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Session 1

Session 1. 1 Check installations 2 Open Mplus 3 Type basic commands 4 Get data read in, spat out &read in again 5 Run an analysis 6 What has it done?. Session 2. 1 Mplus input file command structures 2 Mplus conventions 3 Mplus punctuation CaSeS ; : (.) & green! 4 Common typos in input

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Session 1

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  1. Session 1 1 Check installations2 Open Mplus3 Type basic commands4 Get data read in, spat out &read in again5 Run an analysis6 What has it done?

  2. Session 2 1 Mplus input file command structures2 Mplus conventions 3 Mplus punctuation CaSeS ; : (.) & green!4 Common typos in input 5 Mplus output file structure 6 Output options inc. saves and plots

  3. Session 1 1 Check installations2 Open Mplus3 Type basic commands4 Get data read in, spat out &read in again5 Run an analysis6 What has it done?

  4. Odd1 Even1 Sum1 Case1 Odd2 Even2 Sum2 Case2 7 5 12 1 7 5 12 1 4 4 8 1 4 3 7 1 12 10 22 1 12 12 24 1 5 5 10 1 7 7 14 1 3 7 10 1 3 5 8 1 4 2 6 0 3 1 4 0 3 5 8 1 2 3 5 0 2 2 4 0 3 3 6 0 7 7 14 1 6 8 14 1 3 3 6 0 2 3 5 0 0 2 2 0 3 2 5 0 11 11 22 1 8 8 16 1 12345678901234567890123456789012 12341234XXXX123412341234XXXX1234 DATA: Dunn Statistics in Psychiatry GHQ12 T1 T2 Clinical Psychology students General Health Questionnaire Short self-report questionnaire Used to screen for common mental Disorder (anxiety and depression)

  5. Warning, detour ahead …

  6. Getting (past) the basics … • The importance of total control over data • The value of learning simple FORTRAN formatting statements • LISCOMP, the predecessor to Mplus, • And Mplus itself, is written in FORTRAN • Reading data in uses simple conventions • F / I / G / E / X / T • 34.234 could be read as F6 • 92 read as F2.1 would be 9.1 • Width in columns for the real number • then number of numerals that appear after the decimal point

  7. Overcoming limitations • Of the Mplus demo • It has a limit on the number of variables • Depending on what analysis you are doing these limits are • 4 variables • 6 variables • We shall (largely) work within them • But we can also beat them to make life easier for you

  8. FORTRAN FORMATSTATEMENTS • I X T and / • I1 • Integer single digit • 4X • skip four columns without reading anything • Can jump over data in the middle of a file this way • i.e. columns in text files can be ignored • T10 • Jump from first column to and start reading at column ten, then process rest of format instructions • Can jump over data at the start of a file this way • / is to jump to next line (when data has more “records” lines of data per individidual) 001 1 2 3 4 5 6 rather than 001 1 2 3 4 5 6

  9. Specifications for formatted inputsome F5 some F6 Dunn SiP Book GHQ12 from clinical psychology students Odd1 Even1 Sum1 Case1 Odd2 Even2 Sum2Case2 ------------------------------------------ | 7 5 12 1 7 5 12 1 | 4 4 8 1 4 3 7 1 | 12 10 22 1 12 12 24 1 | 5 5 10 1 7 7 14 1 | 3 7 10 1 3 5 8 1 | 4 2 6 0 3 1 4 0 | 3 5 8 1 2 3 5 0 | 2 2 4 0 3 3 6 0 | 7 7 14 1 6 8 14 1 | 3 3 6 0 2 3 5 0 | 0 2 2 0 3 2 5 0 | 11 11 22 1 8 8 16 1 123451234512345123456123451234561234512345 Numbered columns for field widths (guide for eye and FORTRAN SYNTAX) F5 F5 F5 F6 F5 F6 F5 F5 i.e (3F5,F6,F5,F6,2F5)

  10. End of detour …

  11. Analysis time • Time to begin! • A first orientation to Mplus in action • Data • Input file syntax • Output • Plot • Actually just doing data transformation at this stage • Not doing any analysis

