! Estimate Correlations for DZ Twins by IBD status & MZ twins
! Dutch Adult Twins: Lipid levels

#define nvar 1
#define nvarx2 2
#NGroups 4

G1: DZ IBD2 twins
#include DutchDZ.dat
  Select if pi65cat =2;
  Select
   t1$var
   t2$var ;
 Begin Matrices; 
  M Full nvar nvarx2 Free      ! means
  S Diag nvarx2 nvarx2 Free    ! standard deviations
  R Stnd nvarx2 nvarx2 Free    ! correlations
 End Matrices;
  Matrix M 4 4                 ! starting values 
  Matrix S .5 .5
  Matrix R .5
 Means M;
 Covariance S*R*S';
End

G2: DZ IBD1 twins
#include DutchDZ.dat
  Select if pi65cat =1;
  Select
   t1$var
   t2$var ;
 Begin Matrices;
  M Full nvar nvarx2 Free
  S Diag nvarx2 nvarx2 Free
  R Stnd nvarx2 nvarx2 Free
 End Matrices;
  Matrix M 4 4
  Matrix S .5 .5
  Matrix R .5
 Means M;
 Covariance S*R*S';
End

G3: DZ IBD0 twins
#include DutchDZ.dat
  Select if pi65cat =0;
  Select
   t1$var
   t2$var ;
 Begin Matrices;
  M Full nvar nvarx2 Free
  S Diag nvarx2 nvarx2 Free
  R Stnd nvarx2 nvarx2 Free
 End Matrices;
  Matrix M 4 4
  Matrix S .5 .5
  Matrix R .5
 Means M;
 Covariance S*R*S';
End

G4: MZ twins
#include DutchMZ.dat
  Select
   t1$var
   t2$var ;
 Begin Matrices;
  M Full nvar nvarx2 Free      ! means
  S Diag nvarx2 nvarx2 Free    ! standard deviations
  R Stnd nvarx2 nvarx2 Free    ! correlations
 End Matrices;
  Matrix M 4 4                 ! starting values 
  Matrix S .5 .5
  Matrix R .6
 Means M;
 Covariance S*R*S';
 Option Multiple Issat
End

Save lipidcor.mxs
! Test for linkage
! Set 3 DZ IBD correlations equal
 Equate R 1 2 1 R 2 2 1 R 3 2 1
End 

Get lipidcor.mxs
! Test for residual polygenic variance
! Set DZ IBD2 correlation equal to MZ correlation
 Equate R 1 2 1 R 4 2 1
Exit