First, import and clean data
library(haven)
LarynxSCC_DSS <- read_sav("C:/Users/yul13011/Dropbox/2017-2018/Linda's paper/Revisions/SEER2000on_LarynxSCC_2019Feb22.sav")
LarynxSCC_DSS=LarynxSCC_DSS[LarynxSCC_DSS$`filter_$`==1, ]
LarynxSCC_DSS=LarynxSCC_DSS[, c("DSS_Larynx","SurvivalMonths","Age","Sex","Race_NEW","PrimarySiteLabeled","PrimarySite","LNDx", "AJCC6thStage_NEW","TreatmentGrp","Marital_NEW")]
LarynxSCC_DSS=LarynxSCC_DSS[LarynxSCC_DSS$LNDx!="99",]
LarynxSCC_DSS=LarynxSCC_DSS[LarynxSCC_DSS$Marital_NEW!="6",]
LarynxSCC_DSS=LarynxSCC_DSS[LarynxSCC_DSS$AJCC6thStage_NEW!="8",]
LarynxSCC_DSS$PrimarySite=factor(LarynxSCC_DSS$PrimarySite,
levels=c("320","321","322"),
labels=c("C32.0-Glottis","C32.1-Supraglottis","C32.2-Subglottis"))
LarynxSCC_DSS$Race_NEW=factor(LarynxSCC_DSS$Race_NEW,
levels=c("5","1","2","3","4"),
labels=c("White",
"American Indian/Alaska Native",
"Asian or Pacific Islander",
"Black",
"Unknown"
))
LarynxSCC_DSS$Marital_NEW=factor(LarynxSCC_DSS$Marital_NEW,
levels=c("4","1","2","3","5","7"),
labels=c("Single","Divorced","Married","Separated","Unknown","widowed"))
LarynxSCC_DSS$AJCC6thStage_NEW=factor(LarynxSCC_DSS$AJCC6thStage_NEW,
levels = c("1","2","3","4"))
LarynxSCC_DSS$LNDx=factor(LarynxSCC_DSS$LNDx,
levels = c("0","1"),
labels = c("not examined","examined"))
LarynxSCC_DSS$TreatmentGrp=factor(LarynxSCC_DSS$TreatmentGrp,
levels = c("0","1","2","3"),
labels = c("Radiation only","Local Surgery",
"Local surgery + radiation",
"Open surgery"))
LarynxSCC_DSS$female=ifelse(LarynxSCC_DSS$Sex=="Female",1,0) # create a variable to match on #
LarynxSCC_DSS=data.frame(LarynxSCC_DSS)
Run Cox regression on the unmatched data and check proportional hazards assumption
library(survival)
## Warning: package 'survival' was built under R version 3.5.3
library(survminer)
## Warning: package 'survminer' was built under R version 3.5.3
## Loading required package: ggplot2
## Loading required package: ggpubr
## Loading required package: magrittr
library(dplyr)
## Warning: package 'dplyr' was built under R version 3.5.3
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(timereg)
## Warning: package 'timereg' was built under R version 3.5.3
surv=Surv(time=LarynxSCC_DSS$SurvivalMonths,event= LarynxSCC_DSS$DSS_Larynx)
# Fit cox regression
fit1=coxph(surv~Age+female+Race_NEW+Marital_NEW+
PrimarySite+AJCC6thStage_NEW+TreatmentGrp+LNDx, data=LarynxSCC_DSS)
summary(fit1)