  12. Odd1 Even1 Sum1 Case1 Odd2 Even2 Sum2 Case2 7 5 12 1 7 5 12 1 4 4 8 1 4 3 7 1 12 10 22 1 12 12 24 1 5 5 10 1 7 7 14 1 3 7 10 1 3 5 8 1 4 2 6 0 3 1 4 0 3 5 8 1 2 3 5 0 2 2 4 0 3 3 6 0 7 7 14 1 6 8 14 1 3 3 6 0 2 3 5 0 0 2 2 0 3 2 5 0 11 11 22 1 8 8 16 1 12345678901234567890123456789012 12341234XXXX123412341234XXXX1234 DATA: Dunn Statistics in Psychiatry GHQ12 T1 T2 Clinical Psychology students General Health Questionnaire Short self-report questionnaire Used to screen for common mental Disorder (anxiety and depression)

  13. Odd1 Even1 Sum1 Case1 Odd2 Even2 Sum2 Case2 7 5 12 1 7 5 12 1<snip> 3 3 6 0 2 3 5 011 11 22 1 8 8 16 1 DATA: FILE IS "c:\dunn_ghqoddeven12.dat"; FORMAT IS I4 I4 4x I4 I4 I4 4x I4;

  14. Odd1 Even1 Sum1 Case1 Odd2 Even2 Sum2 Case2 7 5 12 1 7 5 12 1<snip> 3 3 6 0 2 3 5 011 11 22 1 8 8 16 1 DATA: FILE IS "c:\dunn_ghqoddeven12.dat"; FORMAT IS I4 I4 4x I4 I4 I4 4x I4; DEFINE: sum1 = odd1 + even1; diff1= odd1 - even1; !sum2 = odd2 + even2; !diff2= odd2 - even2; VARIABLE: NAMES ARE odd1 even1 case1 odd2 even2 case2; **File actually contains SUM1 & SUM2 variables** USEVARIABLES ARE sum1 diff1; This file is dunn_GHQ12_T1T2_ClinPsych_SiP.inp WARNING - more syntax below in the file estimates a correlation and produces a scatter plot

  15. Odd1 Even1 Sum1 Case1 Odd2 Even2 Sum2 Case2 7 5 12 1 7 5 12 1<snip> 3 3 6 0 2 3 5 011 11 22 1 8 8 16 1 ANALYSIS: ESTIMATOR=ML; MODEL: sum1 with diff1; !sum1 with diff1 sum2 diff2; ! diff1 with sum2 diff2; ! sum2 with diff2; OUTPUT: STDY SAMPSTAT; PLOT: TYPE IS PLOT1; This file is dunn_GHQ12_T1T2_ClinPsych_SiP.inp

  16. ANALYSIS: ESTIMATOR=ML; MODEL: sum1 with diff1; !sum1 with diff1 sum2 diff2; ! diff1 with sum2 diff2; ! sum2 with diff2; OUTPUT: STDY SAMPSTAT; PLOT: TYPE IS PLOT1; This file is dunn_GHQ12_T1T2_ClinPsych_SiP.inp

  17. SUMMARY OF ANALYSIS [dunn_GHQ12_T1T2_ClinPsych_SiP.out] Number of groups 1 Number of observations 12 Number of dependent variables 2 Number of independent variables 0 Number of continuous latent variables 0 Observed dependent variables Continuous SUM1 DIFF1

  18. [dunn_GHQ12_T1T2_ClinPsych_SiP.out] [dunn_GHQ12_T1T2_ClinPsych_SiP.out] Estimator ML Information matrix OBSERVED Maximum number of iterations 1000 Convergence criterion 0.500D-04 Maximum number of steepest descent iterations 20 Input data file(s) c:\dunn_ghqoddeven12.dat Input data format (I4 I4 4X I4 I4 I4 4X I4)

  19. [dunn_GHQ12_T1T2_ClinPsych_SiP.out] SAMPLE STATISTICS [dunn_GHQ12_T1T2_ClinPsych_SiP.out] Means SUM1 DIFF1 ________ ________ 1 10.333 -0.167 Covariances SUM1 DIFF1 ________ ________ SUM1 37.222 DIFF1 3.389 2.972 Correlations SUM1 DIFF1 ________ ________ SUM1 1.000 DIFF1 0.322 1.000

