! F.V. Rijsdijk
! Polychoric Cor Script for CTables, of categorical variables (twin1/twin2)

! Note: the threshold model is different then when using RAW ORD:
! 	           TWIN 2
!	             
!	          0	    1	   2	   	
!    T         0   cell1	| cell2	| cell3	
!    W   	   ___________________________	row threshold 1	
!    I           1   cell4	| cell5	| cell6	
!    N	____________________________	row threshold 2
!    1	2   cell7	| cell8	| cell9	
!		^	^	
! 	      col thr 1	col thr2	

! THRESHOLD MODEL  :
! (1,1) (1,2)  = row thresholds =	TH of twin1	=T
! (2,1) (2,2)  = col thresholds =	TH of twin2 	=U
! So, need to do T_U

#ngroups	2

G1: Correlation matrix for MZ pairs
Data NInputv=2
CTable 3 3
385 23 6 
28 37 4 
3 3 12 

Begin Matrices;
R STAN 2 2	FREE			! MZ cor
T FUL 1 2		FREE		! TH of twin1
U FUL 1 2		FREE		! TH of twin2
End matrices;

COvariance	 	R/		!Model for the MZ correlation

Thresholds 		T_U /		!Model for the thresholds

MA T 
1.8  2.4  				!starting values for the Twin 1 thresholds
MA U 
1.8  2.4  				!starting values for the Twin 2 thresholds
MA  R  .6				!starting value Cor
Interval R 2 1 
options RS
end

G2: Correlation  matrix DZ
Data  NInputv=2
CTable 3 3
334 37 19 
56 32 1 
12 2 10 

Begin Matrices;
R STAN 2 2	FREE			! MZ cor
T FUL 1 2		FREE		! TH of twin1
U FUL 1 2		FREE		! TH of twin2
End matrices;

COvariance	 	R/		!Model for the MZ correlation

Thresholds 		T_U /		!Model for the thresholds

MA T 
1.8  2.4  				!starting values for the Twin 1 thresholds
MA U 
1.8  2.4  				!starting values for the Twin 2 thresholds
MA  R  .6				!starting value Cor
Interval R 2 1 
options RS
end