Hi All,
I'm trying to figure out the cumulative incidence curve in R in some
limited time. I found in package "cmprsk", the command "plot.cuminc" can
get this curve. But I noticed that there is no mark for the censored
time there, comparing with the KM curve by "plot.survfit". Here are my
codes (attached is the data):
----------------
dat<-read.table("F://wendy/BMT data analysis/final
data.txt",header=TRUE,sep="\t")
library(cmprsk)
library(survival)
attach(dat)
par(mfrow=c(2,1))
curve<-cuminc(SURVEFP/365.25,STATREP,Ritux)
plot(curve,xlab="years",curvlab=c("No rituximab",
"Rituximab"),lty=1:2,col=c("red","blue"),mark.time=TRUE)
a<-survfit(Surv(SURVEFP/365.25,STATREP)~Ritux,type="kaplan-meier")
plot(a,main="OS for whole
group",conf.int=F,xlab="years",ylab="probability",lty=1:2,col=c("red","b
lue"))
-------------------
Could you help me with how to put the mark for censored time on
cumulative incidence curve, or maybe how to get the 1-KM curve with the
mark for censored time? This will help me a lot!
Thank you very much!
UPN TYPE STATP SURVP STATNRMP STATREP STATEFP SURVEFP AGE
AGEBMT_med AGEBMT_dec SEX DXCODE DX1 DXBMT? STAGEGRP
BSYMDX BMINVDX PS IPIGROUP INITXGRP PRIXRT INICHEMO
PRIPURAN PRIRITU PRICHOP PRICHEMO PRIRESP DXBMTMON
INIDXBMT CON1_3 CON1_2 STATUS BM_PB CELLDOSE BMTSUB3A
CMV SURVAG STATAG SURVCG STATCG CGVHD_CI STAT_CGCI
AGVHD_CI STAT_AGCI COMPETING_RN STATUSCODE RESIDUALSCT
Ritux
318 AUTO 1 41 1 0 1 41 39 0
2 F 2 2 COMP ADV 0 0 0 1
2 1 1 0 0 1 0 P 1 1
3 0 1 BM 0 3 9 41 9 41
8 41 3 41 3 1 1 0 0
492 ALLO 1 2078 1 0 1 2078 44 0
2 M 2 2 DIS ADV 1 1 0 2
2 1 1 0 0 1 0 P 0 0
2 1 1 BM 1 1 4 2078 0 2078
0 2078 3 2078 3 1 1 1 0
625 ALLO 1 128 1 0 1 128 41 0
2 M 1 1 TRAN-H ADV 1 1 0 1
1 0 1 0 0 1 1 P 0 1
2 1 1 BM 1 1 1 43 1 101
1 101 1 43 3 1 1 0 0
631 ALLO 1 1548 0 1 1 656 36 0
1 F 2 2 DIS ADV 0 1 0 2
1 0 1 0 0 1 1 P 0 0
1 1 1 BM 1 2 1 15 1 1548
0 656 2 15 1 2 1 0 0
637 ALLO 1 16 1 0 1 16 34 0
1 F 2 2 COMP ADV 0 1 0 2
1 0 1 0 0 1 0 C 1 1
2 1 1 BM 1 1 4 16 0 16
8 16 3 16 3 1 1 0 0
