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VCE Features

VCE is completely rewritten in Fortran90

  • comes as executables ready to run
  • controlled by intuitive parameter file
  • sports two methods:
    • does REML optimization with a quasi-Newton procedure using analytical gradients (AG) (i.e. exact first derivatives based on the sparse inverse)
    • estimates (co)variance components with Gibbs sampling (GI)
  • very flexible model definition such as:
    • animal model
    • sire model
    • repeatability model
    • maternal effects model (correlated random effects)
  • inbreeding considered as a default
  • genetic groups (phantom parents)
  • restart facility after abort
  • starting values can override the defaults
  • multiple trait
  • different model for each trait
  • random regression models
  • dominance models
  • optimization ensured to stay within the parameter space
  • no built in limit regarding number of traits, effects (fixed and random), regression which can be nested in another fixed effect
  • automatic reparameterization of rank deficient models to full rank models based on the Cholesky factorization
  • listing of dependent equations