Ravi Varadhan wrote:
Fine detective work, David. Now, you can see the reasons for my frustration - multiplicity of data sets combined with non-existent documentation of the source of data in journal articles (e.g. Kay 1986; Lunn and McNeil 1995).
Best,
Ravi.
Yes that is a big frustration for me, even for projects for which I was
the principal statistician in 1990 for which I did a poor job of
archiving excellent medical datasets for future use. This is a big
advertisement for the reproducible research movement.
David - fantastic job. Based on what you found, the version on our web
site looks as good as any. Now if someone can explain to me why you see
a spike near a serum prostate acid phosphatase (AP) value of 1 when you
use a flexible regression model (e.g., restricted cubic spline) to
relate AP to the log hazard of death in a survival model (see p. 518 in
my book), that would be very helpful.
If you do with(prostate,plot(supsmu(log(ap),1*(status!='alive')))) you
see a minimum at ap=2.37 after anti-logging. If you do
dd <- datadist(prostate); options(datadist='dd')
f <- cph(Surv(dtime,status!='alive') ~ rcs(log(ap),6), data=prostate)
plot(f)
you see a sharp minimum at ap=1.43. With 4 knots the min is a 1.18.
You have to go to 3 knots to get a monotonic fit in log(ap) but AIC is
not as good.
Frank
____________________________________________________________________
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
----- Original Message -----
From: David Winsemius <dwinsem...@comcast.net>
Date: Tuesday, March 24, 2009 10:54 pm
Subject: Re: [R] Green and Byar (1980) Prostate Cancer Data set from Andrews
and Herzberg - Data
To: Rolf Turner <r.tur...@auckland.ac.nz>
Cc: R-help Forum <r-help@r-project.org>, Ravi Varadhan <rvarad...@jhmi.edu>
On Mar 24, 2009, at 8:57 PM, Rolf Turner wrote:
>
> On 25/03/2009, at 12:09 PM, Frank E Harrell Jr wrote:
>
> <snip>
>
>>> (2) Scrolling down to ``Byar and Green prostate cancer data''
>>> appeared
>>> to get
>>> me to the right place. But I couldn't see any signs of any ``R
>>> binary
>>> files''.
>>
>> Please look again. It's under the heading "R". Unfortunately I used
>> .sav suffix for save() files in the old days.
>
> Ah-ha. Oh me of little faith. I have been hanging around (in
> my current work environment) with too many SPSS users, and the
> *.sav extension seems to be the standard for SPSS data files.
> Whence my corrupted thinking.
>
>> The .xls fine opened with no problem in OpenOffice; has 506 rows.
>
> Hmmm. When I opened it with Excel on the Mac I got a spread
> sheet with 503 rows --- the first row being the column names,
> so there were really 502 rows.
The last "patnr" is "506" but there are only 502 lines of data. 471,
473, 475 and 488 are missing.
And the CMU Statlib version for 2002 looks the same.
The version at this site is missing more than 25 cases:
Here are two other copies of the dataset the first of which appears
to
have those missing cases:
This one has patient numbers:
This one has a description of the fields and cites the one above but
has not retained the patient numbers and has apparently only kept the
475 cases with complete data.
>
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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