  20. THE MODEL ESTIMATION TERMINATED NORMALLY TESTS OF MODEL FIT Chi-Square Test of Model Fit Value 0.000 Degrees of Freedom 0 P-Value 0.0000 Chi-Square Test of Model Fit for the Baseline Model Value 1.315 Degrees of Freedom 1 P-Value 0.2515 CFI/TLI CFI 1.000 TLI 1.000 Loglikelihood H0 Value -61.634 H1 Value -61.634 [dunn_GHQ12_T1T2_ClinPsych_SiP.out]

  21. [dunn_GHQ12_T1T2_ClinPsych_SiP.out] MODEL RESULTS Two-Tailed Estimate S.E. Est./S.E. P-Value SUM1 WITH DIFF1 3.389 3.190 1.062 0.288 Means SUM1 10.333 1.761 5.867 0.000 DIFF1 -0.167 0.498 -0.335 0.738 Variances SUM1 37.221 15.195 2.450 0.014 DIFF1 2.972 1.213 2.449 0.014 STANDARDIZED MODEL RESULTS STDY Standardization Two-Tailed Estimate S.E. Est./S.E. P-Value SUM1 WITH DIFF1 0.322 0.259 1.245 0.213 Means SUM1 1.694 0.450 3.761 0.000 DIFF1 -0.097 0.289 -0.334 0.738 Variances SUM1 1.000 0.000 999.000 999.000 DIFF1 1.000 0.000 999.000 999.000

  22. [dunn_GHQ12_T1T2_ClinPsych_SiP.out/gph]

  23. Session 2 1 Mplus input file COMMAND STRUCTURES:2 Mplus conventions 3 Mplus punctuation ; : (.) & green! comment4 Common typos in input 5 Mplus output file structure 6 Output options inc. saves and plots

  24. Command Structures TITLE: DATA: VARIABLE: DEFINE: ANALYSIS: MODEL: OUTPUT: SAVEDATA: PLOT: Simple command structures can be built from the GUI

  25. Conventions Main command structures appear first on lines as BLOCK CAPS: OTHER COMMANDS THEN FOLLOW either IN CAPS or lowercase; All lines end with a ; but lines can run over more than one line and end with a colon;

  26. We’ve seen this already … TITLE: DATA: VARIABLE: DEFINE: ANALYSIS: MODEL: OUTPUT: SAVEDATA: PLOT: Mplus does not mind which Order commands come in …. You do not need them all! Actually you can do a lot With a little!

  27. Mplus is not CaSe SeNsItIvE ! Exclamations - are like comment statements, the editor turns them green

  28. All lines end with a semi-colon The most common typo is probably omitting one of these or typing two;;

  29. { ( [ Mplus parameters } ) } • Variances or Residual Variances • Variable name without brackets • [Means] or Thresholds [catvar$1] • Variable name in square brackets • (round brackets) • Variable name in round brackets • {Scale factors} • Variable name in curly brackets

  30. Mplus output file structure-has to be seen to be believed! OUTPUT: options here govern what you will see in the text output file; SAVEDATA: options here will determine what else is saved in new text files; PLOT: options here will enable you to view graphs of certain things;

  31. OUTPUT: !many more! SAMP STAND RES ! short for residuals) MOD (number) CINT !(three types) TECHn !(14 types-no’s 1 to 14) FSCOEFF FSDETERMINACY + a few more … don’t forget that final colon; PLOT: TYPE IS PLOT1 PLOT2 or PLOT3; ! That’s about it OUTPUT: and PLOT:

  32. SAVEDATA: • You can save • You data (the subset of variables that you modelled only, or these variables plus some more that you want to keep even though you did not use them e.g. IDVARIABLE a subid or AUXILIARY other variables such as sex etc. • You can also save • Factor scores (appended to your data) • Latent class memberships • Cook’s distances or “influence” statistics • There are also other things you can save …. • These depend on what analysis you have constructed

  33. Watch out for the GUIspot here ….. (if you want it)

  34. Watch out for the GUI-2

  35. GUI doesn’t build this part … E1 E2 E3 E4 V1 V2 V3 V4 F1 F2

  36. GHQ T1 T2Psychological Distress E1 E2 E3 E4 Odd 1 Even 1 Odd 2 Even 2 GHQ T1 GHQ T2 Correlation Among GHQ scores at T1 and T2 (could be regression)

