!Fitting genetic parameters jointly to testcross means and variances
!ILS x ISS cross data from Owens (2001)
!Open field activity change scores: saline vs. low dose ethanol

!Single locus model
!
#NGroups 6
!
Generation P1
Data NInput_variables=1 NObservations=27
CMatrix Symmetric 
182.43              ! observed variance
Means
8.88                ! observed mean
Matrices
E full 1 1 free     ! environmental variance parameter
h diag 1 1 fixed    ! h = 1/2 constant
q diag 1 1 fixed    ! q = 1/4 constant
M full 1 1 free     ! midpoint mean
Add full 1 1 free   ! additve effect of single locus
Dom full 1 1 free   ! dominance effect of single locus
!
V full 1 1 free     ! note: separate parameter for P1 variance
!
Covariance V /      ! free parameter for P1 variance
Means M+A /         ! model for the expected mean
Matrix h 
.5                  ! defines h constant = 1/2
Matrix q 
.25                 ! defines q constant = 1/4
Start 5 All         ! supply start values
Options RS ND=4     ! output options: residuals, 4 decimals
End group;
!
!
Generation P2
Data NInput_variables=1 NObservations=17
CMatrix Symmetric 
20.85
Means 
-1.26
Matrices = Group 1
Covariance E /
Means M-A /
Options RS NDecimals=4 
End group;
!
!
Generation F1
Data NInput_variables=1 NObservations=45
CMatrix Symmetric 
36.22
Means
6.81
Matrices = Group 1
Covariance E /
Means M + D /
Options RS NDecimals=4 
End group;
!
!
Generation F2
Data NInput_variables=1 NObservations=106
CMatrix Symmetric 
29.48
Means
4.42
Matrices = Group 1
Covariance E + h @ (A*A') + q @ (D*D') /
Means M + h @ D /
Options RS NDecimals=4
End group;
!
!
Generation B1
Data NInput_variables=1 NObservations=45
CMatrix Symmetric 
31.21
Means
7.7
Matrices = Group 1
Covariance E + q @ (A*A') + q @ (D*D') - h @ (A*D')/
Means M + h @ A + h @ D /
Options RS NDecimals=4
End group;
!
!
Generation B2
Data NInput_variables=1 NObservations=27
CMatrix Symmetric 
25.19
Means
1.83
Matrices = Group 1
Covariance E + q @ (A*A') + q @ (D*D') + h @ (A*D')/
Means M - h @ A + h @ D /
Options RS IT=1000 NDecimals=4
End group;