-------------------------------------------------------------------------------------------------------------------------- log: C:\MyDocs\MPH\LectureNotes\Class do, log and data files\Survival\Framingham.TimeDependentTest.log log type: text opened on: 24 Jan 2008, 10:06:45 . * Framingham.TimeDependent.log . * . * Perform hazard regressions of gender on CHD risk . * using age as the time variable. Explore models . * with time dependent covariates for sex . * . set memory 2m Current memory allocation current memory usage settable value description (1M = 1024k) -------------------------------------------------------------------- set maxvar 5000 max. variables allowed 1.909M set memory 2M max. data space 2.000M set matsize 400 max. RHS vars in models 1.254M ----------- 5.163M . use C:\WDDtext\2.20.Framingham.dta, clear . generate time= followup/365.25 . generate male = sex==1 . label define male 0 "Women" 1 "Men" . label values male male . * . * Calculate the relative risk of CHD for men relative to women using . * age as the time variable. . * . generate follow = age+time . stset follow, failure(chdfate) failure event: chdfate != 0 & chdfate < . obs. time interval: (0, follow] exit on or before: failure ------------------------------------------------------------------------------ 4699 total obs. 0 exclusions ------------------------------------------------------------------------------ 4699 obs. remaining, representing 1473 failures in single record/single failure data 320057.1 total analysis time at risk, at risk from t = 0 earliest observed entry t = 0 last observed exit t = 94 . stcox male failure _d: chdfate analysis time _t: follow Iteration 0: log likelihood = -11477.246 Iteration 1: log likelihood = -11387.924 Iteration 2: log likelihood = -11387.787 Refining estimates: Iteration 0: log likelihood = -11387.787 Cox regression -- Breslow method for ties No. of subjects = 4699 Number of obs = 4699 No. of failures = 1473 Time at risk = 320057.0914 LR chi2(1) = 178.92 Log likelihood = -11387.787 Prob > chi2 = 0.0000 ------------------------------------------------------------------------------ _t | Haz. Ratio Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- male | 2.018537 .1063945 13.33 0.000 1.820417 2.238218 ------------------------------------------------------------------------------ . * . * Perform hazard regression with time dependent covariates for sex . * . tabulate chdfate male Coronary | Heart | male Disease | Women Men | Total -----------+----------------------+---------- Censored | 2,000 1,226 | 3,226 CHD | 650 823 | 1,473 -----------+----------------------+---------- Total | 2,650 2,049 | 4,699 . * . * Split each patient's record into one or more records so that each . * record describes one epoch with constant covariates for the epoch. . * . generate exit = follow . stset exit, id(id) failure(chdfate) id: id failure event: chdfate != 0 & chdfate < . obs. time interval: (exit[_n-1], exit] exit on or before: failure ------------------------------------------------------------------------------ 4699 total obs. 0 exclusions ------------------------------------------------------------------------------ 4699 obs. remaining, representing 4699 subjects 1473 failures in single failure-per-subject data 320057.1 total analysis time at risk, at risk from t = 0 earliest observed entry t = 0 last observed exit t = 94 . stsplit enter, at(50 60 70 80) (10741 observations (episodes) created) . generate male1 = male*( exit <= 50) . generate male2 = male*(enter >= 50 & exit <= 60) . generate male3 = male*(enter >= 60 & exit <= 70) . generate male4 = male*(enter >= 70 & exit <= 80) . generate male5 = male*(enter >= 80) . list id male? enter exit chdfate if id == 924 +--------------------------------------------------------------------------+ | id male1 male2 male3 male4 male5 enter exit chdfate | |--------------------------------------------------------------------------| 9744. | 924 1 0 0 0 0 0 50 . | 9745. | 924 0 1 0 0 0 50 60 . | 9746. | 924 0 0 1 0 0 60 63.23888 CHD | +--------------------------------------------------------------------------+ . generate testmale = male1 + male2 + male3 + male4 + male5 . tabulate chdfate testmale, missing Coronary | Heart | testmale Disease | 0 1 | Total -----------+----------------------+---------- Censored | 2,000 1,226 | 3,226 CHD | 650 823 | 1,473 . | 6,394 4,347 | 10,741 -----------+----------------------+---------- Total | 9,044 6,396 | 15,440 . more . stset exit, id(id) enter(time enter) failure(chdfate) id: id failure event: chdfate != 0 & chdfate < . obs. time interval: (exit[_n-1], exit] enter on or after: time enter exit on or before: failure ------------------------------------------------------------------------------ 15440 total obs. 0 exclusions ------------------------------------------------------------------------------ 15440 obs. remaining, representing 4699 subjects 1473 failures in single failure-per-subject data 320057.1 total analysis time at risk, at risk from t = 0 earliest observed entry t = 0 last observed exit t = 94 . stcox male? failure _d: chdfate analysis time _t: exit enter on or after: time enter id: id Iteration 0: log likelihood = -11477.246 Iteration 1: log likelihood = -11374.206 Iteration 2: log likelihood = -11374.015 Iteration 3: log likelihood = -11374.015 Refining estimates: Iteration 0: log likelihood = -11374.015 Cox regression -- Breslow method for ties No. of subjects = 4699 Number of obs = 15440 No. of failures = 1473 Time at risk = 320057.0914 LR chi2(5) = 206.46 Log likelihood = -11374.015 Prob > chi2 = 0.0000 ------------------------------------------------------------------------------ _t | Haz. Ratio Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- male1 | 4.306581 .9651639 6.52 0.000 2.775663 6.681878 male2 | 2.493208 .2658025 8.57 0.000 2.023072 3.072597 male3 | 1.765886 .1467775 6.84 0.000 1.500418 2.078323 male4 | 1.880939 .2127479 5.59 0.000 1.506946 2.34775 male5 | 1.048225 .2579044 0.19 0.848 .6471809 1.697788 ------------------------------------------------------------------------------ . test male1 = male2 = male3 = male4 = male5 ( 1) male1 - male2 = 0 ( 2) male1 - male3 = 0 ( 3) male1 - male4 = 0 ( 4) male1 - male5 = 0 chi2( 4) = 25.42 Prob > chi2 = 0.0000 . lincom male1 - male2 ( 1) male1 - male2 = 0 ------------------------------------------------------------------------------ _t | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- (1) | .5465743 .2481789 2.20 0.028 .0601525 1.032996 ------------------------------------------------------------------------------ . lincom male2 - male3 ( 1) male2 - male3 = 0 ------------------------------------------------------------------------------ _t | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- (1) | .3449176 .1351832 2.55 0.011 .0799634 .6098718 ------------------------------------------------------------------------------ . lincom male3 - male4 ( 1) male3 - male4 = 0 ------------------------------------------------------------------------------ _t | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- (1) | -.0631188 .1403635 -0.45 0.653 -.3382263 .2119887 ------------------------------------------------------------------------------ . lincom male4 - male5 ( 1) male4 - male5 = 0 ------------------------------------------------------------------------------ _t | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- (1) | .5846729 .2707924 2.16 0.031 .0539295 1.115416 ------------------------------------------------------------------------------ . generate male34 = male3 + male4 . summarize male34 Variable | Obs Mean Std. Dev. Min Max -------------+-------------------------------------------------------- male34 | 15440 .1476684 .3547825 0 1 . stcox male1 male2 male34 male5 failure _d: chdfate analysis time _t: exit enter on or after: time enter id: id Iteration 0: log likelihood = -11477.246 Iteration 1: log likelihood = -11374.29 Iteration 2: log likelihood = -11374.116 Iteration 3: log likelihood = -11374.116 Refining estimates: Iteration 0: log likelihood = -11374.116 Cox regression -- Breslow method for ties No. of subjects = 4699 Number of obs = 15440 No. of failures = 1473 Time at risk = 320057.0914 LR chi2(4) = 206.26 Log likelihood = -11374.116 Prob > chi2 = 0.0000 ------------------------------------------------------------------------------ _t | Haz. Ratio Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- male1 | 4.306581 .9651639 6.52 0.000 2.775663 6.681878 male2 | 2.493208 .2658025 8.57 0.000 2.023072 3.072597 male34 | 1.805429 .1209893 8.82 0.000 1.583207 2.058841 male5 | 1.048225 .2579044 0.19 0.848 .6471809 1.697788 ------------------------------------------------------------------------------ . test male1 = male2 = male34 = male5 ( 1) male1 - male2 = 0 ( 2) male1 - male34 = 0 ( 3) male1 - male5 = 0 chi2( 3) = 25.21 Prob > chi2 = 0.0000 . lincom male1 - male2 ( 1) male1 - male2 = 0 ------------------------------------------------------------------------------ _t | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- (1) | .5465743 .2481789 2.20 0.028 .0601525 1.032996 ------------------------------------------------------------------------------ . lincom male2 - male34 ( 1) male2 - male34 = 0 ------------------------------------------------------------------------------ _t | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- (1) | .3227721 .1259235 2.56 0.010 .0759665 .5695776 ------------------------------------------------------------------------------ . lincom male34 - male5 ( 1) male34 - male5 = 0 ------------------------------------------------------------------------------ _t | Coef. Std. Err. z P>|z| [95% Conf. Interval] -------------+---------------------------------------------------------------- (1) | .5436996 .2550023 2.13 0.033 .0439043 1.043495 ------------------------------------------------------------------------------ . log close log: C:\MyDocs\MPH\LectureNotes\Class do, log and data files\Survival\Framingham.TimeDependentTest.log log type: text closed on: 24 Jan 2008, 10:07:01 -----------------------------------------------------------------------------------------------------------------------