faq.example
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faq.example [2012/05/29 17:30] – shogo | faq.example [2012/05/29 18:15] – shogo | ||
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===== Models ===== | ===== Models ===== | ||
- | Sire model without A | + | **Sire model without A** |
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 2 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
- | Sire model | + | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] |
+ | 1 2 cross | ||
+ | 2 3 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
- | Multiple (2) trait sire model | + | (CO)VARIANCES |
+ | 1 | ||
+ | </ | ||
+ | **Sire model with A** | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 2 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 2 cross | ||
+ | 2 3 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_sire | ||
+ | FILE | ||
+ | sire.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 | ||
+ | </ | ||
+ | **Multiple (2) trait sire model** | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 2 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 1 2 cross | ||
+ | 2 2 3 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_sire | ||
+ | FILE | ||
+ | sire.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | </ | ||
+ | **Animal model** | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 2 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 2 cross | ||
+ | 5 10 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 | ||
+ | </ | ||
+ | **Multiple trait animal model** | ||
+ | < | ||
+ | # Example 1: 2 trait animal | ||
- | Animal | + | DATAFILE |
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 2 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 1 2 cross | ||
+ | 5 5 10 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | </ | ||
+ | < | ||
+ | # Example 2: different | ||
- | Multiple trait animal | + | DATAFILE |
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 3 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 2 2 cross | ||
+ | 5 5 10 cross | ||
+ | 6 7 30 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 3 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
- | Donimance model | + | (CO)VARIANCES |
+ | 1 0 | ||
+ | 0 1 | ||
+ | </ | ||
+ | < | ||
+ | # This one works with Gibbs sampling programs | ||
- | Animal model with UPG | + | DATAFILE |
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 5 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 0 2 cross | ||
+ | 0 2 2 cross | ||
+ | 5 5 10 cross | ||
+ | 6 0 30 cross | ||
+ | 0 7 20 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 3 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 4 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
- | Animal model with inbreeding | + | (CO)VARIANCES |
+ | 1 0 | ||
+ | 0 0 | ||
+ | RANDOM_GROUP | ||
+ | 5 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
- | Repeatability model 1 | + | (CO)VARIANCES |
+ | 0 0 | ||
+ | 0 1 | ||
+ | </ | ||
+ | OR | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 5 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 0 2 cross | ||
+ | 0 2 2 cross | ||
+ | 5 5 10 cross | ||
+ | 6 0 30 cross | ||
+ | 0 7 30 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 3 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 4 5 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
- | Repeatability model 2 | + | (CO)VARIANCES |
+ | 1 0 0 0 | ||
+ | 0 0 0 0 | ||
+ | 0 0 0 0 | ||
+ | 0 0 0 1 | ||
- | Maternal effect | + | # Can you see the difference between these 3 setups in Example 2? |
+ | </ | ||
+ | **Donimance | ||
+ | < | ||
+ | DATAFILE | ||
+ | dom.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 4 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
- | Random regression | + | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] |
+ | 1 1 cross | ||
+ | 4 1 cov | ||
+ | 2 30001 cross | ||
+ | 5 10412 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 100 | ||
+ | RANDOM_GROUP | ||
+ | 3 | ||
+ | RANDOM_TYPE | ||
+ | add_an_upginb | ||
+ | FILE | ||
+ | add.ped | ||
