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Common environmental effects as random

Model

In this example, the author considers a simple maternal model and the maternal effects (\(c\)) do not correlate to each other. The variance components include the animal genetic variance \(\sigma_u^2=20\), the maternal variance \(\sigma_c^2=15\), and the residual variance \(\sigma_e^2=65\).

Files

The data file (data_mr04b.txt) contains the whole table shown in the textbook (p.68). Here is the explanation for each column.

1. Animal ID (piglet)
2. Sire ID
3. Dam ID
4. Sex (1=male and 2=female)
5. Weaning weight (kg)

Pedigree (pedigree_mr04b.txt) can be derived from the above data.

The parameter file should contain 2 random effects.

DATAFILE
data_mr04b.txt
NUMBER_OF_TRAITS
1
NUMBER_OF_EFFECTS
3
OBSERVATION(S)
5
WEIGHT(S)

EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT  [EFFECT NESTED]
4  2 cross
1 15 cross
3  5 cross    # for maternal environmental effect
RANDOM_RESIDUAL VALUES
65.0
RANDOM_GROUP
2
RANDOM_TYPE
add_animal
FILE
pedigree_mr04b.txt
(CO)VARIANCES
20.0
RANDOM_GROUP
3
RANDOM_TYPE
diagonal
FILE

(CO)VARIANCES
15.0
OPTION solv_method FSPAK

Solutions

The results are identical to the textbook.

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