In addition, users can define other functions of covariance components which should be calculated and for which sampling errors should be approximated. This is done in a block entry, beginning with a line containing the code SE+USR (can be abbreviated to SE+), and ending with a line beginning with END. The block should then contain one line for each function to be calculated. The content of the line depends on the type of function. Three types are recognised.
Consider a univariate analysis with repeated records per individual. Fitting additive genetic and permanent environmental effects of the animal, variance components in the model are , and (residual), with running numbers 1, 2 and 3, respectively. WOMBAT automatically calculates the phenotypic variance = and gives it running number 4. To calculate the repeatability and approximate its sampling error, we first need to define the sum of and as a new covariance (which receives running number 5), and then define the repeatability as the ratio of this component and .
HINT: Run WOMBAT with the --setup option to begin with. Inspect the file ListOfCovs generated in this step – this gives a list of running numbers for individual covariance components.