! Simulate the data
! 	30% additive genetic
! 	20% common environment
!    	50% nonshared environment

#NGroups 4

G1: model parameters
Calculation
Begin Matrices;
	X lower 1 1 fixed
	Y lower 1 1 fixed
	Z lower 1 1 fixed
End Matrices;

Matrix X 0.5				!Unsquared Estimate for F of .25
Matrix Y 0.4				!Unsquared Estimate for Q of .16
Matrix Z 0.77				!Unsquared Estimate for E of .59

Begin Algebra;
	F = X*X' ; 
	Q = Y*Y' ;
	E = Z*Z' ;
End Algebra;
End

G2: IBD2 pairs
Calculation
Matrices = Group 1
Covariances F+Q+E	|	F+Q _
			F+Q		|	F+Q+E /
Options MX%E=ibd2.cov		!Stores the MZ Cov. matrix in mzsim.cov
End

G3: IBD1 pairs
Calculation
Matrices = Group 1
 H Full 1 1 
Covariances F+Q+E	|	F+H@Q _
			F+H@Q	|	F+Q+E /
Matrix H 0.5
Options MX%E=ibd1.cov		!Stores the DZ Cov. matrix in mzsim.cov
End

G4: IBD0 pairs
Calculation
Matrices = Group 1
 H Full 1 1 
Covariances F+Q+E	|	F_
			F		|	F+Q+E /
Matrix H 0.5
Options MX%E=ibd0.cov		!Stores the DZ Cov. matrix in mzsim.cov
End


! Second part of script
! Fit the wrong model to the simulated data 
! to calculate power

#NGroups 4
G1 : model parameters
Calculation
Begin Matrices;
	X lower 1 1 free
	Y lower 1 1 fixed		!Dropped C from model for test of power
	Z lower 1 1 free
End Matrices;

Begin Algebra;
	F = X*X' ;
	Q = Y*Y' ; 
	E = Z*Z' ; 
End Algebra;
End

G2 : ibd2 pairs
Data NInput_vars=2 NObservations=350	!Necessary to specify NObservations for baseline
CMatrix Full File=ibd2.cov				!Supplies the covariance matrix from above for MZ
Matrices= Group 1
Covariances F+Q+E	|	F+Q _
			F+Q 	| 	F+Q+E /
Option RSiduals
End

G3 : ibd1 pairs
Data NInput_vars=2 NObservations=350	!Necessary to specify NObservations for baseline
CMatrix Full File=ibd1.cov				!Supplies the covariance matrix from above for MZ
Matrices= Group 1
 H Full 1 1
Covariances F+Q+E	|	F+H@Q _
			F+H@Q 	| 	F+Q+E /
Matix H 0.5
Option RSiduals
End

G4 : ibd0 pairs
Data NInput_vars=2 NObservations=350	!Necessary to specify NObservations for baseline
CMatrix Full File=ibd0.cov				!Supplies the covariance matrix from above for MZ
Matrices= Group 1
 H Full 1 1
Covariances F+Q+E	|	F_
			F 	| 	F+Q+E /
Matix H 0.5
Option RSiduals

! Power for alpha = 0.05 and 1 df
Option Power= 0.05,1  					!Asks for power levels where alpha=.05
End