Chapter 4
The Parameter File

 4.1 Overview
 4.2 General rules
 4.3 Run options
 4.4 Comment line
 4.5 Analysis type
 4.6 Pedigree file
 4.7 Marker counts file
 4.8 Data file
  4.8.1 Simple
  4.8.2 Compact
 4.9 Model of analysis
  4.9.1 Effects fitted
  4.9.2 Traits analysed
 4.10 Covariance components
  4.10.1 Residual covariances
  4.10.2 Covariances for random effects
 4.11 Special information
  4.11.1 Dependencies among fixed effects
  4.11.2 Random effects to be treated as fixed
  4.11.3 Covariance components to be treated as fixed
  4.11.4 Additional functions of covariance components
  4.11.5 Pooling estimates of covariance components
  4.11.6 Genomic relationship matrices
  4.11.7 Miscellaneous
  4.11.8 Penalized estimation