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 Fixed effects
  4.9.3 Fixed covariables
  4.9.4 Random effects
  4.9.5 ‘Subject’ identifier
  4.9.6 ‘Extra’ effects
  4.9.7 Traits analysed
 4.10 Covariance components
  4.10.1 Residual covariances
  4.10.2 Covariances for random effects
 4.11 Additional functions of covariance components
 4.12 Pooling estimates of covariance components
 4.13 Dependencies among fixed effects
 4.14 Random effects to be treated as fixed
 4.15 Covariance components to be treated as fixed
 4.16 Special information
  4.16.1 Weighted analysis
  4.16.2 Covariables that are zero
  4.16.3 Animals that are clones
  4.16.4 Standard errors for fixed and random effect solutions
  4.16.5 Repeated records
  4.16.6 Fitting SNP effects
  4.16.7 Sampling to approximate standard errors
  4.16.8 Fitting “social” genetic effects
  4.16.9 Fitting ‘explicit’ genetic groups
  4.16.10 In core storage
  4.16.11 Calculation of alternative outlier model statistics
  4.16.12 Analyses using a Gaussian Kernel matrix
  4.16.13 Correlations for random regression analyses
  4.16.14 Genomic relationship matrices
  4.16.15 Penalized estimation