## Call:
## coxph(formula = surv ~ Age + female + Race_NEW + Marital_NEW +
## PrimarySite + AJCC6thStage_NEW + TreatmentGrp + LNDx, data = LarynxSCC_DSS)
##
## n= 16288, number of events= 2266
##
## coef exp(coef) se(coef) z
## Age 0.033912 1.034493 0.002172 15.611
## female -0.103079 0.902056 0.054625 -1.887
## Race_NEWAmerican Indian/Alaska Native -0.113446 0.892752 0.302733 -0.375
## Race_NEWAsian or Pacific Islander 0.130016 1.138847 0.117783 1.104
## Race_NEWBlack -0.014558 0.985547 0.059401 -0.245
## Race_NEWUnknown -0.776865 0.459846 0.578163 -1.344
## Marital_NEWDivorced -0.074830 0.927901 0.072972 -1.025
## Marital_NEWMarried -0.363425 0.695291 0.060128 -6.044
## Marital_NEWSeparated 0.077233 1.080294 0.163735 0.472
## Marital_NEWUnknown -0.186985 0.829457 0.128393 -1.456
## Marital_NEWwidowed -0.024129 0.976160 0.080000 -0.302
## PrimarySiteC32.1-Supraglottis 0.315416 1.370829 0.050469 6.250
## PrimarySiteC32.2-Subglottis 0.344408 1.411154 0.136351 2.526
## AJCC6thStage_NEW2 0.587213 1.798967 0.075750 7.752
## AJCC6thStage_NEW3 1.148555 3.153634 0.072458 15.851
## AJCC6thStage_NEW4 1.632233 5.115285 0.070822 23.047
## TreatmentGrpLocal Surgery -0.360669 0.697210 0.129022 -2.795
## TreatmentGrpLocal surgery + radiation -0.246354 0.781646 0.071785 -3.432
## TreatmentGrpOpen surgery -0.023314 0.976955 0.068867 -0.339
## LNDxexamined -0.010435 0.989620 0.067436 -0.155
## Pr(>|z|)
## Age < 2e-16 ***
## female 0.05915 .
## Race_NEWAmerican Indian/Alaska Native 0.70785
## Race_NEWAsian or Pacific Islander 0.26965
## Race_NEWBlack 0.80639
## Race_NEWUnknown 0.17905
## Marital_NEWDivorced 0.30514
## Marital_NEWMarried 1.50e-09 ***
## Marital_NEWSeparated 0.63714
## Marital_NEWUnknown 0.14530
## Marital_NEWwidowed 0.76295
## PrimarySiteC32.1-Supraglottis 4.11e-10 ***
## PrimarySiteC32.2-Subglottis 0.01154 *
## AJCC6thStage_NEW2 9.04e-15 ***
## AJCC6thStage_NEW3 < 2e-16 ***
## AJCC6thStage_NEW4 < 2e-16 ***
## TreatmentGrpLocal Surgery 0.00518 **
## TreatmentGrpLocal surgery + radiation 0.00060 ***
## TreatmentGrpOpen surgery 0.73496
## LNDxexamined 0.87703
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95
## Age 1.0345 0.9667 1.0301
## female 0.9021 1.1086 0.8105
## Race_NEWAmerican Indian/Alaska Native 0.8928 1.1201 0.4932
## Race_NEWAsian or Pacific Islander 1.1388 0.8781 0.9041
## Race_NEWBlack 0.9855 1.0147 0.8772
## Race_NEWUnknown 0.4598 2.1746 0.1481
## Marital_NEWDivorced 0.9279 1.0777 0.8042
## Marital_NEWMarried 0.6953 1.4382 0.6180
## Marital_NEWSeparated 1.0803 0.9257 0.7837
## Marital_NEWUnknown 0.8295 1.2056 0.6449
## Marital_NEWwidowed 0.9762 1.0244 0.8345
## PrimarySiteC32.1-Supraglottis 1.3708 0.7295 1.2417
## PrimarySiteC32.2-Subglottis 1.4112 0.7086 1.0802
## AJCC6thStage_NEW2 1.7990 0.5559 1.5508
## AJCC6thStage_NEW3 3.1536 0.3171 2.7361
## AJCC6thStage_NEW4 5.1153 0.1955 4.4523
## TreatmentGrpLocal Surgery 0.6972 1.4343 0.5414
## TreatmentGrpLocal surgery + radiation 0.7816 1.2794 0.6791
## TreatmentGrpOpen surgery 0.9770 1.0236 0.8536
## LNDxexamined 0.9896 1.0105 0.8671
## upper .95
## Age 1.0389
## female 1.0040
## Race_NEWAmerican Indian/Alaska Native 1.6159
## Race_NEWAsian or Pacific Islander 1.4346
## Race_NEWBlack 1.1072
## Race_NEWUnknown 1.4281
## Marital_NEWDivorced 1.0706
## Marital_NEWMarried 0.7823
## Marital_NEWSeparated 1.4891
## Marital_NEWUnknown 1.0668
## Marital_NEWwidowed 1.1419
## PrimarySiteC32.1-Supraglottis 1.5134
## PrimarySiteC32.2-Subglottis 1.8435
## AJCC6thStage_NEW2 2.0869
## AJCC6thStage_NEW3 3.6349
## AJCC6thStage_NEW4 5.8770
## TreatmentGrpLocal Surgery 0.8978
## TreatmentGrpLocal surgery + radiation 0.8997
## TreatmentGrpOpen surgery 1.1181
## LNDxexamined 1.1295
##
## Concordance= 0.738 (se = 0.005 )
## Likelihood ratio test= 1493 on 20 df, p=<2e-16
## Wald test = 1369 on 20 df, p=<2e-16
## Score (logrank) test = 1569 on 20 df, p=<2e-16
# Evaluate model assumption
temp1=cox.zph(fit1)
print(temp1)
## rho chisq p
## Age -0.08970 19.7404 8.87e-06
## female -0.00218 0.0106 9.18e-01
## Race_NEWAmerican Indian/Alaska Native 0.00508 0.0582 8.09e-01
## Race_NEWAsian or Pacific Islander 0.00883 0.1776 6.73e-01
## Race_NEWBlack 0.03789 3.3098 6.89e-02
## Race_NEWUnknown -0.02778 1.7467 1.86e-01
## Marital_NEWDivorced 0.03582 2.9155 8.77e-02
## Marital_NEWMarried 0.06923 10.8841 9.70e-04
## Marital_NEWSeparated -0.01649 0.6213 4.31e-01
## Marital_NEWUnknown 0.01653 0.6246 4.29e-01
## Marital_NEWwidowed 0.01986 0.8810 3.48e-01
## PrimarySiteC32.1-Supraglottis 0.01137 0.3393 5.60e-01
## PrimarySiteC32.2-Subglottis -0.01089 0.2739 6.01e-01
## AJCC6thStage_NEW2 -0.04826 5.6146 1.78e-02
## AJCC6thStage_NEW3 -0.11943 37.2450 1.04e-09
## AJCC6thStage_NEW4 -0.13714 50.1413 1.43e-12
## TreatmentGrpLocal Surgery -0.08256 16.3496 5.27e-05
## TreatmentGrpLocal surgery + radiation -0.04454 4.5447 3.30e-02
## TreatmentGrpOpen surgery -0.00894 0.2020 6.53e-01
## LNDxexamined 0.03163 2.4550 1.17e-01
## GLOBAL NA 108.5415 3.62e-14
We find out that the data does not satisfy a proportional hazards assumption
