Time Zero as 1st Infection Date
late group: 1st infection between 6m and 1 yr
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 2028 1139 2.20 2.04 2.33
## 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) 2028 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= 2939, number of events= 1648
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.02572 1.02605 0.05333 0.482 0.63
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 1.026 0.9746 0.9242 1.139
##
## Concordance= 0.504 (se = 0.006 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.23 on 1 df, p=0.6301
## Wald test = 0.23 on 1 df, p=0.6296
## Score (logrank) test = 0.23 on 1 df, p=0.6296
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 2028 453 7.11 6.37 NA
## group=Late (>0.5yr) 911 192 NA NA NA
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.5yr) 2028 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.Death) ~
## group, data = dat2)
##
## n= 2939, number of events= 645
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) -0.02228 0.97796 0.08614 -0.259 0.796
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 0.978 1.023 0.826 1.158
##
## Concordance= 0.5 (se = 0.01 )
## Rsquare= 0 (max possible= 0.958 )
## Likelihood ratio test= 0.07 on 1 df, p=0.7956
## Wald test = 0.07 on 1 df, p=0.7959
## Score (logrank) test = 0.07 on 1 df, p=0.7958
late group: 1st infection between 6m and 1.5 yr
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 2028 1139 2.20 2.04 2.33
## group=Late (>0.5yr) 1480 845 1.83 1.63 2.06
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.5yr) 2028 1179 726 397 232 144 89 51 24 5 0
## group=Late (>0.5yr) 1480 842 458 268 142 92 57 29 13 0 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n= 3508, number of events= 1984
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.06995 1.07245 0.04542 1.54 0.124
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 1.072 0.9324 0.9811 1.172
##
## Concordance= 0.51 (se = 0.006 )
## Rsquare= 0.001 (max possible= 1 )
## Likelihood ratio test= 2.36 on 1 df, p=0.1242
## Wald test = 2.37 on 1 df, p=0.1235
## Score (logrank) test = 2.37 on 1 df, p=0.1235
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.5yr) 2028 453 7.11 6.37 NA
## group=Late (>0.5yr) 1480 316 NA 5.59 NA
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.5yr) 2028 1179 726 397 232 144 89 51 24 5 0
## group=Late (>0.5yr) 1480 842 458 268 142 92 57 29 13 0 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n= 3508, number of events= 769
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.5yr) 0.01633 1.01647 0.07332 0.223 0.824
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.5yr) 1.016 0.9838 0.8804 1.174
##
## Concordance= 0.501 (se = 0.01 )
## Rsquare= 0 (max possible= 0.961 )
## Likelihood ratio test= 0.05 on 1 df, p=0.8238
## Wald test = 0.05 on 1 df, p=0.8237
## Score (logrank) test = 0.05 on 1 df, p=0.8237
late group: 1st infection between 3m and 1 yr
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.25yr) 1337 758 2.12 1.95 2.34
## group=Late (>0.25yr) 1602 890 2.09 1.88 2.28
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.25yr) 1337 772 484 268 163 100 59 37 19 4 0
## group=Late (>0.25yr) 1602 935 537 307 161 99 62 32 12 1 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n= 2939, number of events= 1648
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.25yr) 0.008285 1.008319 0.049441 0.168 0.867
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.25yr) 1.008 0.9917 0.9152 1.111
