Boulder 2003
! univariate Mx script for the analysis of one continuous phenotype
! using raw data input file
! MZM, DZM, MZF, DZF, DOSMF, DOSFM twins
! Evaluated models: 
! 1. ACE males, ACE females, DOS A-correlation is not DZ A-correlation
! 2. ACE males, ACE females, DOS A-correlation = DZ A-correlation
! Mx homepage: http://views.vcu.edu/mx

#define nvar 1				! For every instance of the word nvar in the script, 
							! Mx reads 1. This corresponds to one phenotype to be analysed
#define twonvar 1			! twice nvar, used for calculation of means
G1: calculation group
 Data Calc 

  Begin matrices;
     X Lower nvar nvar Free		! MALES additive genetic path coefficient (standard deviation)
     Y Lower nvar nvar Free		! MALES common environmental path coefficient (standard deviation)
     Z Lower nvar nvar Fixed		! MALES unique environmental path coefficient (standard deviation) 

     S Lower nvar nvar Free		! FEMALES additive genetic path coefficient (standard deviation)
     T Lower nvar nvar Free		! FEMALES common environmental path coefficient (standard deviation)
     U Lower nvar nvar Free		! FEMALES unique environmental path coefficient (standard deviation) 

     H Full 1 1	fix			! .5 for dz cov A
     F Full 1 1	free			! free; for dos cov A
  End matrices;

 Matrix H .5				! Matrix H is fixed and contains .5

  Begin algebra;
     A= X*X' ;			  	! MALES additive genetic variance
     C= Y*Y' ;   				! MALES common environmental variance
     E= Z*Z' ;				! MALES unique environmental variance

     K= S*S' ;			  	! FEMALES additive genetic variance
     L= T*T' ;   				! FEMALES common environmental variance
     M= U*U' ;				! FEMALES unique environmental variance

     V = 
     A%(A+C+E) | C%(A+C+E) | E%(A+C+E) _	    !MALES FIRST ROW standardized variance components
     K%(K+L+M) | L%(K+L+M) | M%(K+L+M) ;	    !FEMALES SECOND ROW standardized variance components

  End algebra;

 st 1.5 X 1 1 1			! provide starting values
 st 1.5 Y 1 1 1
 st 1.5 Z 1 1 1
 st 1.5 S 1 1 1			
 st 1.5 T 1 1 1
 st 1.5 U 1 1 1

 st 0.5 F 1 1 1
 Bound 0 0.5 F 1 1 1

end

G2: MZM twins, datagroup
Data NInput_vars= 12				! nr of inputvars per family
 Missing=-1.00						! missing values = -1.00
 REctangular file=all.dat				! read in raw datafile, must be in same directory

 LABELS     							! tell Mx what is found in the datafile
   nih_id country zygot6 rear ageA sexA ldllnA apoblnA apoelnA ageB sexB ldllnB apoblnB apoelnB

 Select if country = 1 ; 				! select Dutch twins, younger sample (Dorret)
 Select if  zygot6 = 1 ; 				! select MZM's
 Select  ldllnA ldllnB ;					! select one phenotype per twin member	
 Matrices = group 1 
     G Full 1 twonvar  free ;				mean phenotypes
 end matrices;

     Means G ;						! model for means

     Covariances						! model for MZM variance/covariances
	A+C+E	| A+C	 _
	A+C	| A+C+E	;

 st 15 G 1 1
Options RSiduals
End

G3: DZM twins, datagroup
Data NInput_vars= 14				! nr of inputvars per family
 Missing=-1							! missing values = -1.00
 REctangular file=all.dat				! read in raw datafile, must be in same directory

 LABELS     							! tell Mx what is found in the datafile
   nih_id country zygot6 rear ageA sexA ldllnA apoblnA apoelnA ageB sexB ldllnB apoblnB apoelnB

 Select if country = 1 and zygot6 = 2 ; 	! select Dutch twins, younger sample (Dorret) and DZM
 
 Select ldllnA ldllnB ;					! select one phenotype per twin member	
 Matrices = group 1 
        G Full 1 twonvar  free ;			! mean phenotypes
 end matrices;

    Means G ;							! model for means
    
    Covariances						! model for DZM variance/covariances
	A+C+E	| H@A+C	 _
	H@A+C	| A+C+E	;