  37. Acronyms / Abbreviations / Fit Chi-Square [Pearson and Likelihood Ratio] CFI/TLI Loglikelihood H0 Value H1 Value Information Criteria Akaike (AIC) Bayesian (BIC) Sample-Size Adjusted BIC (n* = (n + 2) / 24) RMSEA Root Mean Square Error Of Approximation SRMR Standardized Root Mean Square Residual

  38. TITLE: Dunn SiP Book GHQ12 from clinical psychology students Odd1 Even1 Sum1 Case1 Odd2 Even2 Sum2 Case2 7 5 12 1 7 5 12 1 4 4 8 1 4 3 7 1 12 10 22 1 12 12 24 1 5 5 10 1 7 7 14 1 3 7 10 1 3 5 8 1 4 2 6 0 3 1 4 0 3 5 8 1 2 3 5 0 2 2 4 0 3 3 6 0 7 7 14 1 6 8 14 1 3 3 6 0 2 3 5 0 0 2 2 0 3 2 5 0 11 11 22 1 8 8 16 1 DATA: FILE IS "c:\dunn_ghqoddeven12.dat"; FORMAT IS I4 I4 4x I4 I4 I4 4x I4; VARIABLE: NAMES ARE odd1 even1 case1 odd2 even2 case2; USEVARIABLES ARE odd1 even1 odd2 even2;

  39. Out and back: Bob the (re)-builder walk through • Reading data with a fixed format • Same kind of data now, bigger dataset • Do an analysis and save data • Then read back in formatted • hals_ighq.inp • Then • read_savehalstxt.inp

  40. DATA: FILE IS c:\halsghq3.dat; VARIABLE: NAMES ARE GHQ22 GHQ24 GHQ28 AGEYRS IDNUM SEXM1F2; USEVARIABLES ARE AGEYRS GHQ22 GHQ24 GHQ28; CATEGORICAL ARE GHQ22 GHQ24 GHQ28; IDVARIABLE = IDNUM; AUXILIARY = SEXM1F2; MODEL: IGHQ BY GHQ22 GHQ24 GHQ28;!define IGHQ measured BY 3vars IGHQ ON AGEYRS; !Here regressing latent factor ON age SAVEDATA: FILE IS savedata.txt; “Passing out” variables[quick2_rebuild2.inp] Little words IS/ARE are optional

  41. HALSGHQ3.DAT "halsGHQ3.dat“ 1.000 0.000 0.000 65.000 8514 2.000 0.000 0.000 0.000 74.000 7642 1.000 0.000 1.000 0.000 62.000 12249 2.000 2.000 0.000 2.000 46.000 12024 1.000 0.000 0.000 0.000 44.000 8808 2.000 0.000 0.000 1.000 32.000 4863 2.000 1.000 0.000 0.000 22.000 4849 1.000 0.000 0.000 0.000 60.000 8005 2.000 0.000 1.000 0.000 36.000 5923 1.000 0.000 0.000 0.000 58.000 3080 1.000 1.000 0.000 1.000 63.000 4446 1.000 0.000 0.000 0.000 69.000 6357 1.000 <snipped after a dozen lines> GHQ22 GHQ24 GHQ28 AGEYRS IDNUM SEXM1F2

  42. SUMMARY OF ANALYSIS Number of groups 1 Number of observations 6553 Number of dependent variables 3 Number of independent variables 1 Number of continuous latent variables 1 Observed dependent variables Binary and ordered categorical (ordinal) GHQ22 GHQ24 GHQ28 Observed independent variables AGEYRS Observed auxiliary variables SEXM1F2 Continuous latent variables IGHQ Variables with special functions ID variable IDNUM Output .