Try a different model
Fit nonparametric additive hazards model which allows every independent variable to have time-varying effects
LarynxSCC_DSS$age.c=LarynxSCC_DSS$Age-mean(LarynxSCC_DSS$Age)
add1=aalen(surv~I(exp(age.c/10))+female+Race_NEW+Marital_NEW
+PrimarySite+AJCC6thStage_NEW+TreatmentGrp+LNDx,
data=LarynxSCC_DSS,residuals = 1)
summary(add1)
## Additive Aalen Model
##
## Test for nonparametric terms
##
## Test for non-significant effects
## Supremum-test of significance
## (Intercept) Inf
## I(exp(age.c/10)) Inf
## female Inf
## Race_NEWAmerican Indian/Alaska Native Inf
## Race_NEWAsian or Pacific Islander Inf
## Race_NEWBlack Inf
## Race_NEWUnknown Inf
## Marital_NEWDivorced Inf
## Marital_NEWMarried Inf
## Marital_NEWSeparated Inf
## Marital_NEWUnknown Inf
## Marital_NEWwidowed Inf
## PrimarySiteC32.1-Supraglottis Inf
## PrimarySiteC32.2-Subglottis Inf
## AJCC6thStage_NEW2 Inf
## AJCC6thStage_NEW3 Inf
## AJCC6thStage_NEW4 Inf
## TreatmentGrpLocal Surgery Inf
## TreatmentGrpLocal surgery + radiation Inf
## TreatmentGrpOpen surgery Inf
## LNDxexamined Inf
## p-value H_0: B(t)=0
## (Intercept) 0
## I(exp(age.c/10)) 0
## female 0
## Race_NEWAmerican Indian/Alaska Native 0
## Race_NEWAsian or Pacific Islander 0
## Race_NEWBlack 0
## Race_NEWUnknown 0
## Marital_NEWDivorced 0
## Marital_NEWMarried 0
## Marital_NEWSeparated 0
## Marital_NEWUnknown 0
## Marital_NEWwidowed 0
## PrimarySiteC32.1-Supraglottis 0
## PrimarySiteC32.2-Subglottis 0
## AJCC6thStage_NEW2 0
## AJCC6thStage_NEW3 0
## AJCC6thStage_NEW4 0
## TreatmentGrpLocal Surgery 0
## TreatmentGrpLocal surgery + radiation 0
## TreatmentGrpOpen surgery 0
## LNDxexamined 0
##
## Test for time invariant effects
## Kolmogorov-Smirnov test
## (Intercept) 0.03380
## I(exp(age.c/10)) 0.01140
## female 0.02200
## Race_NEWAmerican Indian/Alaska Native 0.03450
## Race_NEWAsian or Pacific Islander 0.03340
## Race_NEWBlack 0.01430
## Race_NEWUnknown 0.03170
## Marital_NEWDivorced 0.01590
## Marital_NEWMarried 0.04520
## Marital_NEWSeparated 0.05670
## Marital_NEWUnknown 0.02550
## Marital_NEWwidowed 0.02720
## PrimarySiteC32.1-Supraglottis 0.03360
## PrimarySiteC32.2-Subglottis 0.12100
## AJCC6thStage_NEW2 0.03630
## AJCC6thStage_NEW3 0.10900
## AJCC6thStage_NEW4 0.18300
## TreatmentGrpLocal Surgery 0.01660
## TreatmentGrpLocal surgery + radiation 0.00931
## TreatmentGrpOpen surgery 0.01930
## LNDxexamined 0.02170
## p-value H_0:constant effect
## (Intercept) 0.258
## I(exp(age.c/10)) 0.098
## female 0.536
## Race_NEWAmerican Indian/Alaska Native 0.929
## Race_NEWAsian or Pacific Islander 0.666
## Race_NEWBlack 0.889
## Race_NEWUnknown 0.716
## Marital_NEWDivorced 0.955
## Marital_NEWMarried 0.090
## Marital_NEWSeparated 0.453
## Marital_NEWUnknown 0.787
## Marital_NEWwidowed 0.897
## PrimarySiteC32.1-Supraglottis 0.254
## PrimarySiteC32.2-Subglottis 0.494
## AJCC6thStage_NEW2 0.109
## AJCC6thStage_NEW3 0.000
## AJCC6thStage_NEW4 0.000
## TreatmentGrpLocal Surgery 0.644
## TreatmentGrpLocal surgery + radiation 0.913
## TreatmentGrpOpen surgery 0.923
## LNDxexamined 0.901
## Cramer von Mises test
## (Intercept) 0.04010
## I(exp(age.c/10)) 0.00486
## female 0.02130
## Race_NEWAmerican Indian/Alaska Native 0.01910
## Race_NEWAsian or Pacific Islander 0.04230
## Race_NEWBlack 0.00677
## Race_NEWUnknown 0.04750
## Marital_NEWDivorced 0.00586
## Marital_NEWMarried 0.07550
## Marital_NEWSeparated 0.09620
## Marital_NEWUnknown 0.01430
## Marital_NEWwidowed 0.01480
## PrimarySiteC32.1-Supraglottis 0.03000
## PrimarySiteC32.2-Subglottis 0.33100
## AJCC6thStage_NEW2 0.03760
## AJCC6thStage_NEW3 0.47000
## AJCC6thStage_NEW4 1.59000
## TreatmentGrpLocal Surgery 0.00428
## TreatmentGrpLocal surgery + radiation 0.00154
## TreatmentGrpOpen surgery 0.00949
## LNDxexamined 0.01010
## p-value H_0:constant effect
## (Intercept) 0.182
## I(exp(age.c/10)) 0.024
## female 0.272
## Race_NEWAmerican Indian/Alaska Native 0.968
## Race_NEWAsian or Pacific Islander 0.581
## Race_NEWBlack 0.758
## Race_NEWUnknown 0.626
## Marital_NEWDivorced 0.907
## Marital_NEWMarried 0.053
## Marital_NEWSeparated 0.506
## Marital_NEWUnknown 0.803
## Marital_NEWwidowed 0.862
## PrimarySiteC32.1-Supraglottis 0.225
## PrimarySiteC32.2-Subglottis 0.378
## AJCC6thStage_NEW2 0.102
## AJCC6thStage_NEW3 0.000
## AJCC6thStage_NEW4 0.000
## TreatmentGrpLocal Surgery 0.794
## TreatmentGrpLocal surgery + radiation 0.928
## TreatmentGrpOpen surgery 0.859
## LNDxexamined 0.865
##
##
##
## Call:
## aalen(formula = surv ~ I(exp(age.c/10)) + female + Race_NEW +
## Marital_NEW + PrimarySite + AJCC6thStage_NEW + TreatmentGrp +
## LNDx, data = LarynxSCC_DSS, residuals = 1)
plot(add1,specific.comps = 3)
