R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("cmprsk-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('cmprsk')
Loading required package: survival
Loading required package: splines
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "crr"
> 
> ### * crr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: crr
> ### Title: Competing Risks Regression
> ### Aliases: crr
> ### Keywords: survival
> 
> ### ** Examples
> 
> # simulated data to test 
> set.seed(10)
> 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] -0.6306  0.2024  0.6384
standard errors:
[1] 0.4043 0.3782 0.4105
two-sided p-values:
[1] 0.12 0.59 0.12
> # 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]  0.01017 -0.17020 -0.58140
standard errors:
[1] 0.4418 0.4799 0.4217
two-sided p-values:
[1] 0.98 0.72 0.17
> # 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] -0.7257  0.1976  0.6392  0.3692 -0.1459
standard errors:
[1] 0.8403 0.3785 0.4116 1.1810 0.3142
two-sided p-values:
[1] 0.39 0.60 0.12 0.75 0.64
> # 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
> 
> 
> 
> cleanEx(); ..nameEx <- "cuminc"
> 
> ### * cuminc
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: cuminc
> ### Title: Cumulative Incidence Analysis
> ### Aliases: cuminc
> ### Keywords: survival
> 
> ### ** Examples
> 
> set.seed(2)
> ss <- rexp(100)
> 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 df
1 0.1110522 0.9459873  2
2 0.1344095 0.9350037  2
Estimates and Variances:
$est
            1         2         3         4
a 1 0.1997374 0.3337599 0.4082169 0.4082169
b 1 0.2582589 0.3116745 0.3116745 0.3116745
c 1 0.2194354 0.2813451 0.2813451 0.2813451
a 2 0.2641725 0.4428692 0.4428692 0.4428692
b 2 0.2669364 0.4479557 0.5280790 0.6082023
c 2 0.2471892 0.4400615 0.4400615 0.4400615

$var
              1           2           3           4
a 1 0.005842447 0.009576915 0.013764577 0.013764577
b 1 0.007508487 0.009432554 0.009432554 0.009432554
c 1 0.006644662 0.009550507 0.009550507 0.009550507
a 2 0.008127032 0.011168223 0.011168223 0.011168223
b 2 0.008030980 0.014868553 0.016688860 0.016481796
c 2 0.006941955 0.016574813 0.016574813 0.016574813

> #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
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  0.46 0.07 0.54 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')