- Early (6m) vs. Late Group
- Time to Tech Failure or Death: Time 0 set at First Infection
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 1689 829 2.73 2.51 2.94
## group=Late (>0.5yr) 911 509 1.91 1.65 2.23
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.5yr) 1689 1179 726 397 232 144 89 51 24 5 0
## group=Late (>0.5yr) 911 528 295 178 92 55 32 18 7 0 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n= 2600, number of events= 1338
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.33596 1.39928 0.05634 5.963 2.48e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 1.399 0.7147 1.253 1.563
##
## Concordance= 0.561 (se = 0.007 )
## Rsquare= 0.013 (max possible= 0.999 )
## Likelihood ratio test= 34.48 on 1 df, p=4.307e-09
## Wald test = 35.56 on 1 df, p=2.476e-09
## Score (logrank) test = 35.89 on 1 df, p=2.085e-09
- Time to Tech failure or Death : Time 0 set at 6 month
## Call: survfit(formula = Surv(Time2Fu, Event) ~ group, data = dat2,
## start.time = early.cut)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 1689 829 2.9 2.73 3.19
## group=Late (>0.5yr) 911 509 2.6 2.34 2.95
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10
## group=Early (<0.5yr) 1303 793 451 251 160 96 57 27 6 0
## group=Late (>0.5yr) 765 446 259 146 77 51 28 13 5 0
## Call:
## coxph(formula = Surv(rep(early.cut, nrow(dat2)), Time2Fu, Event) ~
## group, data = dat2)
##
## n= 2600, number of events= 1338
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.07494 1.07782 0.05632 1.331 0.183
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 1.078 0.9278 0.9652 1.204
##
## Concordance= 0.505 (se = 0.007 )
## Rsquare= 0.001 (max possible= 0.999 )
## Likelihood ratio test= 1.76 on 1 df, p=0.1847
## Wald test = 1.77 on 1 df, p=0.1833
## Score (logrank) test = 1.77 on 1 df, p=0.1832
- Number of Infections After First Infection
## Call:
## coxph(formula = Surv(tstart, tstop, infect) ~ group, data = dat3,
## method = "breslow")
##
## n= 7084, number of events= 4484
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) -0.02065 0.97956 0.03254 -0.635 0.526