652 ALLO 1 17 1 0 1 17 46 1
2 M 1 1 TRAN-H ADV 0 1 0 2
2 1 1 0 0 1 0 C 0 1
2 1 1 BM 1 1 4 17 0 17
8 17 3 17 3 1 1 0 0
759 ALLO 1 156 0 1 1 66 44 0
2 M 1 1 TRAN-H ADV 0 0 0 1
2 1 1 0 0 1 1 C 0 1
1 1 1 BM 0 1 4 156 0 124
1 66 2 66 2 2 1 0 0
826 ALLO 1 52 1 0 1 52 36 0
1 F 1 1 TRAN-H ADV 0 1 0 1
2 1 1 0 0 1 0 P 0 1
1 1 1 BM 1 2 3 20 1 52
8 52 3 20 1 1 1 0 0
918 AUTO 1 289 0 1 1 121 50 1
3 M 2 2 COMP ADV 1 0 0 1
2 1 1 0 0 1 1 P 1 1
2 1 1 PB 1 3 9 289 9 289
0 121 2 121 2 2 1 0 0
985 ALLO 1 166 0 1 1 152 45 1
2 M 1 1 TRAN-C ADV 0 0 0 1
1 0 1 0 0 1 0 P 0 1
1 1 2 BM 0 1 4 166 0 166
0 152 2 152 2 2 2 1 0
1033 ALLO 1 103 0 1 1 85 32 0
1 M 1 2 TRAN-C ADV 0 1 0 2
1 0 3 1 0 0 0 N 0 0
3 0 2 BM 0 2 1 28 1 103
0 85 2 28 1 2 2 1 0
1222 ALLO 1 967 0 1 1 799 32 0
1 F 1 1 TRAN-C ADV 0 1 0 1
2 1 1 0 0 1 1 P 0 1
3 0 2 BM 1 1 4 19 1 826
0 799 2 19 1 2 1 0 0
1225 ALLO 1 639 0 1 1 182 39 0
1 M 1 1 TRAN-H ADV 0 1 0 2
1 1 3 1 0 0 0 P 0 1
1 1 2 BM 0 1 4 639 0 182
1 182 1 182 2 2 2 1 0
1228 AUTO 0 2575 0 0 0 2575 44 1
2 F 2 2 COMP ADV 0 0 0 1
2 1 1 0 0 1 0 C 1 1
2 1 2 PB 1 3 9 2575 9 2575
0 2575 0 2575 0 0 2 1 0
1319 ALLO 1 106 1 0 1 106 53 1
3 M 1 1 TRAN-H LIM 0 0 0 1
2 1 1 0 0 1 0 P 0 1
1 1 2 BM 0 1 4 37 1 104
1 104 1 37 1 1 1 0 0
1321 AUTO 0 2622 0 1 1 962 26 0
0 M 2 2 COMP ADV 1 0 0 1
2 1 1 0 0 1 0 P 0 0
2 1 1 PB 1 3 9 2622 9 2622
0 962 2 962 2 2 1 1 0
1370 AUTO 1 68 0 1 1 61 56 1
3 F 2 2 DIS ADV 1 1 0 2
1 0 1 0 0 1 0 P 0 0
2 1 2 PB 1 3 9 68 9 68
8 61 2 61 2 2 2 1 0
1468 ALLO 0 2212 0 0 0 2212 49 1
2 F 2 2 DIS ADV 0 1 0 1
1 0 1 0 0 1 0 C 0 0
1 1 1 BM 0 1 4 2212 0 100
1 100 1 2212 0 0 1 1 0
1528 ALLO 1 456 0 1 1 245 29 0
0 F 1 2 TRAN-H ADV 0 0 0 2
2 1 1 0 0 1 1 C 0 1
1 1 2 BM 1 1 1 278 0 175
1 175 1 245 2 2 2 1 0
1634 ALLO 1 2074 0 1 1 1324 43 0
2 F 1 1 TRAN-C ADV 1 0 1 2
1 1 1 0 0 1 0 P 0 0
1 1 2 BM 0 1 3 18 1 103
1 103 1 18 1 2 2 1 0
1687 ALLO 1 1461 0 1 1 769 40 0
1 M 1 1 TRAN-H ADV 1 1 0 2
1 0 1 1 0 1 1 P 0 1
1 1 1 BM 0 1 1 24 1 101
1 101 1 24 1 2 1 0 0
1810 ALLO 1 173 0 1 1 104 48 1
2 M 1 1 TRAN-H ADV 0 0 0 1
