Mplus VERSION 6.1 MUTHEN & MUTHEN 10/16/2010 1:09 AM INPUT INSTRUCTIONS Title: Stata2Mplus conversion for all_wide.dta List of variables converted shown below patno : patient age : calculated age (years) count : cases pritreat : prior chemo response 0: sd 1: pd 2: pr 3: u 4: cr tx : treatment arm 1: best supportive care 2: pemetrexed/best supportive care race : race 1: african descent 2: caucasion 3: east/southeast asian 4: hispanic 5: other gender : gender 1: male 2: female stage : stage 1: stage i b 2: stage ia 3: stage ii 4: stage iii 5: stage iv icda : intl class of disease adapted 1: atypical mesothelioma cells (4131) 2: biphasical pleural mesothelioma (3903) 3: epithelial pleural mesothelioma (3692) 4: mixed cell pleural mesothelioma (3693) 5: pleural mesothelioma, nos (3929) 6: sarcomatoid pleural mesothelioma (3691) mets : distant metastasis @study entry 2: m0 3: m1 4: mx lnode : regional lymph nodes @study entry 2: n0 3: n1 4: n2 5: n3 6: nx pmryt : primary tumor @study entry 2: t1a 3: t1b 4: t2 5: t3 6: t4 survcns : overall survival censor flag 0: non-censored 1: censored surv : overall survival opfscns : objective progression-free survival censor flag 0: non-censored 1: censored opfs : objective progression-free survival pfscns : progression-free survival censor flag 0: non-censored 1: censored pfs : progression-free survival ttopdcns : time to objective progressive disease censor flag 0: non-censored 1: censored ttopd : time to objective progressive disease ttpdcns : time to progressive disease censor flag 0: non-censored 1: censored ttpd : time to progressive disease tttfcns : time to treatment failure censor flag 0: non-censored 1: censored tttf : time to treatment failure ttprcns : time to reponse (cr or pr) censor flag 0: non-censored 1: censored ttpr : time to reponse (cr or pr) kps_0 : kps_1 : kps_2 : kps_3 : kps_4 : kps_5 : kps_6 : kps_7 : kps_8 : kps_9 : kps_10 : kps_11 : kps_12 : anrx_0 : 0: anorexia anrx_1 : 1: anorexia anrx_2 : 2: anorexia anrx_3 : 3: anorexia anrx_4 : 4: anorexia anrx_5 : 5: anorexia anrx_6 : 6: anorexia anrx_7 : 7: anorexia anrx_8 : 8: anorexia anrx_9 : 9: anorexia anrx_10 : 10: anorexia anrx_11 : 11: anorexia anrx_12 : 12: anorexia ftg_0 : 0: fatigue ftg_1 : 1: fatigue ftg_2 : 2: fatigue ftg_3 : 3: fatigue ftg_4 : 4: fatigue ftg_5 : 5: fatigue ftg_6 : 6: fatigue ftg_7 : 7: fatigue ftg_8 : 8: fatigue ftg_9 : 9: fatigue ftg_10 : 10: fatigue ftg_11 : 11: fatigue ftg_12 : 12: fatigue cgh_0 : 0: cough cgh_1 : 1: cough cgh_2 : 2: cough cgh_3 : 3: cough cgh_4 : 4: cough cgh_5 : 5: cough cgh_6 : 6: cough cgh_7 : 7: cough cgh_8 : 8: cough cgh_9 : 9: cough cgh_10 : 10: cough cgh_11 : 11: cough cgh_12 : 12: cough dysp_0 : 0: dyspnea dysp_1 : 1: dyspnea dysp_2 : 2: dyspnea dysp_3 : 3: dyspnea dysp_4 : 4: dyspnea dysp_5 : 5: dyspnea dysp_6 : 6: dyspnea dysp_7 : 7: dyspnea dysp_8 : 8: dyspnea dysp_9 : 9: dyspnea dysp_10 : 10: dyspnea dysp_11 : 11: dyspnea dysp_12 : 12: dyspnea hmpty_0 : 0: hemoptysis hmpty_1 : 1: hemoptysis hmpty_2 : 2: hemoptysis hmpty_3 : 3: hemoptysis hmpty_4 : 4: hemoptysis hmpty_5 : 5: hemoptysis hmpty_6 : 6: hemoptysis hmpty_7 : 7: hemoptysis hmpty_8 : 8: