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Univariate Analysis in Mx

Univariate Analysis in Mx. Boulder, 2004. Group Structure. Title Type: Data/ Calculation/ Constraint Reading Data Matrices Declaration Assigning Specifications/ Values Matrix Algebra and/or Means/ Covariances Options End. Additional Commands. ! Comments #NGroups <number of groups>

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Univariate Analysis in Mx

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  1. Univariate Analysis in Mx Boulder, 2004

  2. Group Structure • Title • Type: Data/ Calculation/ Constraint • Reading Data • Matrices Declaration • Assigning Specifications/ Values • Matrix Algebra and/or • Means/ Covariances • Options • End

  3. Additional Commands • ! Comments • #NGroups <number of groups> • #define <name> <number> e.g. #define nvar 1 • #define <$name> <string> • #include filename

  4. Reading Data • Data NInputvars=<n> [NObs=<n>] • Rectangular File= • Missing= • Labels • Select if • Select if zyg =1; • Select Summarized in filename.dat

  5. Matrices Declaration • Begin Matrices; • <Name> <type> <rows> <columns> • … • End Matrices; • Matrix Types: Mx manual p. 56 • Begin Matrices = Group <number>

  6. Matrix Algebra • Begin Algebra; • <matrix name> = <matrix formula>; • <matrix name> = <matrix formula>; • … • End Algebra; • Matrix Operations: Mx Manual p. 59 • Matrix Functions: Mx Manual p. 64

  7. Means/Covariances • Means <formula>; e.g. Means M; dimensions of expected matrix must equal dimensions of observed means • Covariances <formula>; dimensions of expected covariance matrix must equal the square of the number of variables

  8. Mx Script I #NGroups 2 #define nvar 1 #define nsib 2 G1: male MZ twin pairs Data NInput_vars=5 Missing=-1.00 Rectangular File=Agg10.rec Labels ZYG RB10A AGG10A RB10B AGG10B Select if zyg =1 ; ! select MZM twins Select AGG10A AGG10B ; May be put in agg10.dat and included with #Include filename

  9. Mx Script II Begin Matrices; X Symm nsib nsib Free ! covariances I Iden nsib nsib M Full nvar nsib Free ! means End Matrices; Start 2 X 1 1 X 2 2 ! starting values for variances Start 0.5 M 1 1 M 1 2 ! starting values for means Begin Algebra; O= \sqrt(I.X)~&X; ! MZM correlation End Algebra; Means M; ! model for MZM means Covariances X; ! model for MZM (co)variances ! Interval @95 O 2 1 Option RSiduals End

  10. Mx Script III Begin Matrices; Y Symm nsib nsib Free ! covariances I Iden nsib nsib N Full nvar nsib Free ! means End Matrices; Start 2 Y 1 1 X 2 2 ! starting values for variances Start 0.5 N 1 1 N 1 2 ! starting values for means Begin Algebra; P= \sqrt(I.Y)~&Y; ! DZM correlation End Algebra; Means N; ! model for DZM means Covariances Y; ! model for DZM (co)variances ! Interval @95 P 2 1 Option RSiduals End

  11. Mx Script IV ! equate means Equate M 1 1 1 M 1 1 2 N 2 1 1 N 2 1 2 End ! equate means and variances Equate X 1 1 1 X 1 2 2 Y 2 1 1 Y 2 2 2 End

  12. Path Diagram for MZ and DZ twins 1.00 / 0.50 1.00 1.00 / 0.25 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 A1 C1 E1 D1 A2 C2 E2 D2 a c e d a c e d P1 P2

  13. MZ Twins

  14. DZ Twins

  15. Univariate Mx Script I #NGroups 3 #define nvar 1 ! define nvar as number of variables #define nsib 2 Title G1: Model Parameters Calculation Begin Matrices; X Lower nvar nvar Free ! additive genetic structure Y Lower nvar nvar Free ! common environmental structure Z Lower nvar nvar Free ! unique environmental path struct. W Lower nvar nvar Free ! dominance structure H Full 1 1 ! scalar fixed @ .5 for DZ cov of A Q Full 1 1 ! scalar fixed @ .25 for DZ cov of D End Matrices;

  16. Declared Matrices 1.00 / 0.50 [H] 1.00 1.00 / 0.25 [Q] 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 A1 C1 E1 D1 A2 C2 E2 D2 a [X] c [Y] e [Z] d [W] a [X] c [Y] e [Z] d [W] P1 P2

  17. Univariate Mx Script II Matrix H .5 Matrix Q .25 Start .5 all ! starting values for free parameters Begin Algebra; A= X*X' ; ! additive genetic variance C= Y*Y' ; ! common environmental variance E= Z*Z' ; ! unique environmental variance D= W*W’; ! dominance variance V= A+C+E+D; ! total variance P= A|C|E|D; ! put parameters in one matrix S= P@V~; ! standardized variance components End Algebra; Interval @95 S 1 1 – S 1 3 ! confidence intervals End

  18. Univariate Mx Script III G2: male MZ twins, datagroup Data NInput_vars=5 Missing=-1.00 Rectangular File= Agg10.rec Labels ZYG RB10A AGG10A RB10B AGG10B Select if zyg =1; ! select MZM twins Select AGG10A AGG10B ; Begin Matrices = Group 1; M Full nsib nvar Free ! means End Matrices; Start 0.5 M 1 1 M 1 2 ! starting values for means Means M; ! model for means Covariances ! model for MZ variance/covariances A+C+E+D | A+C+D _ A+C +D | A+C+E+D ; Options RSiduals End

  19. Univariate Mx Script IV G3: male DZ twins, datagroup Data NInput_vars= Missing=-1.00 Rectangular File= Agg10.rec Labels ZYG RB10A AGG10A RB10B AGG10B Select if zyg =2; ! select DZM twins Select AGG10A AGG10B ; Begin Matrices = Group 1; M Full nsib nvar Free ! means End Matrices; Start 0.5 M 1 1 M 1 2 ! starting values for means Means M; ! model for means Covariances ! model for DZ variance/covariances A+C+E+D | H@A+C+Q@D _ H@A+C+Q@D | A+C+E+D ; Option RSiduals End

  20. Path Diagram to Matrices

  21. Mx Script V Save satm.mxs ! equate means Equate M 1 1 1 M 1 1 2 N 2 1 1 N 2 1 2 End ! equate means and variances Equate X 1 1 1 X 1 2 2 Y 2 1 1 Y 2 2 2 End Get satm.mxs ! equate variances only Equate X 1 1 1 X 1 2 2 Y 2 1 1 Y 2 2 2 End

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