1 0 1 0 0 1 1 C 0 1
1 1 1 BM 0 1 3 18 1 173
0 104 2 18 1 2 1 0 0
1824 ALLO 1 133 0 1 1 92 29 0
0 M 1 2 TRAN-C ADV 0 1 0 2
1 0 1 1 0 1 1 P 0 1
1 1 2 BM 1 1 2 133 0 133
0 92 2 92 2 2 2 1 0
1867 ALLO 1 285 1 0 1 285 44 1
2 M 2 2 DIS ADV 1 1 1 2
1 0 1 0 0 1 0 P 1 1
1 1 2 BM 0 1 3 21 1 185
1 185 1 21 1 1 1 0 0
1889 ALLO 0 1525 0 0 0 1525 34 0
1 M 1 1 TRAN-H ADV 0 0 0 2
1 0 3 1 1 0 1 P 1 1
1 1 2 BM 0 2 1 25 1 111
1 111 1 25 1 0 2 1 1
1893 ALLO 0 1529 0 0 0 1529 36 0
1 M 2 2 DIS ADV 0 1 0 2
2 1 1 1 0 1 1 C 1 1
1 1 1 PB 1 2 1 17 1 174
1 174 1 17 1 0 1 0 0
1895 ALLO 0 1009 0 0 0 1009 37 0
1 M 1 1 TRAN-H LIM 0 1 0 1
1 0 3 1 1 0 1 P 0 1
1 1 2 BM 1 2 1 1009 0 1009
0 1009 0 1009 0 0 2 1 1
1917 ALLO 1 334 1 0 1 334 46 1
2 M 1 1 TRAN-C ADV 0 1 0 2
1 0 1 1 0 1 1 P 0 1
1 1 2 BM 1 1 4 19 1 111
1 111 1 19 1 1 1 1 0
1958 ALLO 1 38 1 0 1 38 31 0
1 F 2 2 COMP ADV 0 1 0 2
1 0 1 0 0 1 0 C 1 1
1 1 1 BM 0 2 3 10 1 38
8 38 3 10 1 1 1 0 0
1972 ALLO 1 197 1 0 1 197 46 1
2 M 1 1 TRAN-H ADV 0 1 0 2
2 0 1 1 0 1 1 G 1 1
1 1 1 BM 0 2 1 12 1 103
1 103 1 12 1 1 1 0 0
1979 ALLO 0 1275 0 0 0 1275 41 0
2 M 1 1 TRAN-C ADV 0 1 0 1
1 0 3 1 0 0 0 P 0 1
1 1 2 PB 1 1 2 1275 0 159
1 159 1 1275 0 0 2 1 0
2009 AUTO 1 223 0 1 1 82 54 1
3 F 2 2 COMP ADV 0 1 0 1
1 0 1 0 0 1 1 C 1 1
3 0 1 PB 1 3 9 223 9 223
0 82 2 82 2 2 1 0 0
2039 ALLO 1 124 0 1 1 1 55 1
3 M 1 1 TRAN-C ADV 1 0 0 2
1 0 1 1 0 1 1 P 0 1
3 0 1 PB 1 1 4 91 0 91
7 1 2 1 2 2 1 0 0
2061 ALLO 1 91 1 0 1 91 55 1
3 M 1 2 TRAN-H ADV 1 1 0 1
1 0 1 1 1 1 1 N 0 1
1 1 1 BM 0 2 3 36 1 91
8 91 3 36 1 1 1 1 1
2114 ALLO 0 754 0 0 0 754 55 1
3 M 1 1 TRAN-H ADV 1 1 0 2
2 1 1 0 1 1 1 P 0 1
1 1 1 PB 1 1 2 754 0 754
0 754 0 754 0 0 1 1 1
2115 ALLO 0 332 0 0 0 332 42 1
2 F 2 2 COMP ADV 0 1 0 2
1 0 1 0 1 1 1 P 1 1
1 1 1 PB 1 2 4 332 0 100
1 100 1 332 0 0 1 0 1
2117 ALLO 1 98 0 1 1 85 28 0
0 M 2 2 DIS ADV 0 1 0 2
1 0 2 0 0 0 0 P 0 0
1 1 1 PB 1 2 3 20 1 98
8 85 2 20 1 2 1 1 0
2119 ALLO 1 41 1 0 1 41 54 1
3 M 2 2 COMP ADV 0 1 0 1
2 1 1 0 1 1 0 C 1 1
1 1 2 PB 1 2 3 6 1 41
8 41 3 6 1 1 2 1 1
