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R Functions for Competing Risk Analysis and Stratified Analysis in Reduce

Stratified logrank Test

library(survival) f <- survdiff(S ~ treatment + strata(cluster)) chisq <- f$chisq Pval <- 1 - pchisq(chisq, 1)

Cumulative Incidence Function Plots for Competing Risks

library(cmprsk) set.seed(1) n <- 200 treat <- sample(c('a','b'), n, TRUE) event <- sample(c('death','heart attack','censored'), n, TRUE) table(event) time.to.event <- runif(n, .5, 10) f <- cuminc(time.to.event, event, treat, cencode='censored', rho=0) # also has strata argument which doesn't affect plots but affects the test

# Modification of plot.cuminc to allow vector lwd argument plot.cuminc <- function (x, main = " ", curvlab, ylim = c(0, 1), xlim, wh = 2, xlab = "Years", ylab = "Probability", lty = 1:length(x), color = 1, lwd = rep(1, length(x)), ...) { if (is.null(x$Tests)) x <- x[names(x) = "Tests"] nc <- length(x) if (length(lty) < nc) lty <- rep(lty[1], nc) else lty <- lty[1:nc] if (length(color) < nc) color <- rep(color[1], nc) else color <- color[1:nc] lwd <- rep(lwd, length.out=nc) if (missing(curvlab)) { if (mode(names(x)) == "NULL") { curvlab <- as.character(1:nc) } else curvlab <- names(x)[1:nc] } if (missing(xlim)) { xmax <- 0 for (i in 1:nc) { xmax <- max(c(xmax, xi1)) } xlim <- c(0, xmax) } plot(x11, x12, type = "n", ylim = ylim, xlim = xlim, main = main, xlab = xlab, ylab = ylab, bty = "l", ...) if (length(wh) = 2) { wh <- c(xlim[1], ylim[2]) } legend(wh[1], wh[2], legend = curvlab, col = color, lty = lty, lwd=lwd, bty = "n", bg = -999999, ...) for (i in 1:nc) { lines(xi1, xi2, lty = lty[i], col = color[i], lwd=lwd[i],...) } } plot(f) # use all defaults plot(f, xlab='Years', ylab='Cumulative Incidence', color=gray(c(0, .7, 0, .7)), lwd=c(.5, 3, .5, 3), lty=c(1,1,3,3)) Pvalues <- f$Tests[,'pv'] Pvalues Pvalues['heart attack'] f$Tests[,'stat'] g <- timepoints(f, c(2,4)) # get estimates at 2 and 4 years

# Get approximate 0.95 confidence intervals for 2- and 4-y cumulative incidence g$est - 1.96*sqrt(g$var) g$est + 1.96*sqrt(g$var)
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cuminc.pngpng cuminc.png manage 8.0 K 19 Sep 2006 - 17:15 FrankHarrell Example cumulative incidence plot, 2 events, 2 treatments
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Topic revision: r1 - 19 Sep 2006, FrankHarrell
 

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