 Options RSiduals
 
End

G4: MZF twins, datagroup
 Data NInput_vars= 14				! nr of inputvars per family
 REctangular file=all.dat				! read in raw datafile, must be in same directory
Missing=-1.00						! missing values = -1.00

 LABELS     							! tell Mx what is found in the datafile
   nih_id country zygot6 rear ageA sexA ldllnA apoblnA apoelnA ageB sexB ldllnB apoblnB apoelnB

 Select if country = 1 ; 				! select Dutch twins, younger sample (Dorret)
 Select if  zygot6 = 3 ; 				! select MZF's
 Select  ldllnA ldllnB ;					! select one phenotype per twin member	
 Matrices = group 1 
        G Full 1 twonvar  free ;			mean phenotypes
 end matrices;

    Means G | G ;						! model for means
    
    Covariances						! model for MZF variance/covariances
	K+L+M	| K+L	 _
	K+L	| K+L+M	

 Options RSiduals
 

G5: DZF twins, datagroup
 Data NInput_vars= 14				! nr of inputvars per family
 Missing=-1.00						! missing values = -1.00
 REctangular file=all.dat				! read in raw datafile, must be in same directory

 LABELS     							! tell Mx what is found in the datafile
   nih_id country zygot6 rear 
   ageA sexA ldllnA apoblnA apoelnA
   ageB sexB ldllnB apoblnB apoelnB

 Select if country = 1 ; 				! select Dutch twins, younger sample (Dorret)
 Select if  zygot6 = 4 ; 				! select DZF's
 Select  ldllnA ldllnB ;					! select one phenotype per twin member	
 Matrices = group 1 
         G Full 1 twonvar  free ;			! mean phenotypes
 end matrices;

    Means G ;							! model for means
    
    Covariances						! model for DZF variance/covariances
	K+L+M	| K+L	 _
	K+L	| K+L+M	;

 Options RSiduals
End

G6: DOS-MF twins, datagroup
Data NInput_vars= 14				! nr of inputvars per family
 Missing=-1.00						! missing values = -1.00
 CMatrix file=all.dat					! read in raw datafile, must be in same directory

 LABELS     							! tell Mx what is found in the datafile
   

 Select if country = 1 ; 				! select Dutch twins, younger sample (Dorret)
 Select if  zygot6 = 5 ; 				! select DOSmf's
 Select  ldllnA ldllnB ;					! select one phenotype per twin member	
 Matrices = group 1 
        G Full 1 twonvar  free ;			! mean phenotypes
 end matrices;

    Means G ;							! model for means
    
    Covariances						! model for DOSMF variance/covariances
	A+C+E	| F@(X*S')+(Y*T')	 _
	F@(S*X')+(T*Y')	| K+L+M	;

 Options RSiduals
 
End


G7: DOSFM twins, datagroup
 Data NInput_vars= 14				! nr of inputvars per family
 Missing=-1.00						! missing values = -1.00
 REctangular file=all.dat				! read in raw datafile, must be in same directory

 LABELS     							! tell Mx what is found in the datafile
   nih_id country zygot6 rear
   ageA sexA ldllnA apoblnA apoelnA
   ageB sexB ldllnB apoblnB apoelnB

 Select if country = 1 ; 				! select Dutch twins, younger sample (Dorret)
 Select if  zygot6 = 6 ; 				! select DOSfm's
 Select  ldllnA ldllnB ;					! select one phenotype per twin member	
  Matrices = group 1 
       G Full 1 twonvar  free ;			! mean phenotypes
 end matrices;

    Means G ;							! model for means
    
    Covariances						! model for DZ variance/covariances
	K+L+M	| F@(S*X')+(T*Y')	 _
	F@(X*S')+(Y*T')	| A+C+E	;

 Options RSiduals
Option Multiple sat=1399.434,290  	! -2LL of saturated model, will yield chi square for this model
 !Interval @95 V 1 1 1 V 1 1 2 V 1 1 3 V 1 2 1 V 1 2 2 V 1 2 3 P 1 1 1 P 1 2 1 G 1 1 1 F 1 1 1 

End


! FIX DOS COVARIANCE FOR A AT 0.5, WHICH EQUALS THE DZ COVARIANCE
! THIS PROVIDES A TEST OF WHETHER THE SAME GENES ARE EXPRESSED IN MALES AND FEMALES
DROP @.5 F 1 1 1 
end