Bivariate structure

# 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
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

```