- Infection vs. No Infection
- Time dependent covariate model - Tech Failure or Death
## Call:
## coxph(formula = Surv(tstart, tstop, tech.failure.or.death) ~
## infection, data = tdata1)
##
## n= 13835, number of events= 4556
##
## coef exp(coef) se(coef) z Pr(>|z|)
## infection 0.99725 2.71082 0.03317 30.07 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## infection 2.711 0.3689 2.54 2.893
##
## Concordance= 0.598 (se = 0.003 )
## Rsquare= 0.065 (max possible= 0.996 )
## Likelihood ratio test= 932.4 on 1 df, p=0
## Wald test = 903.9 on 1 df, p=0
## Score (logrank) test = 954.6 on 1 df, p=0
- Time dependent covariate model - Death
## Call:
## coxph(formula = Surv(tstart, tstop, death) ~ infection, data = tdata2)
##
## n= 13835, number of events= 2008
##
## coef exp(coef) se(coef) z Pr(>|z|)
## infection 0.62835 1.87451 0.04833 13 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## infection 1.875 0.5335 1.705 2.061
##
## Concordance= 0.558 (se = 0.005 )
## Rsquare= 0.012 (max possible= 0.911 )
## Likelihood ratio test= 170 on 1 df, p=0
## Wald test = 169.1 on 1 df, p=0
## Score (logrank) test = 173 on 1 df, p=0
- Early (6m) vs. Late Group
- Time to Tech Failure Since First Infection
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2, start.time = early.cut)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 1601 748 2.95 2.77 3.26
## group=Late (>0.5yr) 722 326 2.97 2.71 3.53
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10
## group=Early (<0.5yr) 1228 753 410 241 150 91 52 24 5 0
## group=Late (>0.5yr) 549 306 184 98 60 33 18 7 0 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n= 2714, number of events= 1390
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.32712 1.38697 0.05531 5.914 3.34e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 1.387 0.721 1.244 1.546
##
## Concordance= 0.561 (se = 0.007 )
## Rsquare= 0.012 (max possible= 0.999 )
## Likelihood ratio test= 33.94 on 1 df, p=5.693e-09
## Wald test = 34.98 on 1 df, p=3.338e-09
## Score (logrank) test = 35.29 on 1 df, p=2.844e-09
- Time to Death Since First Infection
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2, start.time = early.cut)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 1601 328 NA 7.04 NA
## group=Late (>0.5yr) 722 139 NA NA NA
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10
## group=Early (<0.5yr) 1228 753 410 241 150 91 52 24 5 0
## group=Late (>0.5yr) 549 306 184 98 60 33 18 7 0 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n= 2714, number of events= 582
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.18865 1.20761 0.08722 2.163 0.0305 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 1.208 0.8281 1.018 1.433
##
## Concordance= 0.54 (se = 0.011 )
## Rsquare= 0.002 (max possible= 0.954 )
## Likelihood ratio test= 4.58 on 1 df, p=0.03229
## Wald test = 4.68 on 1 df, p=0.03055
## Score (logrank) test = 4.69 on 1 df, p=0.0303
- Number of Infections After First Infection
## Call:
## coxph(formula = Surv(tstart, tstop, infect) ~ group, data = dat3,
## method = "breslow")
##
## n= 7389, number of events= 4675
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) -0.02031 0.97989 0.03184 -0.638 0.523
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 0.9799 1.021 0.9206 1.043
##
## Concordance= 0.503 (se = 0.004 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.41 on 1 df, p=0.5229
## Wald test = 0.41 on 1 df, p=0.5235
## Score (logrank) test = 0.41 on 1 df, p=0.5235
- Infection Rate for Early (6m) Group
## [1] "1.31 (1.27, 1.35)"
- Infection Rate for Late (6m) Group
## [1] "1.42 (1.37, 1.48)"
- Early (3m) vs. Late Group
- Time to Tech Failure Since First Infection
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2, start.time = early.cut)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.25yr) 1165 581 2.67 2.48 2.93
## group=Late (>0.25yr) 1426 695 2.72 2.42 2.93
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10
## group=Early (<0.25yr) 803 499 274 168 103 60 37 19 4 0
## group=Late (>0.25yr) 974 560 320 171 107 64 33 12 1 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n= 2918, number of events= 1567
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.25yr) 0.1989 1.2201 0.0514 3.87 0.000109 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.25yr) 1.22 0.8196 1.103 1.349
##
## Concordance= 0.537 (se = 0.007 )
## Rsquare= 0.005 (max possible= 1 )
## Likelihood ratio test= 15.14 on 1 df, p=9.994e-05
## Wald test = 14.98 on 1 df, p=0.0001086
## Score (logrank) test = 15.03 on 1 df, p=0.0001058
- Time to Death Since First Infection
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2, start.time = early.cut)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.25yr) 1165 263 NA 6.69 NA
## group=Late (>0.25yr) 1426 290 NA 7.11 NA
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10
## group=Early (<0.25yr) 803 499 274 168 103 60 37 19 4 0
## group=Late (>0.25yr) 974 560 320 171 107 64 33 12 1 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n= 2918, number of events= 634
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.25yr) 0.05408 1.05557 0.07992 0.677 0.499
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.25yr) 1.056 0.9474 0.9025 1.235
##
## Concordance= 0.518 (se = 0.011 )
## Rsquare= 0 (max possible= 0.957 )
## Likelihood ratio test= 0.46 on 1 df, p=0.4983
## Wald test = 0.46 on 1 df, p=0.4987
## Score (logrank) test = 0.46 on 1 df, p=0.4986
- Number of Infections After First Infection
## Call:
## coxph(formula = Surv(tstart, tstop, infect) ~ group, data = dat3,
## method = "breslow")
##
## n= 7670, number of events= 4752
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.25yr) -0.01418 0.98592 0.02911 -0.487 0.626
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.25yr) 0.9859 1.014 0.9313 1.044
##
## Concordance= 0.507 (se = 0.004 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.24 on 1 df, p=0.6263
## Wald test = 0.24 on 1 df, p=0.6263
## Score (logrank) test = 0.24 on 1 df, p=0.6263
- Infection Rate for Early (3m) Group
## [1] "1.34 (1.29, 1.38)"
- Infection Rate for Late (3m) Group
## [1] "1.43 (1.39, 1.47)"