hemoptysis hmpty_9 : 9: hemoptysis hmpty_10 : 10: hemoptysis hmpty_11 : 11: hemoptysis hmpty_12 : 12: hemoptysis pain_0 : 0: pain pain_1 : 1: pain pain_2 : 2: pain pain_3 : 3: pain pain_4 : 4: pain pain_5 : 5: pain pain_6 : 6: pain pain_7 : 7: pain pain_8 : 8: pain pain_9 : 9: pain pain_10 : 10: pain pain_11 : 11: pain pain_12 : 12: pain sx_0 : 0: overall symptoms sx_1 : 1: overall symptoms sx_2 : 2: overall symptoms sx_3 : 3: overall symptoms sx_4 : 4: overall symptoms sx_5 : 5: overall symptoms sx_6 : 6: overall symptoms sx_7 : 7: overall symptoms sx_8 : 8: overall symptoms sx_9 : 9: overall symptoms sx_10 : 10: overall symptoms sx_11 : 11: overall symptoms sx_12 : 12: overall symptoms intfr_0 : 0: interference intfr_1 : 1: interference intfr_2 : 2: interference intfr_3 : 3: interference intfr_4 : 4: interference intfr_5 : 5: interference intfr_6 : 6: interference intfr_7 : 7: interference intfr_8 : 8: interference intfr_9 : 9: interference intfr_10 : 10: interference intfr_11 : 11: interference intfr_12 : 12: interference qol_0 : 0: quality of life qol_1 : 1: quality of life qol_2 : 2: quality of life qol_3 : 3: quality of life qol_4 : 4: quality of life qol_5 : 5: quality of life qol_6 : 6: quality of life qol_7 : 7: quality of life qol_8 : 8: quality of life qol_9 : 9: quality of life qol_10 : 10: quality of life qol_11 : 11: quality of life qol_12 : 12: quality of life Data: File is all_wide.dat ; Variable: Names are patno age count pritreat tx race gender stage icda mets lnode pmryt survcns surv opfscns opfs pfscns pfs ttopdcns ttopd ttpdcns ttpd tttfcns tttf ttprcns ttpr kps_0 kps_1 kps_2 kps_3 kps_4 kps_5 kps_6 kps_7 kps_8 kps_9 kps_10 kps_11 kps_12 anrx_0 anrx_1 anrx_2 anrx_3 anrx_4 anrx_5 anrx_6 anrx_7 anrx_8 anrx_9 anrx_10 anrx_11 anrx_12 ftg_0 ftg_1 ftg_2 ftg_3 ftg_4 ftg_5 ftg_6 ftg_7 ftg_8 ftg_9 ftg_10 ftg_11 ftg_12 cgh_0 cgh_1 cgh_2 cgh_3 cgh_4 cgh_5 cgh_6 cgh_7 cgh_8 cgh_9 cgh_10 cgh_11 cgh_12 dysp_0 dysp_1 dysp_2 dysp_3 dysp_4 dysp_5 dysp_6 dysp_7 dysp_8 dysp_9 dysp_10 dysp_11 dysp_12 hmpty_0 hmpty_1 hmpty_2 hmpty_3 hmpty_4 hmpty_5 hmpty_6 hmpty_7 hmpty_8 hmpty_9 hmpty_10 hmpty_11 hmpty_12 pain_0 pain_1 pain_2 pain_3 pain_4 pain_5 pain_6 pain_7 pain_8 pain_9 pain_10 pain_11 pain_12 sx_0 sx_1 sx_2 sx_3 sx_4 sx_5 sx_6 sx_7 sx_8 sx_9 sx_10 sx_11 sx_12 intfr_0 intfr_1 intfr_2 intfr_3 intfr_4 intfr_5 intfr_6 intfr_7 intfr_8 intfr_9 intfr_10 intfr_11 intfr_12 qol_0 qol_1 qol_2 qol_3 qol_4 qol_5 qol_6 qol_7 qol_8 qol_9 qol_10 qol_11 qol_12; Missing are all (-9999) ; Usev = tx pfs; survival = pfs(all); ! time-to-event outcome timecensored = pfscns (0 = not 1 = right); ! censoring indicator Analysis: process = 4(starts); basehazard = off; ! this specifies proportional-hazard Cox regression with a non-parametric ! baseline hazard function. See UG ex6.21 Model: pfs on tx; Output: tech1 sampstat standardized; Plot: type = plot3; INPUT READING TERMINATED NORMALLY Stata2Mplus conversion for all_wide.dta List of variables converted shown below patno : patient age : calculated age (years) count : cases pritreat : prior chemo response 0: sd 1: pd 2: pr 3: u 4: cr tx : treatment arm 1: best supportive care 2: