JAA 2.0 -- animal model iteration program for solutions and reliabilities
                Upgrade information - DRAFT

I. Misztal, University of Illinois
E-mail address: ignacy@uiuc.edu, tel. (217) 244-3164

last correction:, 10-02-93.


Disclaimer
  This program was developed for my own research. It is believed to be
  reasonably free of serious errors, but few attempts have been made to make
  it resistant to errors in parameter and input files. Please use it at
  your own risk.


Distribution
  The program is free for research applications. Please contact the author for
  information on commercial use.  In any case, please acknowledge the use of
  this program in publications.



The second edition of JAA is able to calculate reliabilities and it 
can accommodate covariables.  See the manual for the previous version 
(JAAMAN) for description of basic JAA program. This update only provides
additional descriptions for the new features.


Reliability
 Models are restricted to those supported by JAA
 (see the JAA manual). Reliabilities are estimated correctly when:
 1. Fixed management effect is first on the parameter list,
 2. animal effect is last on the parameter list,
 3. permament environmental effect (optional) is one before the last,
 4. the animal effect should be ordered as follows:
     a) animals with records,
     b) animals without records,
     c) unknown parent groups.
    A companion program RENUM can compute the desired ordering.
 5. Permanent environmental and animal effects should have the
    same number for same animals.
 6. JAA 2.0 will calculate reliabilities if the parameter file contains
    one additional line, containing 1. The program asks for the number of 
    iterations interactively. 10 rounds should be sufficient.

 The procedure is described in:

           Misztal, I., and G.R. Wiggans. 1988. Approximation of
           prediction error variance in large-scale animal models. J.
           Dairy Sci. 71 (Suppl. 2):27-32.

           Misztal, I., G. R. Wiggans, T.J. Lawlor, and T. Short. 1991.
           Continuous genetic evaluation of dairy cattle. J. Dairy Sci.
           74:2001-2009.

           Misztal, I. 1993. Single and multiple trait implementation
           of animal model for type traits. J. Dairy Science. 76:1421-1432.


Covariable
Covariable is denoted by negative number of levels. Please note that 
the program accepts integer input only, and that real numbers in input
will be truncated to integers.


Example for reliability

Parameter file (iap)
ic
is
pp
4 5 .8 5
2 3 0
3 6 10
4 4 20
1 14 -2
1

Data file (ic)
 1 1 1 1 10
 2 1 2 1 11
 3 2 3 2 15
 4 2 4 3 13
 5 3 5 4 14
 6 3 6 3 12

Pedigree file (is)
 1  12  8 2
 2   1  8 1
 3   2  9 1
 4   7 10 1
 5  12 11 2
 6   1 10 1
 7  13 14 3
 8   5 11 1
 9  13  8 2
 10  7 14 2
 11 13 14 3


Execution (more rounds may be necessary in practice)

[E:\FOR\PEV]jaa20
name of a file with parameters, con - if console:
iap
iteration no.  convergence criterion   last solution
          1        1.000000    0.000000E+00
          2    1.135215E-04    0.000000E+00
          3    1.573324E-04   -1.075020E-01
          4    1.654363E-04   -3.614665E-01
how many more iterations, 0-none?
0
In approximate Prediction Error Variance for animals it will be assumed that:
 first effect is fixed like HYS
 the last effect is animal
  effect before the last is permanent environment
detected       3 unknown parent group(s)

          Calculation of approximate PEV

iteration no. convergence PEV(1)    PEV(2) ....
           1    1.3012     .6620     .6620     .5749     .4878     .4878
more pev rounds?
5
           2     .8661     .6859     .6943     .5899     .4878     .4961
           3     .6385     .7128     .7296     .5998     .4997     .5182
           4     .4624     .7316     .7493     .6132     .5096     .5298
           5     .3375     .7448     .7631     .6244     .5172     .5415
           6     .2443     .7541     .7733     .6319     .5217     .5494
more pev rounds?
0
solutions and reliabilities were stored in file sol

[E:\FOR\PEV]

Solution file (sol)

    10.4747  .000
    13.9940  .000
    13.0449  .000
     -.0277  .000
      .0277  .000
      .0509  .000
     -.0509  .000
      .0498  .000
     -.0498  .000
      .0000  .000
      .0256  .000
     -.0510  .000
      .0250  .000
     -.0302  .274
      .2435  .279
      .4241  .240
     -.4721  .207
      .3785  .216
     -.4765  .243
     -.3796  .067
      .3472  .165
      .3671  .081
     -.5383  .100
      .1273  .075
      .1375  .000
      .0361  .000
     -.3615  .000



Example for regression

Data file (bb)

1 2 10
1 3 16
1 4 20


Execution

[E:\FOR\PEV]jaa20
name of a file with parameters, con - if console:
con
data name:
bb
name of file with animal relationships:
null
name of output file:
pp
no of factors, trait pos., rel. factor,iterations?:
2 3 0 1
 for each factor give position, no of levels,
 and variance ratio, 0 if fixed, negative if relat. matrix
  no of levels < 0 denotes covariable

2 -1 0
1 1 0
iteration no.  convergence criterion   last solution
          1        1.000000    2.298800E-02
how many more iterations, 0-none?
5
          2    1.959441E-05    4.439036E-02
          3    1.703084E-05    6.431834E-02
          4    1.479766E-05    8.287239E-02
          5    1.285323E-05    1.001460E-01
how many more iterations, 0-none?
0
solutions were stored in file sol

[E:\FOR\PEV]


Results (sol)
     5.0777
      .1001