2135 AUTO 1 512 0 1 1 174 57 1
3 F 2 2 COMP LIM 0 0 0 1
1 0 1 0 1 1 0 G 1 1
3 0 2 PB 1 3 9 512 9 512
0 174 2 174 2 2 1 0 1
2141 ALLO 1 679 1 0 1 679 47 1
2 M 1 1 TRAN-H ADV 0 0 0 1
1 0 1 0 1 1 1 G 0 1
1 1 1 BM 1 2 2 15 1 162
1 162 1 15 1 1 1 1 1
2159 AUTO 0 722 0 0 0 722 50 1
3 F 1 1 TRAN-H LIM 0 0 0 1
2 1 1 0 1 1 1 C 1 1
3 0 2 PB 1 3 9 722 9 722
0 722 0 722 0 0 1 0 1
2167 ALLO 0 733 0 0 0 733 39 0
2 F 2 2 DIS ADV 1 1 0 2
1 0 1 1 1 1 1 C 1 1
1 1 2 BM 0 2 3 733 0 124
1 124 1 733 0 0 1 0 1
2173 ALLO 0 643 0 0 0 643 32 0
1 F 2 2 COMP ADV 1 1 0 2
1 0 1 0 1 1 1 P 1 1
1 1 1 PB 1 2 1 643 0 146
1 146 1 643 0 0 1 0 1
2179 ALLO 0 699 0 0 0 699 37 0
2 F 2 2 COMP ADV 0 0 0 1
2 1 1 1 0 1 1 C 1 1
1 1 2 PB 1 1 3 20 1 699
0 699 0 20 1 0 1 0 0
2236 ALLO 0 563 0 0 0 563 49 1
3 F 1 1 TRAN-C ADV 0 1 0 1
1 0 1 1 0 1 1 P 1 1
1 1 2 PB 1 1 3 10 1 563
0 563 0 10 1 0 1 0 0
2250 AUTO 0 386 0 0 0 386 47 1
2 M 1 1 TRAN-C ADV 1 1 0 1
1 0 1 0 1 1 1 P 0 1
2 1 2 PB 1 3 9 386 9 386
0 386 0 386 0 0 1 0 1
2271 ALLO 1 25 1 0 1 25 55 1
3 M 1 1 TRAN-H ADV 0 1 0 1
1 0 1 1 1 1 1 C 0 1
1 1 1 PB 1 1 1 25 9 25
8 25 3 25 3 1 1 1 1
2295 AUTO 0 396 0 0 0 396 48 1
2 M 1 1 TRAN-H LIM 0 0 0 1
2 1 1 1 1 1 1 N 0 1
3 0 1 PB 1 3 9 396 9 396
0 396 0 396 0 0 1 0 1
2304 ALLO 1 295 1 0 1 295 50 1
2 M 2 2 COMP ADV 1 1 0 1
1 0 3 1 1 0 0 P 0 0
1 1 1 PB 1 1 1 21 1 101
1 101 1 21 1 1 1 1 1
2307 AUTO 0 348 0 0 0 348 24 0
0 M 2 2 COMP ADV 1 0 1 2
1 0 1 0 1 1 0 C 1 1
3 0 1 PB 1 3 9 348 9 348
0 348 0 348 0 0 1 0 1
2311 ALLO 1 107 0 1 1 77 40 0
2 M 2 2 COMP LIM 0 0 0 1
2 1 1 0 1 1 0 C 1 1
1 1 1 PB 1 1 1 17 1 107
0 77 2 17 1 2 1 0 1
2340 AUTO 0 317 0 1 1 174 54 1
3 M 1 1 TRAN-H ADV 1 0 0 2
1 0 1 0 0 1 0 P 0 1
2 1 1 PB 1 3 9 317 9 317
0 174 2 174 2 2 1 0 0
2360 AUTO 0 37 0 0 0 37 39 0
2 M 1 2 TRAN-H LIM 0 0 0 1
2 1 1 0 0 1 1 C 1 1
3 0 2 PB 1 3 9 37 9 37
7 37 0 37 0 0 1 0 0
2361 AUTO 0 263 0 0 0 263 54 1
3 M 2 2 COMP ADV 0 0 0 1
1 0 1 1 1 1 1 G 1 1
3 0 2 PB 1 3 9 263 9 263
0 263 0 263 0 0 2 1 1
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