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# Make sure ISwR package is installed library(ISwR) library(survival) library(Hmisc) #library(Design)

data(melanom) contents(melanom) melanom <- upData(melanom, labels=c(status="Patient's Status", days="Observation time", ulc="Tumor Ulceration", thick="Tumor Thickness", sex="Gender"), levels=list(status=c("Dead from Malignant Melanoma", "Alive on Jan 1, 1978", "Dead from Other Causes"), ulc=c("Present", "Absent"), sex=c("Female", "Male")), units=c(days="days", thick="1/100 mm"))

# K-M estimates surv.all <- survfit(Surv(melanom$days, melanom$status=="Dead from Malignant Melanoma")) summary(surv.all) summary(surv.all, censored=TRUE) plot(surv.all)

surv.bysex <- survfit(Surv(melanom$days, melanom$status=="Dead from Malignant Melanoma") ~ melanom$sex) plot(surv.bysex) plot(surv.bysex, conf.int=TRUE, col=c("black", "gray"))

# Cox PH model coxph.m1 <- coxph(Surv(days, status=="Dead from Malignant Melanoma") ~ log(thick) + sex + strata(ulc), data=melanom) plot(survfit(coxph.m1))

# Using Design cph library(Design) f <- cph(Surv(days, status=="Dead from Malignant Melanoma") ~ log(thick) + sex + strat(ulc), data=melanom, surv=TRUE, time.inc=2*365.25, y=TRUE) dd<-datadist(melanom) options(datadist="dd")

survplot(f, ulc=NA)

par(mar=c(5, 5, 0, 3)+0.1, las=1) survplot(f, ulc=NA, ylim=c(0.5, 1.0), xlab="Observation Time (days)", ylab="Cumulative Proportion Without Death from Malignant Melanoma", lwd=2, time.inc=2*365.25, n.risk=TRUE, cex.n.risk=0.85, adj.n.risk=0.5) box(bty="l")

f1 <- cph(Surv(days, status=="Dead from Malignant Melanoma") ~ log(thick) + sex + ulc, data=melanom, surv=TRUE, time.inc=2*365.25, y=TRUE) summary(f1) par(mar=c(5, 4, 4, 2)+0.1) plot(summary(f1))

options(datadist=NULL)
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Topic revision: r1 - 08 Nov 2006, TheresaScott
 

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