Multivariate Cox Analysis
NTX3
cox.NTX3 <- coxph(Surv(Survival.after.begining.ZA.mo, Death.Status) ~ Age.Diagnosis +
Sex + Extra.Mets + NTX3, data = cancerSys.data)
summary(cox.NTX3)
## Call:
## coxph(formula = Surv(Survival.after.begining.ZA.mo, Death.Status) ~
## Age.Diagnosis + Sex + Extra.Mets + NTX3, data = cancerSys.data)
##
## n= 106, number of events= 86
## (41 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Age.Diagnosis 0.0209526 1.0211737 0.0082179 2.550 0.01078 *
## Sex 0.2961432 1.3446627 0.2367167 1.251 0.21092
## Extra.Mets 0.7076370 2.0291907 0.2425613 2.917 0.00353 **
## NTX3 0.0002335 1.0002335 0.0004476 0.522 0.60189
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## Age.Diagnosis 1.021 0.9793 1.0049 1.038
## Sex 1.345 0.7437 0.8455 2.138
## Extra.Mets 2.029 0.4928 1.2614 3.264
## NTX3 1.000 0.9998 0.9994 1.001
##
## Concordance= 0.599 (se = 0.036 )
## Rsquare= 0.141 (max possible= 0.998 )
## Likelihood ratio test= 16.09 on 4 df, p=0.002904
## Wald test = 15.24 on 4 df, p=0.004235
## Score (logrank) test = 15.66 on 4 df, p=0.003512
log(NTX3)
cox.log.NTX3 <- coxph(Surv(Survival.after.begining.ZA.mo, Death.Status) ~ Age.Diagnosis +
Sex + Extra.Mets + log(NTX3), data = cancerSys.data)
summary(cox.log.NTX3)
## Call:
## coxph(formula = Surv(Survival.after.begining.ZA.mo, Death.Status) ~
## Age.Diagnosis + Sex + Extra.Mets + log(NTX3), data = cancerSys.data)
##
## n= 106, number of events= 86
## (41 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Age.Diagnosis 0.019663 1.019858 0.008186 2.402 0.01630 *
## Sex 0.292510 1.339786 0.234740 1.246 0.21273
## Extra.Mets 0.659189 1.933224 0.245260 2.688 0.00719 **
## log(NTX3) 0.135850 1.145510 0.095247 1.426 0.15378
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## Age.Diagnosis 1.020 0.9805 1.0036 1.036
## Sex 1.340 0.7464 0.8457 2.122
## Extra.Mets 1.933 0.5173 1.1954 3.126
## log(NTX3) 1.146 0.8730 0.9504 1.381
##
## Concordance= 0.606 (se = 0.036 )
## Rsquare= 0.155 (max possible= 0.998 )
## Likelihood ratio test= 17.79 on 4 df, p=0.001355
## Wald test = 16.63 on 4 df, p=0.002276
## Score (logrank) test = 16.94 on 4 df, p=0.001986
NTX3 > 100
cox.NTX3.threshold <- coxph(Surv(Survival.after.begining.ZA.mo, Death.Status) ~ Age.Diagnosis +
Sex + Extra.Mets + (NTX3 > 100), data = cancerSys.data)
summary(cox.NTX3.threshold)
## Call:
## coxph(formula = Surv(Survival.after.begining.ZA.mo, Death.Status) ~
## Age.Diagnosis + Sex + Extra.Mets + (NTX3 > 100), data = cancerSys.data)
##
## n= 106, number of events= 86
## (41 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Age.Diagnosis 0.021398 1.021628 0.008105 2.640 0.00829 **
## Sex 0.264429 1.302687 0.236017 1.120 0.26255
## Extra.Mets 0.692272 1.998251 0.243656 2.841 0.00449 **
## NTX3 > 100TRUE 0.221160 1.247523 0.254048 0.871 0.38400
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## Age.Diagnosis 1.022 0.9788 1.0055 1.038
## Sex 1.303 0.7676 0.8202 2.069
## Extra.Mets 1.998 0.5004 1.2395 3.221
## NTX3 > 100TRUE 1.248 0.8016 0.7582 2.053
##
## Concordance= 0.605 (se = 0.036 )
## Rsquare= 0.145 (max possible= 0.998 )
## Likelihood ratio test= 16.56 on 4 df, p=0.00235
## Wald test = 15.74 on 4 df, p=0.003391
## Score (logrank) test = 16.14 on 4 df, p=0.002831
NTX12
cox.NTX12 <- coxph(Surv(Survival.after.begining.ZA.mo, Death.Status) ~ Age.Diagnosis +
Sex + Extra.Mets + NTX12, data = cancerSys.data)
summary(cox.NTX12)