+ | (CO)VARIANCES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 4 | ||
+ | RANDOM_TYPE | ||
+ | par_dom | ||
+ | FILE | ||
+ | dom.ped | ||
+ | (CO)VARIANCES | ||
+ | 2 | ||
+ | </ | ||
+ | **Animal | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 2 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 1 2 cross | ||
+ | 5 5 13 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_an_upg | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | </ | ||
+ | **Animal model with inbreeding** | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 2 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 1 2 cross | ||
+ | 5 5 13 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_an_upginb | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | </ | ||
+ | **Repeatability model 1** | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 3 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 2 cross | ||
+ | 5 5 cross | ||
+ | 5 10 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 | ||
+ | RANDOM_GROUP | ||
+ | 3 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
- | Random regression | + | (CO)VARIANCES |
+ | 1 | ||
+ | </ | ||
+ | **Repeatability | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 3 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 1 2 cross | ||
+ | 5 5 5 cross | ||
+ | 5 5 10 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 3 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
- | Competitive model | + | (CO)VARIANCES |
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | </ | ||
+ | **Maternal effect model** | ||
+ | < | ||
+ | DATAFILE | ||
+ | maternal.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 4 | ||
+ | OBSERVATION(S) | ||
+ | 4 | ||
+ | WEIGHT(S) | ||
+ | |||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 3 946 cross | ||
+ | 1 22473 cross | ||
+ | 2 22473 cross | ||
+ | 2 22473 cross | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 1050 | ||
+ | RANDOM_GROUP | ||
+ | 2 3 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | maternal.ped | ||
+ | (CO)VARIANCES | ||
+ | 450 -100 | ||
+ | -100 340 | ||
+ | RANDOM_GROUP | ||
+ | 4 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 370 | ||
+ | </ | ||
+ | **Random regression model** | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat1 | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 9 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 1 2 cross | ||
+ | 6 6 1 cov | ||
+ | 7 7 1 cov | ||
+ | 2 2 5 cross | ||
+ | 6 6 5 cov 2 2 | ||
+ | 7 7 5 cov 2 2 | ||
+ | 2 2 10 cross | ||
+ | 6 6 10 cov 2 2 | ||
+ | 7 7 10 cov 2 2 | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 4 5 6 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 7 8 9 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 0.1 1 | ||
+ | </ | ||
+ | < | ||
+ | DATAFILE | ||
+ | test.dat2 | ||
+ | NUMBER_OF_TRAITS | ||
+ | 2 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 10 | ||
+ | OBSERVATION(S) | ||
+ | 3 4 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 1 2 cross | ||
+ | 6 6 1 cov | ||
+ | 7 7 1 cov | ||
+ | 8 8 1 cov | ||
+ | 6 6 5 cov 2 2 | ||
+ | 7 7 5 cov 2 2 | ||
+ | 8 8 5 cov 2 2 | ||
+ | 6 6 10 cov 2 2 | ||
+ | 7 7 10 cov 2 2 | ||
+ | 8 8 10 cov 2 2 | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 1 | ||
+ | 1 5 | ||
+ | RANDOM_GROUP | ||
+ | 5 6 7 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 8 9 10 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 1 0.1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 1 0.1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 1 0.1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 1 0.1 | ||
+ | 0.1 0.1 0.1 0.1 0.1 1 | ||
+ | </ | ||
+ | < | ||
+ | test.dat1: example data set using Legendre polynomial | ||
+ | 1 1 21.10000 12.10000 11 -1.73205 2.23607 | ||
+ | 2 2 22.20000 12.20000 12 -1.23718 .59324 | ||
+ | 1 3 21.30000 12.30000 13 -.74231 -.50197 | ||
+ | 2 1 22.10000 12.40000 14 -.24744 -1.04958 | ||
+ | 1 2 21.20000 12.10000 15 .24744 -1.04958 | ||
+ | 2 3 22.30000 12.20000 16 .74231 -.50197 | ||
+ | 1 4 21.40000 12.30000 17 1.23718 .59324 | ||