  43. SAVEDATA INFORMATION Order and format of variables GHQ22 F10.3 GHQ24 F10.3 GHQ28 F10.3 AGEYRS F10.3 IDNUM I6 SEXM1F2 F10.3 Save file savedata.txt Save file format 4F10.3 I6 F10.3 Save file record length 5000 Output .. 1.000 0.000 0.000 65.000 8514 2.000 0.000 0.000 0.000 74.000 7642 1.000 0.000 1.000 0.000 62.000 12249 2.000 2.000 0.000 2.000 46.000 12024 1.000 0.000 0.000 0.000 44.000 8808 2.000 0.000 0.000 1.000 32.000 4863 2.000 1.000 0.000 0.000 22.000 4849 1.000 0.000 0.000 0.000 60.000 8005 2.000 0.000 1.000 0.000 36.000 5923 1.000 0.000 0.000 0.000 58.000 3080 1.000 1.000 0.000 1.000 63.000 4446 1.000 0.000 0.000 0.000 69.000 6357 1.000

  44. INPUT READING TERMINATED NORMALLY SUMMARY OF ANALYSIS Number of groups 1 Number of observations 6553 Number of dependent variables 3 Number of independent variables 1 Number of continuous latent variables 1 Observed dependent variables Binary and ordered categorical (ordinal) GHQ22 GHQ24 GHQ28 Observed independent variables AGEYRS Observed auxiliary variables SEXM1F2 Continuous latent variables IGHQ Variables with special functions ID variable IDNUM Quick2rebuildout.out

  45. (cont) Estimator WLSMV Maximum number of iterations 1000 Convergence criterion 0.500D-04 Maximum number of steepest descent iterations 20 Parameterization DELTA Input data file(s) c:\halsghq3.dat Input data format FREE Quick2rebuildout.out

  46. SUMMARY OF CATEGORICAL DATA PROPORTIONS GHQ22 Category 1 0.444 Category 2 0.343 Category 3 0.167 Category 4 0.046 GHQ24 Category 1 0.713 Category 2 0.202 Category 3 0.062 Category 4 0.023 GHQ28 Category 1 0.523 Category 2 0.329 Category 3 0.120 Category 4 0.027 Quick2rebuildout.out

  47. MODEL ESTIMATION TERMINATED NORMALLY :TESTS OF MODELFIT Chi-Square Test of Model Fit Value 20.172* Degrees of Freedom 2** P-Value 0.0000 Chi-Square Test of Model Fit for the Baseline Model Value 12807.273 Degrees of Freedom 4 P-Value 0.0000 CFI/TLI CFI 0.999 TLI 0.997 Number of Free Parameters 13 RMSEA (Root Mean Square Error Of Approximation) Estimate 0.037 WRMR (Weighted Root Mean Square Residual) Value 0.812 Quick2rebuildout.out

  48. MODEL RESULTS Two-Tailed Estimate S.E. Est./S.E. P-Value IGHQ BY GHQ22 1.000 0.000 999.000 999.000 GHQ24 0.846 0.013 63.991 0.000 GHQ28 0.946 0.014 66.696 0.000 IGHQ ON AGEYRS -0.003 0.001 -3.608 0.000 Thresholds GHQ22$1 -0.344 0.040 -8.706 0.000 GHQ22$2 0.595 0.040 14.912 0.000 GHQ22$3 1.490 0.046 32.627 0.000 GHQ24$1 0.480 0.045 10.725 0.000 GHQ24$2 1.289 0.046 27.834 0.000 GHQ24$3 1.913 0.053 35.945 0.000 GHQ28$1 0.023 0.041 0.551 0.582 GHQ28$2 1.011 0.042 23.950 0.000 GHQ28$3 1.885 0.049 38.205 0.000 Residual Variances IGHQ 0.793 0.013 61.372 0.000 Quick2rebuildout.out

  49. R-SQUARE Observed Residual Variable Estimate Variance GHQ22 0.794 0.207 GHQ24 0.568 0.433 GHQ28 0.710 0.291 Latent Variable Estimate IGHQ 0.003 QUALITY OF NUMERICAL RESULTS Condition Number for the Information Matrix 0.967E-04 (ratio of smallest to largest eigenvalue) Beginning Time: 05:51:15 Ending Time: 05:51:17 Elapsed Time: 00:00:02 Quick2rebuildout.out

  50. Time for some constraints & * @ F by y1*1 (1) y2 (1); F1 by i1 i2 (10) i3 i4 (11); … can be words not numbers

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