##
## Concordance= 0.498 (se = 0.007 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.03 on 1 df, p=0.8669
## Wald test = 0.03 on 1 df, p=0.8669
## Score (logrank) test = 0.03 on 1 df, p=0.8669
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.25yr) 1337 310 7.04 6.37 NA
## group=Late (>0.25yr) 1602 335 NA 5.97 NA
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.25yr) 1337 772 484 268 163 100 59 37 19 4 0
## group=Late (>0.25yr) 1602 935 537 307 161 99 62 32 12 1 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n= 2939, number of events= 645
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.25yr) -0.06951 0.93286 0.07884 -0.882 0.378
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.25yr) 0.9329 1.072 0.7993 1.089
##
## Concordance= 0.51 (se = 0.011 )
## Rsquare= 0 (max possible= 0.958 )
## Likelihood ratio test= 0.78 on 1 df, p=0.3783
## Wald test = 0.78 on 1 df, p=0.378
## Score (logrank) test = 0.78 on 1 df, p=0.3779
late group: 1st infection between 3m and 1.5 yr
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.25yr) 1337 758 2.12 1.95 2.34
## group=Late (>0.25yr) 2171 1226 1.95 1.80 2.17
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.25yr) 1337 772 484 268 163 100 59 37 19 4 0
## group=Late (>0.25yr) 2171 1249 700 397 211 136 87 43 18 1 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ group,
## data = dat2)
##
## n= 3508, number of events= 1984
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.25yr) 0.04182 1.04271 0.04622 0.905 0.366
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.25yr) 1.043 0.959 0.9524 1.142
##
## Concordance= 0.503 (se = 0.006 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.82 on 1 df, p=0.3648
## Wald test = 0.82 on 1 df, p=0.3656
## Score (logrank) test = 0.82 on 1 df, p=0.3656
## Call: survfit(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n events median 0.95LCL 0.95UCL
## group=Early (<0.25yr) 1337 310 7.04 6.37 NA
## group=Late (>0.25yr) 2171 459 NA 5.97 NA
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## group=Early (<0.25yr) 1337 772 484 268 163 100 59 37 19 4 0
## group=Late (>0.25yr) 2171 1249 700 397 211 136 87 43 18 1 0
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## group, data = dat2)
##
## n= 3508, number of events= 769
##
## coef exp(coef) se(coef) z Pr(>|z|)
## groupLate (>0.25yr) -0.03856 0.96217 0.07355 -0.524 0.6
##
## exp(coef) exp(-coef) lower .95 upper .95
## groupLate (>0.25yr) 0.9622 1.039 0.833 1.111
##
## Concordance= 0.507 (se = 0.01 )
## Rsquare= 0 (max possible= 0.961 )
## Likelihood ratio test= 0.27 on 1 df, p=0.6005
## Wald test = 0.27 on 1 df, p=0.6001
## Score (logrank) test = 0.27 on 1 df, p=0.6
Time Zero as 1st Infection Date continuous
include everyone who had a infection in 1 yr
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ Time2Infection.1,
## data = dat2)
##
## n= 2939, number of events= 1648
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Time2Infection.1 0.01347 1.01356 0.08703 0.155 0.877
##
## exp(coef) exp(-coef) lower .95 upper .95
## Time2Infection.1 1.014 0.9866 0.8546 1.202
##
## Concordance= 0.5 (se = 0.008 )
## Rsquare= 0 (max possible= 1 )
## Likelihood ratio test= 0.02 on 1 df, p=0.8771
## Wald test = 0.02 on 1 df, p=0.877
## Score (logrank) test = 0.02 on 1 df, p=0.877
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## Time2Infection.1, data = dat2)
##
## n= 2939, number of events= 645
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Time2Infection.1 -0.07066 0.93178 0.14025 -0.504 0.614
