R help - Oct 2001 - Two questions

Greetings,

		I have two questions that I could not answer from the
documentation.

	A - ecdf and confidence intervals : Is there a (simple) way to generate
confidence intervals (95%) for a ecdf? 

	B - cross-validation of rpart trees : a colleague is using S to
generate decision tree and mentioned to me the use of cross-validation. Is
this function enabled in R ? if so, how should one proceed to do it?

	Thanks,

	Christian

		
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Hi dear R users:

I want to know if any body has implemented the
Dunnett's test for the difference between the control
group and other groups.

Or at least where can I find how to build it in R.

Thank you very much

Kenneth Cabrera
Universidad Nacional de Colombia
Sede Medellin
Facultad de Ciencias.



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At 12:45 PM 10/22/2001 -0400, Christian Blouin wrote:
>         B - cross-validation of rpart trees : a colleague is using S to
>generate decision tree and mentioned to me the use of cross-validation. Is
>this function enabled in R ? if so, how should one proceed to do it?
Well documented in the rpart manuals and rpart help files.  If you are 
using R version 1.30 or higher, under Windows rpart gets installed as part 
of the recommended package distribution.

 >?xpred.rpart

might get you started.

Also

 >?rpart


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>>>>> "Christian" == Christian Blouin <bongo at
havana.biochem.dal.ca> writes:
    Christian> I have two questions that I could not answer from the
    Christian> documentation.

    Christian> A - ecdf and confidence intervals : Is there a (simple) way
    Christian> to generate confidence intervals (95%) for a ecdf?

About two weeks ago, Kjetil Halvorsen (CC'ed above)
sent me code to just do this, and I have improved on the code a bit
with the idea to incorporate into the stepfun package (part of "standard
R").

However, it's content is also linked with the (hidden) pkstwo() function
in ctest's  kolomogorov-smirnov testing.
Also, I think part of this might become an option to ecdf() or plot.ecdf()
rather than the current setup.
Unfortunately, it's not finished for integration into R,
but here is the current code (without help pages) that works quite nicely:

## Fixme: In the following, computing and plotting should be separated

###--> ./ecdf.R plot.ecdf() should get conf.type and conf.int argument!!

ecdf.ksCI <- function(x, main = NULL, sub = NULL,
                      xlab = deparse(substitute(x)), ...)
{
    xlab
    if(is.null(main))
        main <- paste("ecdf(",deparse(substitute(x)),") + 95%
K.S. bands",
                      sep="")
    n <- length(x)
    if(is.null(sub))
        sub <- paste("n = ", n)
    ec <- ecdf(x)
    xx <- get("x", envir=environment(ec))# = sort(x)
    yy <- get("y", envir=environment(ec))
    D <- approx.ksD(n)
    yyu <- pmin(yy+D, 1)
    yyl <- pmax(yy-D, 0)
    ecu <- stepfun(xx, c(yyu, 1) )
    ecl <- stepfun(xx, c(yyl, yyl[n]) )

    ## Plots -- all calling  plot.stepfun

    plot(ec, main = main, sub = sub, xlab = xlab)## no "..." here ??? 
__hmm..__
    plot(ecu, add=TRUE, verticals=TRUE, do.points=FALSE,
         col.hor="red" , col.vert="red", ...)
    plot(ecl, add=TRUE, verticals=TRUE, do.points=FALSE,
         col.hor="red", col.vert="red", ...)
}

approx.ksD <- function(n)
{
    ## approximations for the critical level for Kolmogorov-Smirnov statistic D,
    ## for confidence level 0.95. Taken from Bickel & Doksum, table IX,
p.483
    ## and Lienert G.A.(1975) who attributes to Miller,L.H.(1956), JASA
    ifelse(n > 80,
           1.358 /( sqrt(n) + .12 + .11/sqrt(n)),##Bickel&Doksum, table
IX,p.483

           splinefun(c(1:9, 10, 15, 10 * 2:8),# from Lienert
                     c(.975,   .84189, .70760, .62394, .56328,# 1:5
                       .51926, .48342, .45427, .43001, .40925,# 6:10
                       .33760, .29408, .24170, .21012,# 15,20,30,40
                       .18841, .17231, .15975, .14960)) (n))
}


###-- Example from Kjetil :

ecdf.ksCI( rchisq(50,3) )

--
Martin Maechler <maechler at stat.math.ethz.ch>
http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum  LEO D10	Leonhardstr. 27
ETH (Federal Inst. Technology)	8092 Zurich	SWITZERLAND
phone: x-41-1-632-3408		fax: ...-1228			<><
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