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 0.9796 1.021 0.919 1.044
##
## Concordance= 0.503 (se = 0.004 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.4 on 1 df, p=0.5251
## Wald test = 0.4 on 1 df, p=0.5256
## Score (logrank) test = 0.4 on 1 df, p=0.5256
## Call:
## coxph(formula = Surv(tstart, tstop, infect) ~ group + cluster(ID),
## data = dat3, method = "breslow")
##
## n= 7084, number of events= 4484
##
## coef exp(coef) se(coef) robust se z Pr(>|z|)
## groupLate (>0.5yr) -0.02065 0.97956 0.03254 0.05582 -0.37 0.711
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 0.9796 1.021 0.8781 1.093
##
## Concordance= 0.503 (se = 0.004 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.4 on 1 df, p=0.5251
## Wald test = 0.14 on 1 df, p=0.7114
## Score (logrank) test = 0.4 on 1 df, p=0.5256, Robust = 0.14 p=0.7105
##
## (Note: the likelihood ratio and score tests assume independence of
## observations within a cluster, the Wald and robust score tests do not).
- Time to second infection from first infection
## Call: survfit(formula = Surv(tstop - tstart, infect) ~ group, data = subset(dat3,
## enum == 2))
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 1045 658 0.526 0.465 0.632
## group=Late (>0.5yr) 502 285 0.624 0.487 0.764
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.5yr) 1045 240 85 41 24 21 11 6 3 0 0
## group=Late (>0.5yr) 502 106 37 17 8 5 1 0 0 0 0
## Call:
## coxph(formula = Surv(tstop - tstart, infect) ~ group, data = subset(dat3,
## enum == 2))
##
## n= 1547, number of events= 943
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) -0.03288 0.96766 0.07095 -0.463 0.643
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 0.9677 1.033 0.842 1.112
##
## Concordance= 0.501 (se = 0.008 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.22 on 1 df, p=0.6424
## Wald test = 0.21 on 1 df, p=0.6431
## Score (logrank) test = 0.21 on 1 df, p=0.6431
- Circle length for third and later infections
## Call: survfit(formula = Surv(tstop - tstart, infect) ~ group, data = subset(dat3,
## enum > 3))
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 1427 987 0.274 0.268 0.287
## group=Late (>0.5yr) 567 379 0.312 0.257 0.402
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.5yr) 1427 185 78 28 13 10 5 4 1 0 0
## group=Late (>0.5yr) 567 81 19 14 8 3 2 1 0 0 0
## Call:
## coxph(formula = Surv(tstop - tstart, infect) ~ group, data = subset(dat3,
## enum > 3))
##
## n= 1994, number of events= 1366
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) -0.007876 0.992155 0.060489 -0.13 0.896
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 0.9922 1.008 0.8812 1.117
##
## Concordance= 0.5 (se = 0.007 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.02 on 1 df, p=0.8963
## Wald test = 0.02 on 1 df, p=0.8964
## Score (logrank) test = 0.02 on 1 df, p=0.8964
- Infection Rate for Early (6m) Group
## [1] "1.31 (1.27, 1.34)"
- Infection Rate for Late (6m) Group
## [1] "1.42 (1.36, 1.48)"
- Multivariable Analysis - Tech Failure or Death
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.3397 1.4045 0.0601 5.6537 0.0000
## age 0.0164 1.0165 0.0021 7.9731 0.0000
## genderMale -0.0453 0.9557 0.0589 -0.7693 0.4417
## race2White 0.0410 1.0419 0.0695 0.5897 0.5554
## diab2Yes 0.4221 1.5251 0.1092 3.8652 0.0001
## cause.esrdGN -0.0133 0.9868 0.1357 -0.0980 0.9220
## cause.esrdHTN -0.0191 0.9811 0.1202 -0.1588 0.8739
## cause.esrdOther -0.0427 0.9582 0.1201 -0.3550 0.7226
## pd.typeNew -0.2095 0.8110 0.0677 -3.0960 0.0020
## pd.typeOther -0.1365 0.8724 0.0866 -1.5770 0.1148
## FirstSystemTypeCAPD -0.0590 0.9427 0.0623 -0.9468 0.3437
## cultureGramNeg 0.2023 1.2242 0.0990 2.0424 0.0411
## cultureGramPos 0.1409 1.1513 0.0784 1.7973 0.0723
## Analysis of Deviance Table
## Cox model: response is Surv(Time2Fu - Time2Infection.1, Event)
## Terms added sequentially (first to last)
##
## loglik Chisq Df Pr(>|Chi|)
## NULL -8447.2
## group -8431.6 31.1365 1 2.405e-08 ***
## age -8397.2 68.8841 1 < 2.2e-16 ***
## gender -8397.0 0.4992 1 0.479842
## race2 -8396.9 0.0437 1 0.834385
## diab2 -8366.6 60.6570 1 6.772e-15 ***
## cause.esrd -8366.4 0.4453 3 0.930739
## pd.type -8360.9 10.8617 2 0.004379 **
## FirstSystemType -8360.4 1.1636 1 0.280716
## culture -8358.0 4.7139 2 0.094710 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
- Multivariable Analysis - Death
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.2033 1.2254 0.0951 2.1373 0.0326
## age 0.0411 1.0420 0.0036 11.5470 0.0000
## genderMale 0.0530 1.0545 0.0913 0.5808 0.5614
## race2White 0.0994 1.1045 0.1152 0.8629 0.3882
## diab2Yes 0.4295 1.5365 0.1698 2.5295 0.0114
## cause.esrdGN -0.3652 0.6941 0.2257 -1.6183 0.1056
## cause.esrdHTN -0.2608 0.7705 0.1862 -1.4007 0.1613
## cause.esrdOther -0.2047 0.8149 0.1844 -1.1105 0.2668
## pd.typeNew -0.3625 0.6959 0.1028 -3.5258 0.0004
## pd.typeOther -0.2679 0.7650 0.1355 -1.9777 0.0480
## FirstSystemTypeCAPD 0.0988 1.1038 0.0998 0.9894 0.3225
## cultureGramNeg 0.0364 1.0370 0.1497 0.2428 0.8082
## cultureGramPos -0.0325 0.9680 0.1144 -0.2841 0.7763
## Analysis of Deviance Table
## Cox model: response is Surv(Time2Fu - Time2Infection.1, Event.Death)
## Terms added sequentially (first to last)
##
## loglik Chisq Df Pr(>|Chi|)
## NULL -3536.6
## group -3534.9 3.3201 1 0.068438 .
## age -3454.6 160.5827 1 < 2.2e-16 ***
## gender -3454.5 0.1756 1 0.675148
## race2 -3454.4 0.3197 1 0.571759
## diab2 -3428.0 52.7244 1 3.838e-13 ***
## cause.esrd -3426.0 4.0145 3 0.259899
## pd.type -3420.3 11.4485 2 0.003266 **
## FirstSystemType -3419.8 0.9633 1 0.326355
## culture -3419.6 0.3293 2 0.848203
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1