! covariance structure for 3 sib-pairs - prog modified 06/11/2000
! to form basic script for QTL scans
! using weighted likelihood approach / full ibd distribution
! of sib pairs 

! QTL estimated by  - heterogeneity model -
! the weighted likelihood of 10 covariance matrices  

! global dimensions
! values of ncomb 2sibs = 3; 3sibs=10; 4sibs=36; 5sibs=136; 
!                            6sibs=528; 7sibs=2080 ;8sibs=8256; 9sibs=32896
 #define nvar 1
 #define nsib 2
 #define ncomb 3       !(2**(2*nsib-3))+(2**(nsib-1))-(2**(nsib-2))
 #define nconfig 6     !nsib*ncomb

 Title QTL model two group - DZ's
 calc NGroups=2 
 Matrices
! reads matrix Y of QTL coeficients for covariance matrix from external file
! residual familial and non specific environmental variance
 A Lower nvar nvar Free ! background A and/or C - residual familial
 E Lower nvar nvar Free ! random environment

 Q Full nvar 1 Free      ! qtl effect
 Y Full nconfig nsib  
 B Stan nsib nsib
 I Iden nsib nsib
 U unit ncomb 1
End matrices

!dimensions of B nsib*nsib-((nsib^2-nsib)/2)
Matrix B .5 
Matrix Y File=ibdstr2.out

Begin algebra;

!Variances algebra
!Proportion of total phenotypic variance
 R = (Q*Q')@Y + (E*E')@(U@I) + (A*A')@(U@B) ;
!R=(E*E')@(U@I);
 x=A|Q|E;
End Algebra;

 Option mxx=mix.mat
 option append
 option format=(7(F13.6,1x))
End group

 Title QTL model 4sibs weighted likelihood
 Data  NInput=6 NModel=ncomb
 RECTANGULAR FILE=mxgh2.rec

! READ IN IBD WEIGHTS FOR THE 3 SIBSHIP TYPES


 LABELS famid p1 p2 Z1 Z2 Z3  

              

SELECT p1 p2  Z1 Z2 Z3 /

DEFINITION    Z1 Z2 Z3 /


Matrices;

R computed = R1
N Unit ncomb nsib
! ibds for 2 sibs
! matrices for means model
   !M Full 1 nsib Free      ! mean values
M Full 1 1 Free
Z Full 1 ncomb 
End Matrices;
Specify Z -1 -2 -3;
Begin algebra;
End Algebra;
Means N@M;

Covariance R ;

Weights z;
Option Rsiduals
!start 2 q 1 1 1
start 1 E 1 1 1 !all
Start 0 M 2 1 1 


!Interval q 1 1 1 
Option nd=4
Option multiple it=1000
option samecov issat
End

drop @.0 q 1 1 1
end