temperatureStep {designGG}R Documentation

Calculate the temperature decreasing step for simulated annealing process

Description

Calculate the temperature decreasing step for simulated annealing process. This is a subfunction needed for designGG, but is not directly used.

Usage

temperatureStep(startTemp, maxTempStep, endTemp, nIterations)

Arguments

startTemp

starting temperature of simulated annealing process.

maxTempStep

maximum temperature decreasing step for simulated annealing process. The parameter ensures that the multiplicative cooling factor is not smaller than this value. If nIterations is too small, the preferred final temperature (endTemp) may not be reached. See Wit and McClure (2004) for details.

endTemp

ending temperature of simulated annealing process. An important optimization parameter. Setting this parameter closer to zero. See Wit and McClure (2004) for details

nIterations

number of iterations in the simulated annealing method.

Value

A temperature decreasing step in the simulated annealing process.

Author(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>

References

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. BMC Bioinformatics 10:188(2009)
http://gbic.biol.rug.nl/designGG
Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical genomics: the added value from environmental perturbation, Trends Genet (2008) 24:518-524.
E. Wit and J. McClure. Statistics for Microarrays: Design, Analysis and Inference. (2004) Chichester: Wiley.

See Also

designGG


[Package designGG version 1.1 Index]