Bivariate structure
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Bivariate structure
I have been having problems with the following Bivariate
analysis. The first trait is a random regression of
fat on weight. Ftting an animal genetic and permanent environment
effect of animal for slope and intercept. This is a simple
linear regression (simulated data). The second trait is weight
of first fat measure for an animal. Here a simple additive genetic
effect of animal is fit.
Sample records on two animals
4501 4501 975.15 786.43 975.15
4501 4501 1075.15 869.60 .
4501 4501 1175.15 1000.74 .
4501 4501 1275.15 1133.56 .
4502 4502 1119.13 674.90 1119.13
4502 4502 1219.13 812.53 .
4502 4502 1319.13 943.30 .
4502 4502 1419.13 1120.03 .
Here is the .as file
Random regression of fat on weight 5/750 sires
animal !P #Animal
an2 3750 !I #Another animal
weight !-1142.123 !/411.1376 #weight standardised lbs
fat #ultrasonic fat measure in mm/100
start !M. #start weight !M. indicates missing
../../../../FatWt/One/Boost_New2/ped.dat # reading the pedigree file
one.dat !maxit 1000 # reading data file
fat start ~ Trait Tr|1.weight !r -weight.animal Tr.animal Tr|1.weight.animal,
-weight.an2 Tr|1.an2 Tr|1.weight.an2
1 2 2
0
Trait 0 US 2500 1 5018
Tr.animal 2
3 0 US 10621 1 42 4202 1 11467
animal
Tr|1.an2 2
2 0 US 13380 6972 19395
3750
The error is
Fault 1Covariance Structure Factor, order
The log file from a run is (-del options)
animal !P
an2 3750 !I
weight !-1142.123 !/411.1376
fat
start !M.
3 - 1142.1230
3 / 411.1376
5 MISS 0.0000
../../../../FatWt/One/Boost_New2/ped.dat
A-inverse retrieved from ainverse.bin
PEDIGREE [] has 8250 animals, 19500 Non zero elements
Bivariate analysis of fat and start
i,factor,nlev,flevel,inter1..4, plusnn,gmcstr
1 animal 1 8250 -1 -1 0 1 0 1
2 an2 1 3750 3750 0 1 0 0 1
3 weight 1 1 1 0 2 0 0 1
4 fat 1 1 1 0 3 0 5 1
5 start 1 1 1 0 4 2 0 1
6 Trait 0 2 -8 0 0 0 0 1
7 Tr_1.weight 0 1 6 3 -1 1 0 1
8 weight.anima 0 8250 3 1 1 8250 0 1
9 Tr.animal 0 16500 6 1 2 8250 0 1
10 Tr_1.weight. 0 8250 6 8 -1 8250 0 1
11 weight.an2 0 3750 3 2 1 3750 0 1
12 Tr_1.an2 0 3750 6 2 -1 3750 0 1
13 Tr_1.weight. 0 3750 6 11 -1 3750 0 1
41646 683292 491647
Data being held on scratch file to increase RAM available
1 7 0 1 6 3 -1 1 1.000
1 3 1 1 1 0 2 0 1.000
1 1 3 491649
1 6 0 2 -8 0 0 0 1.000
1 2 6 491650
1 9 0 16500 6 1 2 8250 1.000
1 1 1 8250 -1 -1 0 1 1.000
1 3 1 491651
1 6 0 2 -8 0 0 0 1.000
1 3 6 491652
1 10 0 8250 6 8 -1 8250 1.000
1 8 0 8250 3 1 1 8250 1.000
1 1 1 8250 -1 -1 0 1 1.000
1 4 1 491652
1 3 1 1 1 0 2 0 1.000
1 4 3 491653
1 12 0 3750 6 2 -1 3750 1.000
1 2 1 3750 3750 0 1 0 1.000
1 5 2 491653
1 13 0 3750 6 11 -1 3750 1.000
1 11 0 3750 3 2 1 3750 1.000
1 2 1 3750 3750 0 1 0 1.000
1 6 2 491654
1 3 1 1 1 0 2 0 1.000
1 6 3 491655
1 786.4 2 -0.4 3 1.0 4505 1.021005 -0.424755 1.0
28505 -0.4
2 7 0 1 6 3 -1 1 1.000
2 6 0 2 -8 0 0 0 1.000
2 2 6 491656
2 9 0 16500 6 1 2 8250 1.000
2 1 1 8250 -1 -1 0 1 1.000
2 3 1 491657
2 6 0 2 -8 0 0 0 1.000
2 3 6 491658
2 10 0 8250 6 8 -1 8250 1.000
2 12 0 3750 6 2 -1 3750 1.000
2 13 0 3750 6 11 -1 3750 1.000
1 975.2 4 1.012755 1.0
1 869.6 2 -0.2 3 1.0 4505 1.021005 -0.224755 1.0
28505 -0.2
1 0.0 4 1.012755 1.0
1 1000.7 2 0.1 3 1.0 4505 1.021005 0.124755 1.0
28505 0.1
1 0.0 4 1.012755 1.0
1 1133.6 2 0.3 3 1.0 4505 1.021005 0.324755 1.0
28505 0.3
1 0.0 4 1.012755 1.0
41646 683292 491647 1991647
Data occupies 1500000 positions
0 1.0 0 1 0.000
7 1.0 0 2 0.000
10 1.0 0 16500 0.100
17 1.0 0 8250 0.100
20 1.0 0 3750 0.100
27 1.0 0 3750 0.100
150000 0 0 0 0 1 0 0 1
9771.23904582797 -2528.29955619919 1771.47219493205
2 3 9 8 0 1 0 0 1
300000 300000 300000
3 0 US 10621 1 42 4202 1 11467 ...
9771.23904582797 -2528.29955619919 1771.47219493205
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
animal ...
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
Covariance Structure Factor, order
Last line read was: Tr|1.an2 2 0 0 0 0
13 1 150000300000 8000
fat one.dat
Model specification: TERM LEVELS GAMMAS
Tr_1.weight 1 0.00 Trait 2 0.00 Tr.animal 16500 0.00
Tr_1.weight. 8250 0.00 Tr_1.an2 3750 0.10 Tr_1.weight. 3750 0.10
SECTIONS 300000 7 1
TYPE 0 0 203 -1 0 0
STRUCT 150000 0 0 0 0 1 0 0
2 3 9 8 0 1 0 0
3 6 9 11 0 1 0 0
8250 0 -2 0 0 1 2 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
Final parameter values 0.00000 0.00000 0.10000
0.10000 1.000002500.00000 1.000005018.00000********** 1.00000
42.000004202.00000 1.00000**********
Fault 1Covariance Structure Factor, order
Finished: Fri Apr 3 17:07:33 1998 Covariance Structure Factor, order
For some reason is does not like the way I hve set up the G structure but
don't know what is wrong.
Any hints would be appreciated.
Stephen Miller
Currently at AGBU