##
## exp(coef) exp(-coef) lower .95 upper .95
## Time2Infection.1 0.9318 1.073 0.7078 1.227
##
## Concordance= 0.502 (se = 0.013 )
## Rsquare= 0 (max possible= 0.958 )
## Likelihood ratio test= 0.25 on 1 df, p=0.6137
## Wald test = 0.25 on 1 df, p=0.6144
## Score (logrank) test = 0.25 on 1 df, p=0.6144
include everyone who had a infection in 1.5 yr
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event) ~ Time2Infection.1,
## data = dat2)
##
## n= 3508, number of events= 1984
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Time2Infection.1 0.10324 1.10875 0.05361 1.926 0.0541 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## Time2Infection.1 1.109 0.9019 0.9982 1.232
##
## Concordance= 0.51 (se = 0.007 )
## Rsquare= 0.001 (max possible= 1 )
## Likelihood ratio test= 3.67 on 1 df, p=0.05535
## Wald test = 3.71 on 1 df, p=0.05414
## Score (logrank) test = 3.71 on 1 df, p=0.05409
## Call:
## coxph(formula = Surv(Time2Fu - Time2Infection.1, Event.Death) ~
## Time2Infection.1, data = dat2)
##
## n= 3508, number of events= 769
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Time2Infection.1 0.008771 1.008810 0.087511 0.1 0.92
##
## exp(coef) exp(-coef) lower .95 upper .95
## Time2Infection.1 1.009 0.9913 0.8498 1.198
##
## Concordance= 0.498 (se = 0.012 )
## Rsquare= 0 (max possible= 0.961 )
## Likelihood ratio test= 0.01 on 1 df, p=0.9202
## Wald test = 0.01 on 1 df, p=0.9202
## Score (logrank) test = 0.01 on 1 df, p=0.9202
GramNeg versus GramPos
## Call: survfit(formula = Surv(Time2Fu, Event) ~ culture, data = dat2)
##
## 306 observations deleted due to missingness
## n events median 0.95LCL 0.95UCL
## culture=CNEG 582 301 2.76 2.53 3.30
## culture=GramNeg 615 357 2.19 1.98 2.64
## culture=GramPos 2005 1132 2.63 2.46 2.80
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## culture=CNEG 582 432 279 158 87 54 33 18 6 2 0
## culture=GramNeg 615 440 246 128 72 45 34 21 11 5 0
## culture=GramPos 2005 1567 960 547 312 173 107 61 30 8 0
## Call:
## coxph(formula = Surv(Time2Fu, Event) ~ culture, data = dat2)
##
## n= 3202, number of events= 1790
## (306 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## cultureGramNeg 0.24176 1.27349 0.07829 3.088 0.00201 **
## cultureGramPos 0.07756 1.08064 0.06486 1.196 0.23176
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## cultureGramNeg 1.273 0.7852 1.0923 1.485
## cultureGramPos 1.081 0.9254 0.9517 1.227
##
## Concordance= 0.525 (se = 0.006 )
## Rsquare= 0.003 (max possible= 1 )
## Likelihood ratio test= 10.47 on 2 df, p=0.005339
## Wald test = 10.73 on 2 df, p=0.00468
## Score (logrank) test = 10.76 on 2 df, p=0.004608
## Call: survfit(formula = Surv(Time2Fu, Event.Death) ~ culture, data = dat2)
##
## 306 observations deleted due to missingness
## n events median 0.95LCL 0.95UCL
## culture=CNEG 582 133 NA 5.60 NA
## culture=GramNeg 615 112 NA NA NA
## culture=GramPos 2005 456 7.49 6.42 NA
## yr1 yr2 yr3 yr4 yr5 yr6 yr7 yr8 yr9 yr10 NA
## culture=CNEG 582 432 279 158 87 54 33 18 6 2 0
## culture=GramNeg 615 440 246 128 72 45 34 21 11 5 0
## culture=GramPos 2005 1567 960 547 312 173 107 61 30 8 0
## Call:
## coxph(formula = Surv(Time2Fu, Event.Death) ~ culture, data = dat2)
##
## n= 3202, number of events= 701
## (306 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## cultureGramNeg -0.09013 0.91381 0.12830 -0.702 0.482
## cultureGramPos -0.01340 0.98669 0.09856 -0.136 0.892
##
## exp(coef) exp(-coef) lower .95 upper .95
## cultureGramNeg 0.9138 1.094 0.7106 1.175
## cultureGramPos 0.9867 1.013 0.8134 1.197
##
## Concordance= 0.503 (se = 0.01 )
## Rsquare= 0 (max possible= 0.959 )
## Likelihood ratio test= 0.63 on 2 df, p=0.7309
## Wald test = 0.62 on 2 df, p=0.7348
## Score (logrank) test = 0.62 on 2 df, p=0.7346