Table of Contents

Models

Animal model

DATAFILE
data.test
TRAITS
3
FIELDS_PASSED TO OUTPUT
5 6
WEIGHT(S)

RESIDUAL VARIANCE
5
EFFECT
1 cross alpha
EFFECT
2 cross alpha
RANDOM
animal
FILE
test.ped
FILE_POS
1 2 3 0 0
PED_DEPTH
5
(CO)VARIANCES
1

Multiple trait animal model

DATAFILE
data.test
TRAITS
3 4
FIELDS_PASSED TO OUTPUT
5 6
WEIGHT(S)

RESIDUAL VARIANCE
5 2
2 4
EFFECT
1 1 cross alpha
EFFECT
2 2 cross alpha
RANDOM
animal
FILE
test.ped
FILE_POS
1 2 3 0 0
PED_DEPTH
5
(CO)VARIANCES
2 1
1 2

Animal model with UPG

DATAFILE
data.test
TRAITS
3
FIELDS_PASSED TO OUTPUT
5 6
WEIGHT(S)

RESIDUAL VARIANCE
5
EFFECT
1 cross alpha
EFFECT
2 cross alpha
RANDOM
animal
FILE
test.ped
FILE_POS
1 2 3 0 4
PED_DEPTH
5
GEN_INT
1 3 10
UPG_TYPE
yob
1990 1995 2000 2005
(CO)VARIANCES
1

Repeatability model 1

DATAFILE
data.test
TRAITS
3 4
FIELDS_PASSED TO OUTPUT
5 6
WEIGHT(S)

RESIDUAL VARIANCE
5 2
2 4
EFFECT
1 1 cross alpha
EFFECT
2 2 cross alpha
RANDOM
animal
FILE
test.ped
FILE_POS
1 2 3 0 0
PED_DEPTH
5
(CO)VARIANCES
2 1
1 2
EFFECT
2 2 cross alpha
RANDOM
diagonal
(CO)VARIANCES_PE
2 1
1 2

Repeatability model 2

DATAFILE
data.test
TRAITS
3 4
FIELDS_PASSED TO OUTPUT
5 6
WEIGHT(S)

RESIDUAL VARIANCE
5 2
2 4
EFFECT
1 1 cross alpha
EFFECT
2 2 cross alpha
RANDOM
animal
OPTIONAL
pe
FILE
test.ped
FILE_POS
1 2 3 0 0
PED_DEPTH
5
(CO)VARIANCES
2 1
1 2
(CO)VARIANCES_PE
2 1
1 2

Random regression model 1

DATAFILE
rrm.dat
TRAITS
9
FIELDS_PASSED TO OUTPUT

WEIGHT(S)

RESIDUAL_VARIANCE
1
EFFECT
7 cross alpha
EFFECT
2 cov
EFFECT
3 cov
EFFECT
4 cov
EFFECT
5 cov
EFFECT
6 cross alpha
RANDOM
animal
OPTIONAL
pe
FILE
rrm.ped
RANDOM_REGRESSION
data
RR_POSITION
2 3 4 5
rrm.dat
 1 -1.00000 1.00000 -1.00000 1.00000  1 1 1 11
 2 -0.77778 0.40741 -0.00960 -0.29249  2 1 1 12
 3 -0.55556 -0.03704 0.40466 -0.36565  3 1 1 13
 4 -0.33333 -0.33333 0.40741 0.01235  4 2 1 13
 5 -0.11111 -0.48148 0.16324 0.32937  5 2 1 12
 6 0.11111 -0.48148 -0.16324 0.32937  6 2 1 11
 7 0.33333 -0.33333 -0.40741 0.01235  7 3 1 12
 8 0.55556 -0.03704 -0.40466 -0.36565  8 3 1 13
 9 0.77778 0.40741 0.00960 -0.29249  9 3 1 14
 10 1.00000 1.00000 1.00000 1.00000  10 3 1 15
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rrm.ped
1 0 0
2 0 0
3 0 0
4 0 0
5 1 0
6 1 4
7 2 0
8 2 4
9 2 0
10 3 5
renf90.par
DATAFILE
 renf90.dat
NUMBER_OF_TRAITS
           1
NUMBER_OF_EFFECTS
          13
OBSERVATION(S)
    1
WEIGHT(S)
 
EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT[EFFECT NESTED]
 6         3 cross 
 7 1 cov 
 8 1 cov 
 9 1 cov 
 10 1 cov 
 2         10 cov 11
 3         10 cov 11
 4         10 cov 11
 5         10 cov 11
 2         10 cov 11
 3         10 cov 11
 4         10 cov 11
 5         10 cov 11
RANDOM_RESIDUAL VALUES
       1.0000000
 RANDOM_GROUP
     6     7     8     9
 RANDOM_TYPE
 add_animal   
 FILE
renadd06.ped                                                
(CO)VARIANCES
       1.0000000       0.1000000       0.1000000       0.1000000
       0.1000000       1.0000000       0.1000000       0.1000000
       0.1000000       0.1000000       1.0000000       0.1000000
       0.1000000       0.1000000       0.1000000       1.0000000
 RANDOM_GROUP
    10    11    12    13
 RANDOM_TYPE
 diagonal     
 FILE
                                                            
(CO)VARIANCES
       1.0000000       0.1000000       0.1000000       0.1000000
       0.1000000       1.0000000       0.1000000       0.1000000
       0.1000000       0.1000000       1.0000000       0.1000000
       0.1000000       0.1000000       0.1000000       1.0000000

Maternal effect model

DATAFILE
data.test
TRAITS
3 4
FIELDS_PASSED TO OUTPUT
5 6
WEIGHT(S)

RESIDUAL VARIANCE
5 2
2 4
EFFECT
1 1 cross alpha
EFFECT
2 2 cross alpha
RANDOM
animal
OPTIONAL
mat
FILE
test.ped
FILE_POS
1 2 3 0 0
PED_DEPTH
5
(CO)VARIANCES
2 1 1 1
1 2 1 1
1 1 2 1
1 1 1 2