#ngroups 24 ! ! Ascertainment correction, estimating pi ! G1: Model parameters Calc Begin Matrices; H Full 1 1 Q Full 1 1 U unit 1 1 ! M Stan 2 2 Free ! L Stan 2 2 Free X Lower 1 1 Free Y Lower 1 1 Free Z Lower 1 1 Free W Lower 1 1 O Zero 1 1 End Matrices; Begin Algebra; A= X*X'; C= Y*Y'; E= Z*Z'; D= W*W'; L= A+C+D+E | H@A+C+Q@D _ H@A+C+Q@D | A+C+D+E ; ! DZ cov matrix M= A+C+D+E | A+C+D _ A+C+D | A+C+D+E ; ! MZ cov matrix End Algebra; Matrix H .5 Matrix Q .25 Start .6 all Bound 0 1 x 1 1 y 1 1 Bound 0.1 1 z 1 1 Intervals A 1 1 1 C 1 1 1 E 1 1 1 End #repeat 11 G2: MZ twin pairs Data Ninput=9 Labels studyid studyyr zygosity twin1 twin2 asc freq pihat threshold Ordinal File=scz_mx.1.dat Select if studyid = $repeat_number Select if zygosity = 1; Select twin1 twin2 asc freq pihat threshold ; Definition Asc Freq Pihat Threshold ; Begin Matrices= Group 1; F full 1 1 ! Frequency G full 1 4 ! to select ascertainment prob P full 1 1 ! ascertainment probability p T full 1 1 ! threshold End Matrices; Begin Algebra; S= (P) _ (P) _ P+P-P*P ; ! Vector of ascertainment probabilities J= (P+P)*\mnor(U_O_T_T_U)-P*P*\mnor(M_O|O_T|T_T|T_U|U); End Algebra: Specify F Freq Specify P Pihat Specify T threshold Matrix G 1 1 1 1 Specify G asc 0 asc 0 Covariances M; Thresholds T|T ; Frequency F ; #if repeat_number < 4 ! pihat is not 1 so weight is needed Weight \part(S,G)%J ; #elseif repeat_number = 9 ! pihat is not 1 so weight is needed Weight \part(S,G)%J ; #elseif repeat_number = 7 ! population sample, so no weight required ! Weight \part(S,G)%J ; #elseif repeat_number = 10 ! population sample, so no weight required ! Weight \part(S,G)%J ; #else ! pihat is 1 but -- not sampled Weight \part(S,G)%J ; #endif Options RSidual End G3: DZ twin pairs Data Ninput=9 Labels studyid studyyr zygosity twin1 twin2 asc freq pihat threshold Ordinal File=scz_mx.1.dat Select if studyid = $repeat_number Select if zygosity = 2 Select twin1 twin2 asc freq pihat threshold ; Definition Asc Freq Pihat Threshold ; Begin Matrices= Group 1 ; F full 1 1 ! Frequency G full 1 4 =G2 ! To select ascertainment probability P full 1 1 ! ascertainment probability p T full 1 1 ! threshold End Matrices; Specify F Freq Matrix G 1 1 1 1 Specify G asc 0 asc 0 Specify P Pihat Specify T threshold Begin Algebra; S= (P) _ (P) _ P+P-P*P ; ! Vector of ascertainment probabilities K= (P+P)*\mnor(U_O_T_T_U)-P*P*\mnor(L_O|O_T|T_T|T_U|U); End Algebra: Covariances L; Thresholds T|T ; Frequency F ; #if repeat_number < 4 ! pihat is not 1 so weight is needed Weight \part(S,G)%K ; #elseif repeat_number = 9 ! pihat is not 1 so weight is needed Weight \part(S,G)%K ; #elseif repeat_number = 10 ! population sample, so no weight required (could estimate threshold) ! Weight \part(S,G)%K ; #elseif repeat_number = 7 ! population sample, so no weight required (could estimate threshold) ! Weight \part(S,G)%K ; #else ! pihat is 1 but -- not sampled Weight \part(S,G)%K ; #endif Options RSidual NDecimals=4 Option jiggle func=1.e-12 End #end repeat Group 24 Constraint Constraint Begin Matrices = Group 2 U Unit 1 1 End matrices; Constraint U = A+C+E+D; Option multiple issat End Drop @.4461 Y 1 1 1 End Matrix 1 Y 0.18708286933869706927918743661583 End