AJCC6thStage_NEW failed the tests for constant effect
Fit semi-parametric additive hazards model
LarynxSCC_DSS$age.c=LarynxSCC_DSS$Age-mean(LarynxSCC_DSS$Age)
add2=aalen(surv~const(I(exp(age.c/10)))+const(female)+const(Race_NEW)+const(Marital_NEW)
+const(PrimarySite)+AJCC6thStage_NEW+const(TreatmentGrp)+const(LNDx),
data=LarynxSCC_DSS)
summary(add2)
## Additive Aalen Model
##
## Test for nonparametric terms
##
## Test for non-significant effects
## Supremum-test of significance p-value H_0: B(t)=0
## (Intercept) 4.14 0
## AJCC6thStage_NEW2 7.40 0
## AJCC6thStage_NEW3 13.40 0
## AJCC6thStage_NEW4 20.00 0
##
## Test for time invariant effects
## Kolmogorov-Smirnov test
## (Intercept) 0.0103
## AJCC6thStage_NEW2 0.0467
## AJCC6thStage_NEW3 0.1170
## AJCC6thStage_NEW4 0.1910
## p-value H_0:constant effect
## (Intercept) 0.334
## AJCC6thStage_NEW2 0.000
## AJCC6thStage_NEW3 0.000
## AJCC6thStage_NEW4 0.000
## Cramer von Mises test
## (Intercept) 0.00362
## AJCC6thStage_NEW2 0.07710
## AJCC6thStage_NEW3 0.56400
## AJCC6thStage_NEW4 1.80000
## p-value H_0:constant effect
## (Intercept) 0.296
## AJCC6thStage_NEW2 0.000
## AJCC6thStage_NEW3 0.000
## AJCC6thStage_NEW4 0.000
##
## Parametric terms :
## Coef. SE Robust SE
## const(I(exp(age.c/10))) 6.11e-04 5.21e-05 5.87e-05
## const(female) -5.04e-04 1.99e-04 2.03e-04
## const(Race_NEW)American Indian/Alaska Native -5.14e-04 9.80e-04 8.91e-04
## const(Race_NEW)Asian or Pacific Islander 7.32e-04 4.62e-04 4.68e-04
## const(Race_NEW)Black -6.12e-05 2.33e-04 2.30e-04
## const(Race_NEW)Unknown -1.16e-03 7.73e-04 8.84e-04
## const(Marital_NEW)Divorced 8.86e-05 3.17e-04 3.30e-04
## const(Marital_NEW)Married -8.97e-04 2.30e-04 2.36e-04
## const(Marital_NEW)Separated 6.45e-04 7.67e-04 7.69e-04
## const(Marital_NEW)Unknown -3.52e-04 4.10e-04 3.99e-04
## const(Marital_NEW)widowed 5.38e-04 3.80e-04 3.84e-04
## const(PrimarySite)C32.1-Supraglottis 1.24e-03 2.12e-04 2.17e-04
## const(PrimarySite)C32.2-Subglottis 1.63e-03 8.42e-04 8.76e-04
## const(TreatmentGrp)Local Surgery -6.94e-04 1.98e-04 2.11e-04
## const(TreatmentGrp)Local surgery + radiation -6.06e-04 1.59e-04 1.61e-04
## const(TreatmentGrp)Open surgery -1.19e-04 3.37e-04 3.35e-04
## const(LNDx)examined -1.79e-04 3.76e-04 3.75e-04
## z P-val lower2.5%
## const(I(exp(age.c/10))) 10.400 0.00e+00 5.09e-04
## const(female) -2.480 1.31e-02 -8.94e-04
## const(Race_NEW)American Indian/Alaska Native -0.577 5.64e-01 -2.43e-03
## const(Race_NEW)Asian or Pacific Islander 1.560 1.18e-01 -1.74e-04
## const(Race_NEW)Black -0.266 7.90e-01 -5.18e-04
## const(Race_NEW)Unknown -1.320 1.88e-01 -2.68e-03
## const(Marital_NEW)Divorced 0.269 7.88e-01 -5.33e-04
## const(Marital_NEW)Married -3.810 1.41e-04 -1.35e-03
## const(Marital_NEW)Separated 0.839 4.02e-01 -8.58e-04
## const(Marital_NEW)Unknown -0.882 3.78e-01 -1.16e-03
## const(Marital_NEW)widowed 1.400 1.61e-01 -2.07e-04
## const(PrimarySite)C32.1-Supraglottis 5.700 1.20e-08 8.24e-04
## const(PrimarySite)C32.2-Subglottis 1.870 6.21e-02 -2.03e-05
## const(TreatmentGrp)Local Surgery -3.290 9.87e-04 -1.08e-03
## const(TreatmentGrp)Local surgery + radiation -3.780 1.60e-04 -9.18e-04
## const(TreatmentGrp)Open surgery -0.356 7.22e-01 -7.80e-04
## const(LNDx)examined -0.477 6.33e-01 -9.16e-04
## upper97.5%
## const(I(exp(age.c/10))) 0.000713
## const(female) -0.000114
## const(Race_NEW)American Indian/Alaska Native 0.001410
## const(Race_NEW)Asian or Pacific Islander 0.001640
## const(Race_NEW)Black 0.000395
## const(Race_NEW)Unknown 0.000355
## const(Marital_NEW)Divorced 0.000710
## const(Marital_NEW)Married -0.000446
## const(Marital_NEW)Separated 0.002150
## const(Marital_NEW)Unknown 0.000452
## const(Marital_NEW)widowed 0.001280
## const(PrimarySite)C32.1-Supraglottis 0.001660
## const(PrimarySite)C32.2-Subglottis 0.003280
## const(TreatmentGrp)Local Surgery -0.000306
## const(TreatmentGrp)Local surgery + radiation -0.000294
## const(TreatmentGrp)Open surgery 0.000542
## const(LNDx)examined 0.000558
##
## Call:
## aalen(formula = surv ~ const(I(exp(age.c/10))) + const(female) +
## const(Race_NEW) + const(Marital_NEW) + const(PrimarySite) +
## AJCC6thStage_NEW + const(TreatmentGrp) + const(LNDx), data = LarynxSCC_DSS)
PS Matching and check balance
library(MatchIt)
## Warning: package 'MatchIt' was built under R version 3.5.3
library("optmatch")
## Warning: package 'optmatch' was built under R version 3.5.3
## The optmatch package has an academic license. Enter relaxinfo() for more information.
library(cobalt)
## Warning: package 'cobalt' was built under R version 3.5.3
##
## Attaching package: 'cobalt'
## The following object is masked from 'package:MatchIt':
##
## lalonde
# Now try full matching #
m.out=matchit(female~Age+TreatmentGrp+Race_NEW+Marital_NEW+LNDx, data=LarynxSCC_DSS,
method="full",exact = c("PrimarySite","AJCC6thStage_NEW",options("optmatch_max_problem_size" = Inf)))
