1. reformated the read.pheno.data Rscript
2. deleted the restricted parameter, i.e. use.grand.mean, it means not
allowing to use grand mean to instead of missing level value and
checking whether it is full level when the population type is pyramided
lines.
3. implemented single site analysis on phenotypic data and created a
Rscript doSSA.R for that purpose. And made the return value as an object
of class SingleSiteAnalysis.