+ | 2 5 22.50000 12.40000 18 1.73205 2.23607 | ||
+ | </ | ||
+ | < | ||
+ | test.dat2: example data set using linear spline | ||
+ | 1 1 21.100000 12.100000 11 1.000000 .000000 .000000 | ||
+ | 2 2 22.200000 12.200000 12 .666667 .333333 .000000 | ||
+ | 1 3 21.300000 12.300000 13 .333333 .666667 .000000 | ||
+ | 2 1 22.100000 12.400000 14 .000000 1.000000 .000000 | ||
+ | 1 2 21.200000 12.100000 15 .000000 .750000 .250000 | ||
+ | 2 3 22.300000 12.200000 16 .000000 .500000 .500000 | ||
+ | 1 4 21.400000 12.300000 17 .000000 .250000 .750000 | ||
+ | 2 5 22.500000 12.400000 18 .000000 .000000 1.000000 | ||
+ | </ | ||
+ | **Random regression model with heterogeneous residual variances** | ||
+ | < | ||
+ | ### using airemlf90 | ||
+ | |||
+ | # Example 1: with intercept | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 9 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 2 cross | ||
+ | 6 1 cov | ||
+ | 7 1 cov | ||
+ | 5 5 cross | ||
+ | 6 5 cov 5 | ||
+ | 7 5 cov 5 | ||
+ | 5 10 cross | ||
+ | 6 10 cov 5 | ||
+ | 7 10 cov 5 | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 4 5 6 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 | ||
+ | 0.1 1 0.1 | ||
+ | 0.1 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 7 8 9 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 | ||
+ | 0.1 1 0.1 | ||
+ | 0.1 0.1 1 | ||
+ | OPTION hetres_pos 6 7 | ||
+ | OPTION hetres_pol 4.0 1.0 0.1 | ||
+ | </ | ||
+ | < | ||
+ | ### using airemlf90 | ||
+ | |||
+ | # Example 2: with no intercept | ||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 7 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 2 cross | ||
+ | 6 1 cov | ||
+ | 7 1 cov | ||
+ | 6 5 cov 5 | ||
+ | 7 5 cov 5 | ||
+ | 6 10 cov 5 | ||
+ | 7 10 cov 5 | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 4 5 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 6 7 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 | ||
+ | 0.1 1 | ||
+ | OPTION hetres_pos 6 7 | ||
+ | OPTION hetres_pol 1.0 0.1 | ||
+ | </ | ||
+ | < | ||
+ | ### using gibbs3f90 | ||
+ | |||
+ | DATAFILE | ||
+ | test.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 9 | ||
+ | OBSERVATION(S) | ||
+ | 3 | ||
+ | WEIGHT(S) | ||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] | ||
+ | 1 2 cross | ||
+ | 6 1 cov | ||
+ | 7 1 cov | ||
+ | 5 5 cross | ||
+ | 6 5 cov 5 | ||
+ | 7 5 cov 5 | ||
+ | 5 10 cross | ||
+ | 6 10 cov 5 | ||
+ | 7 10 cov 5 | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 10 | ||
+ | RANDOM_GROUP | ||
+ | 4 5 6 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 | ||
+ | 0.1 1 0.1 | ||
+ | 0.1 0.1 1 | ||
+ | RANDOM_GROUP | ||
+ | 7 8 9 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | animal.ped | ||
+ | (CO)VARIANCES | ||
+ | 1 0.1 0.1 | ||
+ | 0.1 1 0.1 | ||
+ | 0.1 0.1 1 | ||
+ | OPTION hetres_int 8 5 | ||
+ | </ | ||
+ | **Competitive model** | ||
+ | < | ||
+ | DATAFILE | ||
+ | competition.dat | ||
+ | NUMBER_OF_TRAITS | ||
+ | 1 | ||
+ | NUMBER_OF_EFFECTS | ||
+ | 19 | ||
+ | OBSERVATION(S) | ||
+ | 24 | ||
+ | WEIGHT(S) | ||
+ | |||
+ | EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT[EFFECT NESTED] | ||
+ | 2 88 cross | ||
+ | 3 362 cross | ||
+ | 21 2409 cross | ||
+ | 4 8004 cross | ||
+ | 22 0 cov 5 | ||
+ | 22 0 cov 6 | ||
+ | 22 0 cov 7 | ||
+ | 22 0 cov 8 | ||
+ | 22 0 cov 9 | ||
+ | 22 0 cov 10 | ||
+ | 22 0 cov 11 | ||
+ | 22 0 cov 12 | ||
+ | 22 0 cov 13 | ||
+ | 22 0 cov 14 | ||
+ | 22 0 cov 15 | ||
+ | 22 0 cov 16 | ||
+ | 22 0 cov 17 | ||
+ | 22 0 cov 18 | ||
+ | 22 8004 cov 19 | ||
+ | RANDOM_RESIDUAL VALUES | ||
+ | 1225.8 | ||
+ | RANDOM_GROUP | ||
+ | 4 5 | ||
+ | RANDOM_TYPE | ||
+ | add_animal | ||
+ | FILE | ||
+ | renadd04.ped | ||
+ | (CO)VARIANCES | ||
+ | 267.03 25.313 | ||
+ | 25.313 104.44 | ||
+ | RANDOM_GROUP | ||
+ | 2 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 89.187 | ||
+ | RANDOM_GROUP | ||
+ | 3 | ||
+ | RANDOM_TYPE | ||
+ | diagonal | ||
+ | FILE | ||
+ | |||
+ | (CO)VARIANCES | ||
+ | 167.34 | ||
+ | </ | ||
faq.example.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1