## Warning in optmatch::fullmatch(d, ...): Without 'data' argument the order of the match is not guaranteed
## to be the same as your original data.
summary(m.out,standardize = T)
##
## Call:
## matchit(formula = female ~ Age + TreatmentGrp + Race_NEW + Marital_NEW +
## LNDx, data = LarynxSCC_DSS, method = "full", exact = c("PrimarySite",
## "AJCC6thStage_NEW", options(optmatch_max_problem_size = Inf)))
##
## Summary of balance for all data:
## Means Treated Means Control
## distance 0.2438 0.1830
## Age 63.4412 65.2972
## TreatmentGrpRadiation only 0.6499 0.6099
## TreatmentGrpLocal Surgery 0.0659 0.0769
## TreatmentGrpLocal surgery + radiation 0.1447 0.1667
## TreatmentGrpOpen surgery 0.1396 0.1465
## Race_NEWAmerican Indian/Alaska Native 0.0047 0.0050
## Race_NEWAsian or Pacific Islander 0.0202 0.0313
## Race_NEWBlack 0.1443 0.1425
## Race_NEWUnknown 0.0013 0.0043
## Marital_NEWDivorced 0.1447 0.1304
## Marital_NEWMarried 0.3958 0.5754
## Marital_NEWSeparated 0.0154 0.0135
## Marital_NEWUnknown 0.0432 0.0403
## Marital_NEWwidowed 0.2335 0.0784
## LNDxexamined 0.1708 0.1479
## Std. Mean Diff. eCDF Med eCDF Mean
## distance 0.4972 0.1703 0.1494
## Age -0.1562 0.0146 0.0239
## TreatmentGrpRadiation only 0.0837 0.0200 0.0200
## TreatmentGrpLocal Surgery -0.0446 0.0055 0.0055
## TreatmentGrpLocal surgery + radiation -0.0626 0.0110 0.0110
## TreatmentGrpOpen surgery -0.0198 0.0034 0.0034
## Race_NEWAmerican Indian/Alaska Native -0.0033 0.0001 0.0001
## Race_NEWAsian or Pacific Islander -0.0794 0.0056 0.0056
## Race_NEWBlack 0.0052 0.0009 0.0009
## Race_NEWUnknown -0.0869 0.0015 0.0015
## Marital_NEWDivorced 0.0406 0.0071 0.0071
## Marital_NEWMarried -0.3672 0.0898 0.0898
## Marital_NEWSeparated 0.0158 0.0010 0.0010
## Marital_NEWUnknown 0.0144 0.0015 0.0015
## Marital_NEWwidowed 0.3667 0.0776 0.0776
## LNDxexamined 0.0608 0.0114 0.0114
## eCDF Max
## distance 0.2327
## Age 0.0731
## TreatmentGrpRadiation only 0.0399
## TreatmentGrpLocal Surgery 0.0111
## TreatmentGrpLocal surgery + radiation 0.0220
## TreatmentGrpOpen surgery 0.0069
## Race_NEWAmerican Indian/Alaska Native 0.0002
## Race_NEWAsian or Pacific Islander 0.0112
## Race_NEWBlack 0.0018
## Race_NEWUnknown 0.0031
## Marital_NEWDivorced 0.0143
## Marital_NEWMarried 0.1796
## Marital_NEWSeparated 0.0019
## Marital_NEWUnknown 0.0029
## Marital_NEWwidowed 0.1551
## LNDxexamined 0.0229
##
##
## Summary of balance for matched data:
## Means Treated Means Control
## distance 0.2438 0.2438
## Age 63.4412 62.9968
## TreatmentGrpRadiation only 0.6499 0.6528
## TreatmentGrpLocal Surgery 0.0659 0.0677
## TreatmentGrpLocal surgery + radiation 0.1447 0.1313
## TreatmentGrpOpen surgery 0.1396 0.1481
## Race_NEWAmerican Indian/Alaska Native 0.0047 0.0019
## Race_NEWAsian or Pacific Islander 0.0202 0.0129
## Race_NEWBlack 0.1443 0.1928
## Race_NEWUnknown 0.0013 0.0015
## Marital_NEWDivorced 0.1447 0.1327
## Marital_NEWMarried 0.3958 0.3990
## Marital_NEWSeparated 0.0154 0.0168
## Marital_NEWUnknown 0.0432 0.0489
## Marital_NEWwidowed 0.2335 0.2286
## LNDxexamined 0.1708 0.1750
## Std. Mean Diff. eCDF Med eCDF Mean
## distance -0.0001 0.0036 0.0061
## Age 0.0374 0.0084 0.0103
## TreatmentGrpRadiation only -0.0062 0.0046 0.0046
## TreatmentGrpLocal Surgery -0.0076 0.0030 0.0030
## TreatmentGrpLocal surgery + radiation 0.0379 0.0052 0.0052
## TreatmentGrpOpen surgery -0.0245 0.0036 0.0036
## Race_NEWAmerican Indian/Alaska Native 0.0410 0.0010 0.0010
## Race_NEWAsian or Pacific Islander 0.0519 0.0020 0.0020
## Race_NEWBlack -0.1378 0.0164 0.0164
## Race_NEWUnknown -0.0059 0.0002 0.0002
## Marital_NEWDivorced 0.0339 0.0130 0.0130
## Marital_NEWMarried -0.0064 0.0106 0.0106
## Marital_NEWSeparated -0.0110 0.0016 0.0016
## Marital_NEWUnknown -0.0279 0.0056 0.0056
## Marital_NEWwidowed 0.0116 0.0004 0.0004
## LNDxexamined -0.0111 0.0004 0.0004
## eCDF Max
## distance 0.0232
## Age 0.0376
## TreatmentGrpRadiation only 0.0092
## TreatmentGrpLocal Surgery 0.0060
## TreatmentGrpLocal surgery + radiation 0.0104
## TreatmentGrpOpen surgery 0.0072
## Race_NEWAmerican Indian/Alaska Native 0.0020
## Race_NEWAsian or Pacific Islander 0.0040
## Race_NEWBlack 0.0328
## Race_NEWUnknown 0.0004
## Marital_NEWDivorced 0.0260
## Marital_NEWMarried 0.0212
## Marital_NEWSeparated 0.0032
## Marital_NEWUnknown 0.0112
## Marital_NEWwidowed 0.0008
## LNDxexamined 0.0008
##
## Percent Balance Improvement:
## Std. Mean Diff. eCDF Med
## distance 99.9757 97.8863
## Age 76.0527 42.4724
## TreatmentGrpRadiation only 92.5818 76.9688
## TreatmentGrpLocal Surgery 83.0604 45.7825
## TreatmentGrpLocal surgery + radiation 39.5055 52.7730
## TreatmentGrpOpen surgery -23.7070 -4.9869
## Race_NEWAmerican Indian/Alaska Native -1131.0098 -774.2415
## Race_NEWAsian or Pacific Islander 34.7183 64.1833
## Race_NEWBlack -2540.5865 -1688.1333
## Race_NEWUnknown 93.2343 87.0363
## Marital_NEWDivorced 16.5275 -82.1622
## Marital_NEWMarried 98.2520 88.1965
## Marital_NEWSeparated 30.2355 -64.3722
## Marital_NEWUnknown -94.6024 -283.8825
## Marital_NEWwidowed 96.8497 99.4844
## LNDxexamined 81.6945 96.5056
## eCDF Mean eCDF Max
## distance 95.9160 90.0313
## Age 56.8591 48.5676
## TreatmentGrpRadiation only 76.9688 76.9688
## TreatmentGrpLocal Surgery 45.7825 45.7825
## TreatmentGrpLocal surgery + radiation 52.7730 52.7730
## TreatmentGrpOpen surgery -4.9869 -4.9869
## Race_NEWAmerican Indian/Alaska Native -774.2415 -774.2415
## Race_NEWAsian or Pacific Islander 64.1833 64.1833
## Race_NEWBlack -1688.1333 -1688.1333
## Race_NEWUnknown 87.0363 87.0363
## Marital_NEWDivorced -82.1622 -82.1622
## Marital_NEWMarried 88.1965 88.1965
## Marital_NEWSeparated -64.3722 -64.3722
## Marital_NEWUnknown -283.8825 -283.8825
## Marital_NEWwidowed 99.4844 99.4844
## LNDxexamined 96.5056 96.5056
##
## Sample sizes:
## Control Treated
## All 13115 3173
## Matched 13115 3173
## Unmatched 0 0
## Discarded 0 0
m.data_full=match.data(m.out,group="all",distance = "distance",weights="weights",subclass = "subclass")
# Check balance by graphical evidence
bal.plot(m.out,var.name = "distance",which="both",type="histogram")+
scale_fill_discrete(name="Sex",labels=c("Male","Female"))+
ggtitle("")+xlab("Propensity Score")