pemetrexed/best supportive care race : race 1: african descent 2: caucasion 3: east/southeast asian 4: hispanic 5: other gender : gender 1: male 2: female stage : stage 1: stage i b 2: stage ia 3: stage ii 4: stage iii 5: stage iv icda : intl class of disease adapted 1: atypical mesothelioma cells (4131) 2: biphasical pleural mesothelioma (3903) 3: epithelial pleural mesothelioma (3692) 4: mixed cell pleural mesothelioma (3693) 5: pleural mesothelioma, nos (3929) 6: sarcomatoid pleural mesothelioma (3691) mets : distant metastasis @study entry 2: m0 3: m1 4: mx lnode : regional lymph nodes @study entry 2: n0 3: n1 4: n2 5: n3 6: nx pmryt : primary tumor @study entry 2: t1a 3: t1b 4: t2 5: t3 6: t4 survcns : overall survival censor flag 0: non-censored 1: censored surv : overall survival opfscns : objective progression-free survival censor flag 0: non-censored 1: censored opfs : objective progression-free survival pfscns : progression-free survival censor flag 0: non-censored 1: censored pfs : progression-free survival ttopdcns : time to objective progressive disease censor flag 0: non-censored 1: censored ttopd : time to objective progressive disease ttpdcns : time to progressive disease censor flag 0: non-censored 1: censored ttpd : time to progressive disease tttfcns : time to treatment failure censor flag 0: non-censored 1: censored tttf : time to treatment failure ttprcns : time to reponse (cr or pr) censor flag 0: non-censored 1: censored ttpr : time to reponse (cr or pr) kps_0 : kps_1 : kps_2 : kps_3 : kps_4 : kps_5 : kps_6 : kps_7 : kps_8 : kps_9 : kps_10 : kps_11 : kps_12 : anrx_0 : 0: anorexia anrx_1 : 1: anorexia anrx_2 : 2: anorexia anrx_3 : 3: anorexia anrx_4 : 4: anorexia anrx_5 : 5: anorexia anrx_6 : 6: anorexia anrx_7 : 7: anorexia anrx_8 : 8: anorexia anrx_9 : 9: anorexia anrx_10 : 10: anorexia anrx_11 : 11: anorexia anrx_12 : 12: anorexia ftg_0 : 0: fatigue ftg_1 : 1: fatigue ftg_2 : 2: fatigue ftg_3 : 3: fatigue ftg_4 : 4: fatigue ftg_5 : 5: fatigue ftg_6 : 6: fatigue ftg_7 : 7: fatigue ftg_8 : 8: fatigue ftg_9 : 9: fatigue ftg_10 : 10: fatigue ftg_11 : 11: fatigue ftg_12 : 12: fatigue cgh_0 : 0: cough cgh_1 : 1: cough cgh_2 : 2: cough cgh_3 : 3: cough cgh_4 : 4: cough cgh_5 : 5: cough cgh_6 : 6: cough SUMMARY OF ANALYSIS Number of groups 1 Number of observations 243 Number of dependent variables 1 Number of independent variables 1 Number of continuous latent variables 0 Observed dependent variables Time-to-event (survival) PFS Observed independent variables TX Variables with special functions Time-censoring variables PFSCNS Estimator MLR Information matrix OBSERVED Optimization Specifications for the Quasi-Newton Algorithm for Continuous Outcomes Maximum number of iterations 100 Convergence criterion 0.100D-05 Optimization Specifications for the EM Algorithm Maximum number of iterations 500 Convergence criteria Loglikelihood change 0.100D-02 Relative loglikelihood change 0.100D-05 Derivative 0.100D-02 Optimization Specifications for the M step of the EM Algorithm for Categorical Latent variables Number of M step iterations 1 M step convergence criterion 0.100D-02 Basis for M step termination