version 2.1-7

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: cmprsk
-Version: 2.1-5
-Date: 2004-oct-6
+Version: 2.1-7
+Date: 2006-dec-24
 Title: Subdistribution Analysis of Competing Risks
 Author: Bob Gray <[email protected]>
 Maintainer: Bob Gray <[email protected]>
-Depends: R (>= 1.4.0), survival
+Depends: R (>= 1.9.0), survival
 Description: Estimation, testing and regression modeling of
  subdistribution functions in competing risks, as described in Gray
  (1988), A class of K-sample tests for comparing the cumulative
@@ -13,4 +13,4 @@ Description: Estimation, testing and regression modeling of
  of a competing risk, JASA, 94:496-509.
 License: GPL version 2 or newer
 URL: http://www.r-project.org, http://biowww.dfci.harvard.edu/~gray
-Packaged: Wed Oct  6 10:33:45 2004; gray
+Packaged: Sun Dec 24 12:16:26 2006; gray

R/cmprsk.R

@@ -360,7 +360,7 @@ timepoints <- function(w,times) {
 }
 
 plot.cuminc <-  function(x,main=" ",curvlab,ylim=c(0,1),xlim,wh=2,xlab="Years",
-ylab="Probability",lty=1:length(x),color=1,...) {
+ylab="Probability",lty=1:length(x),color=1,lwd = par('lwd'),...) {
 # x is a list containing curves to be plotted. Each component of
 # x is a list with the first component containing the x values
 # and the second component the y values.  main = main title in the plot
@@ -369,6 +369,7 @@ ylab="Probability",lty=1:length(x),color=1,...) {
   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(lwd) < nc) lwd <- rep(lwd[1],nc) else lwd <- lwd[1:nc]
   if (length(color) < nc) color <- rep(color[1],nc) else color <- color[1:nc]
   if (missing(curvlab)) {
     if (mode(names(x))=="NULL") {
@@ -387,8 +388,15 @@ ylab="Probability",lty=1:length(x),color=1,...) {
   if (length(wh) != 2) {
       wh <- c(xlim[1],ylim[2])
   }
-  legend(wh[1],wh[2],legend=curvlab,col=color,lty=lty,bty="n",bg=-999999,...)
+  u <- list(...)
+  if (length(u)>0) {
+    i <- pmatch(names(u),names(formals(legend)),0)
+    do.call('legend',c(list(x=wh[1],y=wh[2],legend=curvlab,col=color,lty=lty,lwd=lwd,bty="n",bg=-999999),u[i>0]))
+  } else {
+    do.call('legend',list(x=wh[1],y=wh[2],legend=curvlab,col=color,lty=lty,lwd=lwd,bty="n",bg=-999999))
+  }
+#  legend(wh[1],wh[2],legend=curvlab,col=color,lty=lty,bty="n",bg=-999999,...)
   for (i in 1:nc) {
-    lines(x[[i]][[1]],x[[i]][[2]],lty=lty[i],col=color[i],...)
+    lines(x[[i]][[1]],x[[i]][[2]],lty=lty[i],col=color[i],lwd=lwd[i],...)
   }
 }

man/crr.Rd

@@ -129,34 +129,11 @@ ftime <- rexp(200)
 fstatus <- sample(0:2,200,replace=TRUE)
 cov <- matrix(runif(600),nrow=200)
 print(z <- crr(ftime,fstatus,cov))
-# convergence:  TRUE 
-# coefficients:
-# [1]  0.8470 -0.3473 -0.6913
-# standard errors:
-# [1] 0.4027 0.4402 0.4916
-# two-sided p-values:
-# [1] 0.035 0.430 0.160
-# for failures of type 2
 z.p <- predict(z,rbind(c(.1,.5,.8),c(.1,.5,.2)))
 plot(z.p,lty=1,color=2:3)
 crr(ftime,fstatus,cov,failcode=2)
-# convergence:  TRUE 
-# coefficients:
-# [1] -0.4638  0.4896  0.2331
-# standard errors:
-# [1] 0.3896 0.4540 0.4256
-# two-sided p-values:
-# [1] 0.23 0.28 0.58
 # quadratic in time for first cov
 crr(ftime,fstatus,cov,cbind(cov[,1],cov[,1]),function(Uft) cbind(Uft,Uft^2))
-# convergence:  TRUE 
-# coefficients:
-# [1]  1.3360 -0.3484 -0.6852 -1.1210  0.3897
-# standard errors:
-# [1] 0.8657 0.4405 0.4909 1.6860 0.6271
-# two-sided p-values:
-# [1] 0.12 0.43 0.16 0.51 0.53
-#last 2 values are the coefs of the cov[,1]*t and cov[,1]*t^2 terms
 #additional examples in test.R
 }
 \keyword{survival}

man/cuminc.Rd

@@ -93,28 +93,6 @@ gg <- factor(sample(1:3,100,replace=TRUE),1:3,c('a','b','c'))
 cc <- sample(0:2,100,replace=TRUE)
 strt <- sample(1:2,100,replace=TRUE)
 print(xx <- cuminc(ss,cc,gg,strt))
-#Tests:
-#      stat        pv
-#1 3.393977 0.1832345
-#2 1.989511 0.3698139
-#Estimates and Variances:
-#$est
-#            1         2         3         4         5
-#a 1 0.1311269 0.2699184 0.3420625 0.3420625 0.3420625
-#b 1 0.2176471 0.2615686        NA        NA        NA
-#c 1 0.3816280 0.4889137 0.5723581        NA        NA
-#a 2 0.2257601 0.2972171 0.4415053 0.4415053 0.4415053
-#b 2 0.3117647 0.5878431        NA        NA        NA
-#c 2 0.2160508 0.2607532 0.2607532        NA        NA
-#
-#$var
-#              1           2           3          4          5
-#a 1 0.003922836 0.009113464 0.012507959 0.01250796 0.01250796
-#b 1 0.005528913 0.006916070          NA         NA         NA
-#c 1 0.009854126 0.012351948 0.015575726         NA         NA
-#a 2 0.005947601 0.007356628 0.014479506 0.01447951 0.01447951
-#b 2 0.007033454 0.010927780          NA         NA         NA
-#c 2 0.006497566 0.007867543 0.007867543         NA         NA
 plot(xx,lty=1,color=1:6)
 # see also test.R, test.out
 }

man/plot.cuminc.Rd

@@ -9,7 +9,7 @@ list input, for example, the output from \code{cuminc()}.
 }
 \usage{
 plot.cuminc(x, main=" ", curvlab, ylim=c(0, 1), xlim, wh=2, xlab="Years", 
-ylab="Probability", lty=1:length(x), color=1, \dots)
+ylab="Probability", lty=1:length(x), color=1, lwd=par('lwd'), \dots)
 }
 \arguments{
 \item{x}{
@@ -53,7 +53,11 @@ used for all.
   vector of colors.  If \code{length(color)<nc}, then the \code{color[1]} is
   used for all.
   }
-\item{...}{
+\item{lwd}{
+  vector of line widths.  If \code{length(lwd)<nc}, then \code{lwd[1]}
+  is used for all.
+  }
+  \item{...}{
 additional arguments passed to the initial call of the plot function.
 }}
 \value{