## Scale for 'fill' is already present. Adding another scale for 'fill',
## which will replace the existing scale.
# Balance is good #
Run additive hazards models on the post-matching data
surv2=Surv(time=m.data_full$SurvivalMonths,event= m.data_full$DSS_Larynx)
fit2=coxph(surv2~Age+female+Race_NEW+Marital_NEW+
PrimarySite+AJCC6thStage_NEW+TreatmentGrp+LNDx, data=m.data_full,weights=weights)
summary(fit2)
## Call:
## coxph(formula = surv2 ~ Age + female + Race_NEW + Marital_NEW +
## PrimarySite + AJCC6thStage_NEW + TreatmentGrp + LNDx, data = m.data_full,
## weights = weights)
##
## n= 16288, number of events= 2266
##
## coef exp(coef) se(coef)
## Age 0.0249215 1.0252346 0.0022551
## female -0.0124816 0.9875960 0.0531394
## Race_NEWAmerican Indian/Alaska Native 0.2168965 1.2422155 0.3909311
## Race_NEWAsian or Pacific Islander -0.1541069 0.8571804 0.1941255
## Race_NEWBlack -0.0762215 0.9266109 0.0560435
## Race_NEWUnknown -0.8449916 0.4295610 1.1611683
## Marital_NEWDivorced -0.1213746 0.8857021 0.0738707
## Marital_NEWMarried -0.3957535 0.6731726 0.0634560
## Marital_NEWSeparated 0.2340891 1.2637571 0.1537547
## Marital_NEWUnknown -0.3150317 0.7297657 0.1298756
## Marital_NEWwidowed -0.0670477 0.9351506 0.0706845
## PrimarySiteC32.1-Supraglottis 0.3235159 1.3819781 0.0517275
## PrimarySiteC32.2-Subglottis 0.5943498 1.8118525 0.1247383
## AJCC6thStage_NEW2 0.5381740 1.7128764 0.0817326
## AJCC6thStage_NEW3 1.0675630 2.9082834 0.0771864
## AJCC6thStage_NEW4 1.6208445 5.0573595 0.0742454
## TreatmentGrpLocal Surgery -0.1152530 0.8911407 0.1257914
## TreatmentGrpLocal surgery + radiation -0.0005749 0.9994253 0.0758042
## TreatmentGrpOpen surgery 0.0725655 1.0752633 0.0687561
## LNDxexamined -0.0429823 0.9579283 0.0656775
## z Pr(>|z|)
## Age 11.051 < 2e-16 ***
## female -0.235 0.8143
## Race_NEWAmerican Indian/Alaska Native 0.555 0.5790
## Race_NEWAsian or Pacific Islander -0.794 0.4273
## Race_NEWBlack -1.360 0.1738
## Race_NEWUnknown -0.728 0.4668
## Marital_NEWDivorced -1.643 0.1004
## Marital_NEWMarried -6.237 4.47e-10 ***
## Marital_NEWSeparated 1.522 0.1279
## Marital_NEWUnknown -2.426 0.0153 *
## Marital_NEWwidowed -0.949 0.3428
## PrimarySiteC32.1-Supraglottis 6.254 3.99e-10 ***
## PrimarySiteC32.2-Subglottis 4.765 1.89e-06 ***
## AJCC6thStage_NEW2 6.585 4.56e-11 ***
## AJCC6thStage_NEW3 13.831 < 2e-16 ***
## AJCC6thStage_NEW4 21.831 < 2e-16 ***
## TreatmentGrpLocal Surgery -0.916 0.3595
## TreatmentGrpLocal surgery + radiation -0.008 0.9939
## TreatmentGrpOpen surgery 1.055 0.2912
## LNDxexamined -0.654 0.5128
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## exp(coef) exp(-coef) lower .95
## Age 1.0252 0.9754 1.02071
## female 0.9876 1.0126 0.88991
## Race_NEWAmerican Indian/Alaska Native 1.2422 0.8050 0.57735
## Race_NEWAsian or Pacific Islander 0.8572 1.1666 0.58591
## Race_NEWBlack 0.9266 1.0792 0.83022
## Race_NEWUnknown 0.4296 2.3280 0.04412
## Marital_NEWDivorced 0.8857 1.1290 0.76632
## Marital_NEWMarried 0.6732 1.4855 0.59445
## Marital_NEWSeparated 1.2638 0.7913 0.93495
## Marital_NEWUnknown 0.7298 1.3703 0.56576
## Marital_NEWwidowed 0.9352 1.0693 0.81417
## PrimarySiteC32.1-Supraglottis 1.3820 0.7236 1.24874
## PrimarySiteC32.2-Subglottis 1.8119 0.5519 1.41888
## AJCC6thStage_NEW2 1.7129 0.5838 1.45934
## AJCC6thStage_NEW3 2.9083 0.3438 2.49997
## AJCC6thStage_NEW4 5.0574 0.1977 4.37246
## TreatmentGrpLocal Surgery 0.8911 1.1222 0.69642
## TreatmentGrpLocal surgery + radiation 0.9994 1.0006 0.86144
## TreatmentGrpOpen surgery 1.0753 0.9300 0.93970
## LNDxexamined 0.9579 1.0439 0.84223
## upper .95
## Age 1.0298
## female 1.0960
## Race_NEWAmerican Indian/Alaska Native 2.6727
## Race_NEWAsian or Pacific Islander 1.2540
## Race_NEWBlack 1.0342
## Race_NEWUnknown 4.1823
## Marital_NEWDivorced 1.0237
## Marital_NEWMarried 0.7623
## Marital_NEWSeparated 1.7082
## Marital_NEWUnknown 0.9413
## Marital_NEWwidowed 1.0741
## PrimarySiteC32.1-Supraglottis 1.5294
## PrimarySiteC32.2-Subglottis 2.3137
## AJCC6thStage_NEW2 2.0105
## AJCC6thStage_NEW3 3.3833
## AJCC6thStage_NEW4 5.8495
## TreatmentGrpLocal Surgery 1.1403
## TreatmentGrpLocal surgery + radiation 1.1595
## TreatmentGrpOpen surgery 1.2304
## LNDxexamined 1.0895
##
## Concordance= 0.724 (se = 0.01 )
## Likelihood ratio test= 1266 on 20 df, p=<2e-16
## Wald test = 1139 on 20 df, p=<2e-16
## Score (logrank) test = 1307 on 20 df, p=<2e-16
ggforest(fit1,data=LarynxSCC_DSS)
