Radiationdata: Two-column coordinates(X,Y) extracted from published Kaplan...

In NaLiuStat/IPDfromKM: An implementation that maps digitized survival curves back to individual patient data(IPD)

Description

The dataset is extracted from a published Kaplan Meier image by ScanIt software. Locoreginal control events were studied in 424 head and neck cancer patients: 213 in Radiotherapy treatment group and 211 in the Radiotherapy plus cetuximab group. There are 145 pairs of coordinates extracted from the radiation treatment arm, and 136 pairs of coordinates are extracted from the radiation plus arm. For both datasets, the first columns are the times, and the second columns are the survival rates at those time points(in percentage). For each group, there are six patients numbers at risk reported at the months of 0, 10, 20, 30, 40, and 50. Three vectors (i.e., trisk, nrisk.radio and nrisk.radioplus) record those numbers.

Usage

Radiationdata

Format

List of two dataframes (radio and radioplus) and three vectors

References

Bonner JA, Harari PM, Giralt J, Azarnia N, Shin DM, Cohen RB, Jones CU, Sur R, Raben D, Jassem J, Ove R, Kies MS, Baselga J, Youssoufian H, Amellal N, Rowinsky EK, Ang KK: Radiotherapy plus Cetuximab for Squamous-Cell Carcinoma of the Head and Neck. N Engl J Med. 2006, 354: 567-78. 10.1056/NEJMoa053422.

Examples

radio <- Radiationdata$radio
radioplus <- Radiationdata$radioplus
trisk <- Radiationdata$trisk
nrisk_radio <- Radiationdata$nrisk.radio
nrisk_radioplus <- Radiationdata$nrisk.radioplus
plot(radio,xlab="time",ylab="survival rates",type="l",
    lty=2,col="cyan4",xlim=c(1,70),main="Curves extracted by ScanIt software")
lines(radioplus,type="l",col="red4",lty=1)
legend("topright", c("Radiotherapy", "Radiotherapy plus cetuximab"),
      col = c("cyan4","red4"),lty=c(2,1),text.col = "green4")
text(40,80,"Reported Hazard Ratio with 95% CI: 0.69 (0.52,0.89)")

pre_radio <- preprocess(dat=radio, trisk=trisk,nrisk=nrisk_radio,maxy=100)
est_radio <- getIPD(prep=pre_radio,armind=0,tot.events=NULL)
pre_radio_plus <- preprocess(dat=radioplus, trisk=trisk,nrisk=nrisk_radioplus,maxy=100)
est_radio_plus <- getIPD(prep=pre_radio_plus,armind=1,tot.events=NULL)
library(survival)
library(survminer)
mixdat <- rbind(est_radio$IPD,est_radio_plus$IPD)
coxfit <- coxph(Surv(time,status)~treat,data=mixdat)
fit <- survfit(Surv(time, status) ~ treat,data = mixdat)
ggsurvplot(fit, data = mixdat, risk.table = TRUE)

NaLiuStat/IPDfromKM documentation built on Oct. 30, 2019, 10:09 p.m.