ITERATION Optimization Specifications for the M step of the EM Algorithm for Censored, Binary or Ordered Categorical (Ordinal), Unordered Categorical (Nominal) and Count Outcomes Number of M step iterations 1 M step convergence criterion 0.100D-02 Basis for M step termination ITERATION Maximum value for logit thresholds 15 Minimum value for logit thresholds -15 Minimum expected cell size for chi-square 0.100D-01 Maximum number of iterations for H1 2000 Convergence criterion for H1 0.100D-03 Optimization algorithm EMA Integration Specifications Type STANDARD Number of integration points 15 Dimensions of numerical integration 0 Adaptive quadrature ON Base Hazard OFF Cholesky OFF Input data file(s) all_wide.dat Input data format FREE SUMMARY OF DATA COVARIANCE COVERAGE OF DATA Minimum covariance coverage value 0.100 SAMPLE STATISTICS SAMPLE STATISTICS Means TX ________ 1 1.506 Covariances TX ________ TX 0.251 Correlations TX ________ TX 1.000 THE MODEL ESTIMATION TERMINATED NORMALLY MODEL FIT INFORMATION Number of Free Parameters 1 Loglikelihood H0 Value -450.517 H0 Scaling Correction Factor 1.062 for MLR Information Criteria Akaike (AIC) 903.034 Bayesian (BIC) 906.527 Sample-Size Adjusted BIC 903.357 (n* = (n + 2) / 24) MODEL RESULTS Two-Tailed Estimate S.E. Est./S.E. P-Value PFS ON TX -0.325 0.139 -2.339 0.019 STANDARDIZED MODEL RESULTS STDYX Standardization Two-Tailed Estimate S.E. Est./S.E. P-Value PFS ON TX -1.000 0.000 ********* 0.000 STDY Standardization Two-Tailed Estimate S.E. Est./S.E. P-Value PFS ON TX -2.000 0.091 -22.045 0.000 STD Standardization Two-Tailed Estimate S.E. Est./S.E. P-Value PFS ON TX -0.325 0.139 -2.339 0.019 QUALITY OF NUMERICAL RESULTS Condition Number for the Information Matrix 0.100E+01 (ratio of smallest to largest eigenvalue) TECHNICAL 1 OUTPUT PARAMETER SPECIFICATION NU PFS#1 PFS TX ________ ________ ________ 1 0 0 0 LAMBDA PFS#1 PFS TX ________ ________ ________ PFS#1 0 0 0 PFS 0 0 0 TX 0 0 0 THETA PFS#1 PFS TX ________ ________ ________ PFS#1 0 PFS 0 0 TX 0 0 0 ALPHA PFS#1 PFS TX ________ ________ ________ 1 0 0 0 BETA PFS#1 PFS TX ________ ________ ________ PFS#1 0 0 0 PFS 0 0 1 TX 0 0 0 PSI PFS#1 PFS TX ________ ________ ________ PFS#1 0 PFS 0 0 TX 0 0 0 STARTING VALUES NU PFS#1 PFS TX ________ ________ ________ 1 0.000 0.000 0.000 LAMBDA PFS#1 PFS TX ________ ________ ________ PFS#1 1.000 0.000 0.000 PFS 0.000 1.000 0.000 TX 0.000 0.000 1.000 THETA PFS#1 PFS TX ________ ________ ________ PFS#1 0.000 PFS 0.000 0.000 TX 0.000 0.000 0.000 ALPHA PFS#1 PFS TX ________ ________ ________ 1 -20.000 0.000 0.000 BETA PFS#1 PFS TX ________ ________ ________ PFS#1 0.000 0.000 0.000 PFS 0.000 0.000 0.000 TX 0.000 0.000 0.000 PSI PFS#1 PFS TX ________ ________ ________ PFS#1 0.000 PFS 0.000 0.000 TX 0.000 0.000 0.125 PLOT INFORMATION The following plots are available: Histograms (sample values) Scatterplots (sample values) Survival curves Beginning Time: 01:09:20 Ending Time: 01:09:20 Elapsed Time: 00:00:00 MUTHEN & MUTHEN 3463 Stoner Ave. Los Angeles, CA 90066 Tel: (310) 391-9971 Fax: (310) 391-8971 Web: www.StatModel.com Support: Support@StatModel.com Copyright (c) 1998-2010 Muthen & Muthen