## Warning: Removed 6 rows containing missing values (geom_errorbar).
temp1=cox.zph(fit2)
print(temp1)
## rho chisq p
## Age -0.08115 17.5677 2.77e-05
## female -0.02855 1.8809 1.70e-01
## Race_NEWAmerican Indian/Alaska Native 0.01263 0.5999 4.39e-01
## Race_NEWAsian or Pacific Islander 0.00174 0.0189 8.91e-01
## Race_NEWBlack 0.01866 0.7199 3.96e-01
## Race_NEWUnknown -0.03039 8.4490 3.65e-03
## Marital_NEWDivorced 0.03456 2.7899 9.49e-02
## Marital_NEWMarried 0.07274 13.7118 2.13e-04
## Marital_NEWSeparated -0.01387 0.3899 5.32e-01
## Marital_NEWUnknown 0.01514 0.5415 4.62e-01
## Marital_NEWwidowed 0.02127 0.8711 3.51e-01
## PrimarySiteC32.1-Supraglottis 0.02367 1.5595 2.12e-01
## PrimarySiteC32.2-Subglottis 0.01260 0.3125 5.76e-01
## AJCC6thStage_NEW2 -0.05526 8.5787 3.40e-03
## AJCC6thStage_NEW3 -0.13718 55.9945 7.27e-14
## AJCC6thStage_NEW4 -0.14456 61.5838 4.24e-15
## TreatmentGrpLocal Surgery -0.08996 18.6807 1.55e-05
## TreatmentGrpLocal surgery + radiation -0.03759 3.6229 5.70e-02
## TreatmentGrpOpen surgery -0.00600 0.0910 7.63e-01
## LNDxexamined 0.01782 0.7453 3.88e-01
## GLOBAL NA 138.4661 9.88e-20
m.data_full$age.c=m.data_full$Age-mean(m.data_full$Age)
add3=aalen(surv2~I(exp(age.c/10))+female+Race_NEW+Marital_NEW+TreatmentGrp+LNDx,
data=m.data_full, m.data_full$weights,residuals = 1)
## Warning in times > start.time: longer object length is not a multiple of
## shorter object length
summary(add3)
## Additive Aalen Model
##
## Test for nonparametric terms
##
## Test for non-significant effects
## Supremum-test of significance
## (Intercept) Inf
## I(exp(age.c/10)) Inf
## female Inf
## Race_NEWAmerican Indian/Alaska Native Inf
## Race_NEWAsian or Pacific Islander Inf
## Race_NEWBlack Inf
## Race_NEWUnknown Inf
## Marital_NEWDivorced Inf
## Marital_NEWMarried Inf
## Marital_NEWSeparated Inf
## Marital_NEWUnknown Inf
## Marital_NEWwidowed Inf
## TreatmentGrpLocal Surgery Inf
## TreatmentGrpLocal surgery + radiation Inf
## TreatmentGrpOpen surgery Inf
## LNDxexamined Inf
## p-value H_0: B(t)=0
## (Intercept) 0
## I(exp(age.c/10)) 0
## female 0
## Race_NEWAmerican Indian/Alaska Native 0
## Race_NEWAsian or Pacific Islander 0
## Race_NEWBlack 0
## Race_NEWUnknown 0
## Marital_NEWDivorced 0
## Marital_NEWMarried 0
## Marital_NEWSeparated 0
## Marital_NEWUnknown 0
## Marital_NEWwidowed 0
## TreatmentGrpLocal Surgery 0
## TreatmentGrpLocal surgery + radiation 0
## TreatmentGrpOpen surgery 0
## LNDxexamined 0
##
## Test for time invariant effects
## Kolmogorov-Smirnov test
## (Intercept) 0.12600
## I(exp(age.c/10)) 0.00878
## female 0.03270
## Race_NEWAmerican Indian/Alaska Native 0.03280
## Race_NEWAsian or Pacific Islander 0.03560
## Race_NEWBlack 0.04380
## Race_NEWUnknown 0.03770
## Marital_NEWDivorced 0.04360
## Marital_NEWMarried 0.08340
## Marital_NEWSeparated 0.04550
## Marital_NEWUnknown 0.06860
## Marital_NEWwidowed 0.06160
## TreatmentGrpLocal Surgery 0.06430
## TreatmentGrpLocal surgery + radiation 0.04380
## TreatmentGrpOpen surgery 0.02830
## LNDxexamined 0.07550
## p-value H_0:constant effect
## (Intercept) 0.000
## I(exp(age.c/10)) 0.250
## female 0.606
## Race_NEWAmerican Indian/Alaska Native 0.938
## Race_NEWAsian or Pacific Islander 0.622
## Race_NEWBlack 0.447
## Race_NEWUnknown 0.538
## Marital_NEWDivorced 0.556
## Marital_NEWMarried 0.038
## Marital_NEWSeparated 0.789
## Marital_NEWUnknown 0.223
## Marital_NEWwidowed 0.508
## TreatmentGrpLocal Surgery 0.001
## TreatmentGrpLocal surgery + radiation 0.013
## TreatmentGrpOpen surgery 0.683
## LNDxexamined 0.038
## Cramer von Mises test
## (Intercept) 0.74100
## I(exp(age.c/10)) 0.00244
## female 0.02710
## Race_NEWAmerican Indian/Alaska Native 0.01840
## Race_NEWAsian or Pacific Islander 0.04830
## Race_NEWBlack 0.10400
## Race_NEWUnknown 0.07480
## Marital_NEWDivorced 0.05800
## Marital_NEWMarried 0.30800
## Marital_NEWSeparated 0.02290
## Marital_NEWUnknown 0.17700
## Marital_NEWwidowed 0.15700
## TreatmentGrpLocal Surgery 0.18200
## TreatmentGrpLocal surgery + radiation 0.07770
## TreatmentGrpOpen surgery 0.03060
## LNDxexamined 0.27500
## p-value H_0:constant effect
## (Intercept) 0.001
## I(exp(age.c/10)) 0.124
## female 0.675
## Race_NEWAmerican Indian/Alaska Native 0.972
## Race_NEWAsian or Pacific Islander 0.525
## Race_NEWBlack 0.404
## Race_NEWUnknown 0.510
## Marital_NEWDivorced 0.584
## Marital_NEWMarried 0.075
## Marital_NEWSeparated 0.937
## Marital_NEWUnknown 0.283
## Marital_NEWwidowed 0.428
## TreatmentGrpLocal Surgery 0.002
## TreatmentGrpLocal surgery + radiation 0.011
## TreatmentGrpOpen surgery 0.484
## LNDxexamined 0.021
##
##
##
## Call:
## aalen(formula = surv2 ~ I(exp(age.c/10)) + female + Race_NEW +
## Marital_NEW + TreatmentGrp + LNDx, data = m.data_full, start.time = m.data_full$weights,
## residuals = 1)
Stage and LDX failed test for constant effect