## Call:
## coxph(formula = Surv(Survival.after.begining.ZA.mo, Death.Status) ~
## Age.Diagnosis + Sex + Extra.Mets + NTX12, data = cancerSys.data)
##
## n= 51, number of events= 41
## (96 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Age.Diagnosis 0.0184254 1.0185961 0.0128402 1.435 0.1513
## Sex 0.3708548 1.4489727 0.4105095 0.903 0.3663
## Extra.Mets 0.6222906 1.8631909 0.3525074 1.765 0.0775 .
## NTX12 0.0010300 1.0010305 0.0008444 1.220 0.2225
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## Age.Diagnosis 1.019 0.9817 0.9933 1.045
## Sex 1.449 0.6901 0.6481 3.240
## Extra.Mets 1.863 0.5367 0.9337 3.718
## NTX12 1.001 0.9990 0.9994 1.003
##
## Concordance= 0.643 (se = 0.051 )
## Rsquare= 0.172 (max possible= 0.995 )
## Likelihood ratio test= 9.66 on 4 df, p=0.04664
## Wald test = 9.29 on 4 df, p=0.05415
## Score (logrank) test = 9.85 on 4 df, p=0.04296
log(NTX12)
cox.log.NTX12 <- coxph(Surv(Survival.after.begining.ZA.mo, Death.Status) ~ Age.Diagnosis +
Sex + Extra.Mets + log(NTX12), data = cancerSys.data)
summary(cox.log.NTX12)
## Call:
## coxph(formula = Surv(Survival.after.begining.ZA.mo, Death.Status) ~
## Age.Diagnosis + Sex + Extra.Mets + log(NTX12), data = cancerSys.data)
##
## n= 51, number of events= 41
## (96 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Age.Diagnosis 0.01769 1.01785 0.01269 1.394 0.163
## Sex 0.36474 1.44014 0.41170 0.886 0.376
## Extra.Mets 0.55634 1.74427 0.36877 1.509 0.131
## log(NTX12) 0.16380 1.17797 0.14409 1.137 0.256
##
## exp(coef) exp(-coef) lower .95 upper .95
## Age.Diagnosis 1.018 0.9825 0.9928 1.043
## Sex 1.440 0.6944 0.6426 3.227
## Extra.Mets 1.744 0.5733 0.8467 3.593
## log(NTX12) 1.178 0.8489 0.8882 1.562
##
## Concordance= 0.63 (se = 0.051 )
## Rsquare= 0.172 (max possible= 0.995 )
## Likelihood ratio test= 9.62 on 4 df, p=0.0474
## Wald test = 8.96 on 4 df, p=0.06205
## Score (logrank) test = 9.42 on 4 df, p=0.05147
NTX12 > 100
cox.NTX12.threshold <- coxph(Surv(Survival.after.begining.ZA.mo, Death.Status) ~ Age.Diagnosis +
Sex + Extra.Mets + (NTX12 > 100), data = cancerSys.data)
summary(cox.NTX12.threshold)
## Call:
## coxph(formula = Surv(Survival.after.begining.ZA.mo, Death.Status) ~
## Age.Diagnosis + Sex + Extra.Mets + (NTX12 > 100), data = cancerSys.data)
##
## n= 51, number of events= 41
## (96 observations deleted due to missingness)
##
## coef exp(coef) se(coef) z Pr(>|z|)
## Age.Diagnosis 0.01698 1.01713 0.01276 1.331 0.1831
## Sex 0.40195 1.49473 0.41912 0.959 0.3375
## Extra.Mets 0.60042 1.82289 0.35886 1.673 0.0943 .
## NTX12 > 100TRUE 0.44395 1.55885 0.39757 1.117 0.2642
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95 upper .95
## Age.Diagnosis 1.017 0.9832 0.9920 1.043
## Sex 1.495 0.6690 0.6574 3.399
## Extra.Mets 1.823 0.5486 0.9022 3.683
## NTX12 > 100TRUE 1.559 0.6415 0.7151 3.398
##
## Concordance= 0.64 (se = 0.051 )
## Rsquare= 0.171 (max possible= 0.995 )
## Likelihood ratio test= 9.55 on 4 df, p=0.04875
## Wald test = 9.21 on 4 df, p=0.056
## Score (logrank) test = 9.68 on 4 df, p=0.04613