during the simulated annealing process.
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" (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".
|
Draw a plot that visualizeds the scores (y-axis) at each iteration during the simulated annealing process (x-axis 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) 24:518-524.
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