Fit semi-parametric additive hazards model
add4=aalen(surv2~const(I(exp(age.c/10)))+const(female)+const(Race_NEW)+const(Marital_NEW)
+const(PrimarySite)+AJCC6thStage_NEW+const(TreatmentGrp)+LNDx,
data=LarynxSCC_DSS,m.data_full$weights)
## Warning in times > start.time: longer object length is not a multiple of
## shorter object length
summary(add4)
## Additive Aalen Model
##
## Test for nonparametric terms
##
## Test for non-significant effects
## Supremum-test of significance p-value H_0: B(t)=0
## (Intercept) 4.40 0.000
## AJCC6thStage_NEW2 7.23 0.000
## AJCC6thStage_NEW3 13.20 0.000
## AJCC6thStage_NEW4 19.30 0.000
## LNDxexamined 2.96 0.087
##
## Test for time invariant effects
## Kolmogorov-Smirnov test
## (Intercept) 0.1020
## AJCC6thStage_NEW2 0.0789
## AJCC6thStage_NEW3 0.1990
## AJCC6thStage_NEW4 0.4000
## LNDxexamined 0.0229
## p-value H_0:constant effect
## (Intercept) 0.001
## AJCC6thStage_NEW2 0.000
## AJCC6thStage_NEW3 0.000
## AJCC6thStage_NEW4 0.000
## LNDxexamined 0.826
## Cramer von Mises test
## (Intercept) 0.4670
## AJCC6thStage_NEW2 0.4020
## AJCC6thStage_NEW3 2.9900
## AJCC6thStage_NEW4 11.8000
## LNDxexamined 0.0152
## p-value H_0:constant effect
## (Intercept) 0.000
## AJCC6thStage_NEW2 0.000
## AJCC6thStage_NEW3 0.000
## AJCC6thStage_NEW4 0.000
## LNDxexamined 0.768
##
## Parametric terms :
## Coef. SE Robust SE
## const(I(exp(age.c/10))) 5.93e-04 5.15e-05 5.79e-05
## const(female) -5.23e-04 1.98e-04 2.01e-04
## const(Race_NEW)American Indian/Alaska Native -4.54e-04 9.80e-04 8.98e-04
## const(Race_NEW)Asian or Pacific Islander 6.75e-04 4.57e-04 4.69e-04
## const(Race_NEW)Black -4.05e-05 2.32e-04 2.29e-04
## const(Race_NEW)Unknown -1.12e-03 7.73e-04 8.83e-04
## const(Marital_NEW)Divorced 6.92e-05 3.17e-04 3.29e-04
## const(Marital_NEW)Married -9.10e-04 2.30e-04 2.35e-04
## const(Marital_NEW)Separated 5.39e-04 7.58e-04 7.66e-04
## const(Marital_NEW)Unknown -3.45e-04 4.10e-04 4.00e-04
## const(Marital_NEW)widowed 4.48e-04 3.77e-04 3.80e-04
## const(PrimarySite)C32.1-Supraglottis 1.22e-03 2.11e-04 2.17e-04
## const(PrimarySite)C32.2-Subglottis 1.48e-03 8.28e-04 8.58e-04
## const(TreatmentGrp)Local Surgery -7.73e-04 1.92e-04 2.05e-04
## const(TreatmentGrp)Local surgery + radiation -6.01e-04 1.59e-04 1.60e-04
## const(TreatmentGrp)Open surgery -1.75e-04 3.34e-04 3.31e-04
## z P-val lower2.5%
## const(I(exp(age.c/10))) 10.200 0.00e+00 0.000492
## const(female) -2.610 9.13e-03 -0.000911
## const(Race_NEW)American Indian/Alaska Native -0.505 6.14e-01 -0.002370
## const(Race_NEW)Asian or Pacific Islander 1.440 1.50e-01 -0.000221
## const(Race_NEW)Black -0.177 8.59e-01 -0.000495
## const(Race_NEW)Unknown -1.270 2.03e-01 -0.002640
## const(Marital_NEW)Divorced 0.210 8.34e-01 -0.000552
## const(Marital_NEW)Married -3.870 1.09e-04 -0.001360
## const(Marital_NEW)Separated 0.704 4.81e-01 -0.000947
## const(Marital_NEW)Unknown -0.862 3.89e-01 -0.001150
## const(Marital_NEW)widowed 1.180 2.38e-01 -0.000291
## const(PrimarySite)C32.1-Supraglottis 5.620 1.88e-08 0.000806
## const(PrimarySite)C32.2-Subglottis 1.720 8.48e-02 -0.000143
## const(TreatmentGrp)Local Surgery -3.760 1.70e-04 -0.001150
## const(TreatmentGrp)Local surgery + radiation -3.770 1.66e-04 -0.000913
## const(TreatmentGrp)Open surgery -0.528 5.97e-01 -0.000830
## upper97.5%
## const(I(exp(age.c/10))) 0.000694
## const(female) -0.000135
## const(Race_NEW)American Indian/Alaska Native 0.001470
## const(Race_NEW)Asian or Pacific Islander 0.001570
## const(Race_NEW)Black 0.000414
## const(Race_NEW)Unknown 0.000395
## const(Marital_NEW)Divorced 0.000691
## const(Marital_NEW)Married -0.000459
## const(Marital_NEW)Separated 0.002020
## const(Marital_NEW)Unknown 0.000459
## const(Marital_NEW)widowed 0.001190
## const(PrimarySite)C32.1-Supraglottis 0.001630
## const(PrimarySite)C32.2-Subglottis 0.003100
## const(TreatmentGrp)Local Surgery -0.000397
## const(TreatmentGrp)Local surgery + radiation -0.000289
## const(TreatmentGrp)Open surgery 0.000480
##
## Call:
## aalen(formula = surv2 ~ const(I(exp(age.c/10))) + const(female) +
## const(Race_NEW) + const(Marital_NEW) + const(PrimarySite) +
## AJCC6thStage_NEW + const(TreatmentGrp) + LNDx, data = LarynxSCC_DSS,
## start.time = m.data_full$weights)