From diggsb at ohsu.edu  Mon Oct 20 20:02:00 2008
From: diggsb at ohsu.edu (Brian Diggs)
Date: Mon, 20 Oct 2008 11:02:00 -0700
Subject: [Rd] (PR#13180) Wrong behavior of lines.survfit for
 conf.int="only"
In-Reply-To: <alpine.LFD.2.00.0810201826140.24959@gannet.stats.ox.ac.uk>
References: <20081020155505.22BD5283416C@mail.pubhealth.ku.dk>
	<48FCB2B3.7060807@biostat.ku.dk>
	<alpine.LFD.2.00.0810201826140.24959@gannet.stats.ox.ac.uk>
Message-ID: <D90C24824765F143934E4DE78009D6174DF4A7@EX-BE05.ohsu.edu>

Thank you.  I was confused because survival was a standard (recommended) package, so I thought r-bugs was the appropriate place.  I have contacted the maintainer of the package with this information.  My thanks also to Peter Dalgaard for de-base64-coding my message; I have no idea how or why it got encoded that way.  Additionally, this was meant as a follow-up to PR#13171. Both PR#13171 and PR#13180 can be considered dealt with.  Please accept my apologies for messing the process up so much.


--
Brian Diggs, Ph.D.
Senior Research Associate, Department of Surgery, Oregon Health & Science University


-----Original Message-----
From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
Sent: Monday, October 20, 2008 10:29 AM
To: Peter Dalgaard
Cc: Brian Diggs; R-bugs at r-project.org; r-devel at stat.math.ethz.ch
Subject: Re: [Rd] (PR#13180) Wrong behavior of lines.survfit for conf.int="only"

Note that survival is a contributed package: only the maintainer can alter 
it (or at least, if someone else does the change will get lost -- it has 
happened before).  So it is not useful to report on it on R-bugs (see the 
FAQ and the posting guide).


On Mon, 20 Oct 2008, Peter Dalgaard wrote:

> diggsb at ohsu.edu wrote:
>> SSBkb3dubG9hZGVkIHRoZSBzb3VyY2UgZm9yIHN1cnZpdmFsIGFuZCBJIHRoaW5rIEkgZm91bmQg
>> dGhlIGJ1Zy4gIEkgaGF2ZSBub3QgdHJpZWQgdG8gYnVpbGQgdGhlIHBhY2thZ2Ugd2l0aCB0aGlz
>> IGNoYW5nZSB0byB0ZXN0IGl0LCBidXQganVzdCBkZWZpbmluZyB0aGUgZnVuY3Rpb24gd2l0aCB0
>> aGlzIGNoYW5nZSBzZWVtcyB0byB3b3JrLg0KDQpUaGUgY29kZQ0KDQoJaWYgKGNvbmYuaW50PT0n
>> b25seScpIHsNCgkgICAgY29uZi5pbnQgPC0gVFJVRQ0KCSAgICBwbG90LnN1cnY8LSBUUlVFDQoJ
>> ICAgIH0NCg0KU2hvdWxkIGJlDQoNCglpZiAoY29uZi5pbnQ9PSdvbmx5Jykgew0KCSAgICBjb25m
>> LmludCA8LSBUUlVFDQoJICAgIHBsb3Quc3VydjwtIEZBTFNFDQoJICAgIH0NCg0KLS1CcmlhbiBE
>> aWdncw0KDQo=
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> Argh! Jitterbug...must...die...
>
> [pd at titmouse2]$ base64 -d
> SSBkb3dubG9hZGVkIHRoZSBzb3VyY2UgZm9yIHN1cnZpdmFsIGFuZCBJIHRoaW5rIEkgZm91bmQg
> ....
> aWdncw0KDQo=
>
> I downloaded the source for survival and I think I found the bug.  I have not 
> tried to build the package with this change to test it, but just defining the 
> function with this change seems to work.
>
> The code
>
> 	if (conf.int=='only') {
> 	    conf.int <- TRUE
> 	    plot.surv<- TRUE
> 	    }
>
> Should be
>
> 	if (conf.int=='only') {
> 	    conf.int <- TRUE
> 	    plot.surv<- FALSE
> 	    }
>
> --Brian Diggs
>
>
>
>
> --
>   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
>  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] (PR#13180) Wrong behavior of lines.survfit for conf.int="only"
Brian Diggs