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("mfp-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('mfp')
Loading required package: survival
Loading required package: splines
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "GBSG"
> 
> ### * GBSG
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: GBSG
> ### Title: German Breast Cancer Study Group
> ### Aliases: GBSG
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     data(GBSG)
>     mfp(Surv(rfst, cens) ~ fp(age, df = 2, select = 0.05)
+                  + fp(prm, df = 4, select = 0.05), family = cox, data = GBSG)
Call:
mfp(formula = Surv(rfst, cens) ~ fp(age, df = 2, select = 0.05) + 
    fp(prm, df = 4, select = 0.05), data = GBSG, family = cox)


Fractional polynomials:
    df.initial select alpha df.final power1 power2
prm          4   0.05  0.05        2      0      .
age          2   0.05  0.05        0      .      .

        coef exp(coef) se(coef)     z       p
prm.1 -0.215     0.807   0.0297 -7.23 4.8e-13

Likelihood ratio test=50.9  on 1 df, p=9.68e-13 n= 686 
> 
> 
> 
> 
> cleanEx(); ..nameEx <- "bodyfat"
> 
> ### * bodyfat
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: bodyfat
> ### Title: percentage of body fat determined by underwater weighing
> ### Aliases: bodyfat
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     data(bodyfat)
>     bodyfat$height[bodyfat$case==42] <- 69.5   # apparent error
>     bodyfat <- bodyfat[-which(bodyfat$case==39),]  # cp. Royston $\amp$ Sauerbrei, 2004
>     mfp(siri ~ fp(age, df = 4, select = 0.1) + fp(weight, df = 4, select = 0.1)
+                  + fp(height, df = 4, select = 0.1), family = gaussian, data = bodyfat)
Call:
mfp(formula = siri ~ fp(age, df = 4, select = 0.1) + fp(weight, 
    df = 4, select = 0.1) + fp(height, df = 4, select = 0.1), 
    data = bodyfat, family = gaussian)


Fractional polynomials:
       df.initial select alpha df.final power1 power2
weight          4    0.1  0.05        2   -0.5      .
height          4    0.1  0.05        1      1      .
age             4    0.1  0.05        1      1      .

Coefficients:
Intercept   weight.1   height.1      age.1  
   203.13   -1239.24      -1.37       0.13  

Degrees of Freedom: 250 Total (i.e. Null);  247 Residual
Null Deviance:	    17300 
Residual Deviance: 6860 	AIC: 1550 
> 
> 
> 
> cleanEx(); ..nameEx <- "fp"
> 
> ### * fp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: fp
> ### Title: Fractional Polynomial Transformation
> ### Aliases: fp
> 
> 
> ### ** Examples
> 
> ## Not run: 
> ##D         fp(x, df = 4, select = 0.05, scale = FALSE)
> ## End(Not run)
> 
> 
> 
> cleanEx(); ..nameEx <- "mfp"
> 
> ### * mfp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: mfp
> ### Title: Fit a Multiple Fractional Polynomial Model
> ### Aliases: mfp
> ### Keywords: models
> 
> ### ** Examples
> 
>         data(GBSG)
>         f <- mfp(Surv(rfst, cens) ~ fp(age, df = 4, select = 0.05)
+                  + fp(prm, df = 4, select = 0.05), family = cox, data = GBSG)
>         print(f)
Call:
mfp(formula = Surv(rfst, cens) ~ fp(age, df = 4, select = 0.05) + 
    fp(prm, df = 4, select = 0.05), data = GBSG, family = cox)


Fractional polynomials:
    df.initial select alpha df.final power1 power2
prm          4   0.05  0.05        2      0      .
age          4   0.05  0.05        4     -2   -0.5

          coef exp(coef) se(coef)     z       p
prm.1   -0.215  8.07e-01   0.0298 -7.22 5.4e-13
age.1 4070.015       Inf 833.4929  4.88 1.0e-06
age.2  -49.603  2.87e-22  12.4620 -3.98 6.9e-05

Likelihood ratio test=68.3  on 3 df, p=9.77e-15 n= 686 
>         survfit(f$fit)  # use proposed coxph model fit for survival curve estimation
Call: survfit.coxph(object = f$fit)

      n  events  median 0.95LCL 0.95UCL 
    672     299    1814    1589    2034 
> 
> 
> 
> cleanEx(); ..nameEx <- "plot.mfp"
> 
> ### * plot.mfp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: plot.mfp
> ### Title: Plots for mfp objects
> ### Aliases: plot.mfp
> 
> 
> ### ** Examples
> 
>         data(GBSG)
>         f <- mfp(Surv(rfst, cens) ~ fp(age, df = 4, select = 0.05)
+                  + fp(prm, df = 4, select = 0.05), family = cox, data = GBSG)
>         par(mfrow=c(2,2), mar=c(4,4,1,1), mgp=c(1.5,0.75,0))
>       plot(f, var="age")
> 
> 
> 
> graphics::par(get("par.postscript", env = .CheckExEnv))
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  4.09 0.22 4.34 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')