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