faq.renum_example
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 : : : : : :
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
faq.renum_example.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1