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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

> ### * <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("relsurv-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('relsurv')
Loading required package: survival
Loading required package: splines
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "invtime"
> 
> ### * invtime
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: invtime
> ### Title: Inverse transforming of time in Relative Survival
> ### Aliases: invtime
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> invtime(y = 0.1, age = 23011, sex = "male", year = 9497, ratetable = slopop)
[[1]]
[1] 63

[[2]]
[1] "male"

[[3]]
[1] 9497

$Y
[1] 0.1

$T
[1] 5106

> 
> 
> 
> cleanEx(); ..nameEx <- "plotrszph"
> 
> ### * plotrszph
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: plot.rs.zph
> ### Title: Graphical Inspection of Proportional Hazards Assumption in
> ###   Relative Survival Models
> ### Aliases: plot.rs.zph
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> data(rdata)
> fit <- rsadd(Surv(time,cens)~sex+as.factor(agegr)+ratetable(age=age*365,sex=sex,
+        year=year),ratetable=slopop,data=rdata,int=5)
> rszph <- rs.zph(fit)
> plot(rszph)
> 
> 
> 
> cleanEx(); ..nameEx <- "resid"
> 
> ### * resid
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: residuals.rsadd
> ### Title: Calculate Residuals for a rsadd Fit
> ### Aliases: residuals.rsadd resid.com
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> data(rdata)
> fit <- rsadd(Surv(time,cens)~sex+ratetable(age=age*365,sex=sex,year=year),
+        ratetable=slopop,data=rdata,int=5)
> sresid <- residuals.rsadd(fit)
> 
> 
> 
> cleanEx(); ..nameEx <- "rsadd"
> 
> ### * rsadd
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: rsadd
> ### Title: Fit an Additive model for Relative Survival
> ### Aliases: rsadd print.rsadd summary.rsadd print.summary.rsadd maxlik
> ###   glmxp lik.fit
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> data(rdata)
> rsadd(Surv(time,cens)~sex+as.factor(agegr)+ratetable(age=age*365,sex=sex,
+       year=year),ratetable=slopop,data=rdata,int=5)

Call: rsadd(formula = Surv(time, cens) ~ sex + as.factor(agegr) + ratetable(age = age * 
    365, sex = sex, year = year), data = rdata, ratetable = slopop, 
    int = 5)


Coefficients:
                  sex  as.factor.agegr.61.70  as.factor.agegr.70.95  
               0.8945                 0.3995                 0.4760  
  as.factor.agegr..53               fu [0,1)               fu [1,2)  
              -0.1295                -4.0644                -4.8102  
             fu [2,3)               fu [3,4)               fu [4,5)  
              -4.8513                -5.2646                -4.8030  
> 
> 
> 
> cleanEx(); ..nameEx <- "rsbr"
> 
> ### * rsbr
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: rs.br
> ### Title: Test the Proportional Hazards Assumption for Relative Survival
> ###   Regression Models
> ### Aliases: rs.br plot.rs.br print.rs.br
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> data(rdata)
> fit <- rsadd(Surv(time,cens)~sex+ratetable(age=age*365,sex=sex,year=year),
+        ratetable=slopop,data=rdata,int=5)
> rsbr <- rs.br(fit)
> print(rsbr)
      max    p
sex 0.542 0.93
> plot(rsbr)
> 
> 
> 
> cleanEx(); ..nameEx <- "rsmul"
> 
> ### * rsmul
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: rsmul
> ### Title: Fit Andersen et al Multiplicative Regression Model for Relative
> ###   Survival
> ### Aliases: rsmul
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> data(rdata)
> rsmul(Surv(time,cens)~sex+as.factor(agegr)+ratetable(age=age*365,
+       sex=sex,year=year),ratetable=slopop,data=rdata)
Call:
rsmul(formula = Surv(time, cens) ~ sex + as.factor(agegr) + ratetable(age = age * 
    365, sex = sex, year = year), data = rdata, ratetable = slopop)


                         coef exp(coef) se(coef)      z       p
sex                    0.6356     1.888    0.101  6.302 2.9e-10
as.factor.agegr.61.70 -0.0474     0.954    0.129 -0.367 7.1e-01
as.factor.agegr.70.95 -0.5346     0.586    0.132 -4.060 4.9e-05
as.factor.agegr..53    0.4759     1.609    0.149  3.204 1.4e-03

Likelihood ratio test=66.3  on 4 df, p=1.39e-13  n= 8160 
> 
> 
> 
> cleanEx(); ..nameEx <- "rstrans"
> 
> ### * rstrans
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: rstrans
> ### Title: Fit Cox Proportional Hazards Model in Transformed Time
> ### Aliases: rstrans
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> data(rdata)
> rstrans(Surv(time,cens)~sex+as.factor(agegr)+ratetable(age=age*365,
+         sex=sex,year=year),ratetable=slopop,data=rdata)
Call:
rstrans(formula = Surv(time, cens) ~ sex + as.factor(agegr) + 
    ratetable(age = age * 365, sex = sex, year = year), data = rdata, 
    ratetable = slopop)


                         coef exp(coef) se(coef)      z       p
sex                    0.5353     1.708    0.101  5.291 1.2e-07
as.factor(agegr)61-70  0.0947     1.099    0.131  0.722 4.7e-01
as.factor(agegr)70-95 -0.1577     0.854    0.139 -1.132 2.6e-01
as.factor(agegr)<53    0.3201     1.377    0.151  2.126 3.4e-02

Likelihood ratio test=30.7  on 4 df, p=3.51e-06  n= 1040 
> 
> 
> 
> cleanEx(); ..nameEx <- "rszph"
> 
> ### * rszph
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: rs.zph
> ### Title: Behaviour of Covariates in Time for Relative Survival Regression
> ###   Models
> ### Aliases: rs.zph
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(slopop)
> data(rdata)
> fit <- rsadd(Surv(time,cens)~sex+ratetable(age=age*365,sex=sex,year=year),
+        ratetable=slopop,data=rdata,int=5)
> rszph <- rs.zph(fit)
> 
> 
> 
> cleanEx(); ..nameEx <- "slopop"
> 
> ### * slopop
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: slopop
> ### Title: Census Data Set for the Slovene Population
> ### Aliases: slopop
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(slopop)
> 
> 
> 
> cleanEx(); ..nameEx <- "transrate"
> 
> ### * transrate
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: transrate
> ### Title: Reorganize Data into a Ratetable Object
> ### Aliases: transrate
> ### Keywords: survival
> 
> ### ** Examples
> 
> men <- cbind(exp(-365*exp(-14.5+.08*(0:100))),exp(-365*exp(-14.7+.085*(0:100))))
> women <- cbind(exp(-365*exp(-15.5+.085*(0:100))),exp(-365*exp(-15.7+.09*(0:100))))
> table <- transrate(men,women,yearlim=c(1980,1990),int.length=10)
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  18.73 8.99 27.84 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')