user_defined_files_for_covariances_of_random_effects

There is an option (originally included in `REMLF90`

by Miguel Perez Enciso) included to include covariance structures, say **T**, computed from outside. This covariance structures will be included in the mixed model equations for the corresponding random effect. This option works in all programs (BLUP, REML, Gibbs… ).

This is useful in several cases, including for example:

- plant breeding (with tetra or hexa-ploids or self-fertilization),
- uncertain parentships,
- kernel methods such as RKHS,
- genomic relationship matrices (although the latter are correctly included using genomic options)
- autoregressive covariance structures.

The inclusion is rather simple. One has to include a random effect of the type, either

`user_file`

if the file contains the*inverse*of the covariance structure, that is, it contains**T**^{-1},`user_file_inv`

if the file contains the covariance structure, that is, it contains**T**. If this is the case,**T**is inverted,

and declare a file (in this example, `Gi`

) with the covariance structure:

RANDOM_GROUP # genomic 2 RANDOM_TYPE user_file FILE # matrix file Gi

The file has to have the form (row, col, value) in Ascii (i.e. plain text), stored as lower- or upper- triangle, e.g., this is valid:

1 1 1 1 2 0.5 2 2 1

but this is **not valid**:

1 1 1 1 2 0.5 2 1 0.5 2 2 1

Elements of **T** not stored in the file are assumed to be zero. Therefore, *the file with the covariance structure is not necessarily very large* . For instance, matrix

1.0 0.0 0.5 0.0 0.5 0.0 0.5 0.0 1.1

can be stored as:

1 1 1.0 1 3 0.5 2 2 0.5 3 3 1.1

user_defined_files_for_covariances_of_random_effects.txt · Last modified: 2018/05/22 14:25 by ignacio