the object
produced by contents( ) and remove the value levels components, then
pass the smaller object to latex().
Frank
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some hint why you consider this to be a VERY bad fit? It
appears a rather good fit to me, despite the test case apparently not
being construct with any curvature which is what the rcs modeling
strategy should be detecting.
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Frank E Harrell Jr Professor and Chair School
way?
Respectfully,
sp
--- On Tue, 12/23/08, Frank E Harrell Jr f.harr...@vanderbilt.edu wrote:
From: Frank E Harrell Jr f.harr...@vanderbilt.edu
Subject: Re: [R] newbie problem using Design.rcs
To: David Winsemius dwinsem...@comcast.net
Cc: to_rent_2...@yahoo.com, r-help@r-project.org
Date
{ } you will need to do print(Function(f))
Note this is a simplified version of the rcs with 2 redundant terms to
avoid writing in terms of differences in cubes.
Frank
Sincerely,
sp
--- On Tue, 12/23/08, Frank E Harrell Jr f.harr...@vanderbilt.edu wrote:
From: Frank E Harrell Jr f.harr
://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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REGRESSION MODELING STRATEGIES
presented by
Frank E. Harrell, Jr., Ph.D.
Professor and Chair
Department of Biostatistics
Vanderbilt University School of Medicine
February 2 - 6, 2009
Vanderbilt University Medical Center Campus
Five-Session Short Course by Frank Harrell, Jr., Ph.D., Professor
Felix Schönbrodt wrote:
*Von: *Frank E Harrell Jr f.harr...@vanderbilt.edu
mailto:f.harr...@vanderbilt.edu
*Datum: *18. Dezember 2008 14:49:53 MEZ
*An: *Meir Preiszler pm...@itamar-medical.com
mailto:pm...@itamar-medical.com
*Kopie: *r-h...@r-project.org mailto:r-help@r-project.org
*Betreff
to truly quantify
the conservativeness of Fisher's test;``the test size of FET was less
than 0.035 for nearly all sample sizes before 50 and did not approach
0.05 even for sample sizes over 100.'';conservativeness of ``exact''
methods}
}
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-guide.html
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whereas transcan is good for single conditional mean imputation.
Frank
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to discard
ties in x.
The Fortran code that comes with Hmisc can also be viewed to see the
exact algorithms.
Frank
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.
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PLEASE do read the posting
guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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E Harrell Jr Professor and Chair School of Medicine
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PLEASE do read the posting guide
read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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from rpart will be badly biased away from 1.0.
Unbiasing them will be tricky.
Frank
Home Address:
Brusselsepoortstraat 85
9000
Gent
Belgium
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and
discrimination indexes. Note that AUC is not a great objective
function; that's why we have the log likelihood.
Frank
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.
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PLEASE do read the posting
Frank E Harrell Jr wrote:
[EMAIL PROTECTED] wrote:
Hi,
I am trying to read a SAS version 9.1.3 SAS dataset into R (to preserve
the SAS labels), but am unable to do so (I have read in a CSV version).
I first created a transport file using the SAS code:
libname ces2 'D:\CES Analysis
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
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://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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R
Dylan Beaudette wrote:
On Mon, Dec 1, 2008 at 5:48 AM, Frank E Harrell Jr
[EMAIL PROTECTED] wrote:
David Winsemius wrote:
On Nov 30, 2008, at 10:23 PM, Dylan Beaudette wrote:
Hi, I am using the rcs() function in the Design library to model
non-linearity that is not well characterized
it retrieves
the imputed values. Also see the example in documentation for transcan
in which the command impute(xt, imputation=1) to retrieve one of the
multiple imputations.
Note that you can say library(Design) (omit the quotes) to access both
Design and Hmisc.
Frank
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Charlie Brush wrote:
Frank E Harrell Jr wrote:
Charlie Brush wrote:
I am doing multiple imputation with Hmisc, and
can't figure out how to replace the NA values with
the imputed values.
Here's a general ourline of the process:
set.seed(23)
library(mice)
library(Hmisc)
library(Design
, self-contained, reproducible code.
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Daniel Brewer wrote:
Hello,
I was just wondering whether there is a quick way to divide a vector of
data into four groups defined by the quantiles?
i.e.
0-25%
25-50%
50-75%
75-100%
Many thanks
Dan
library(Hmisc)
cut2(x, g=4)
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and the simple forward probability of a positive diagnosis,
e.g., from a basic logistic regression model if you start with a cohort
study) vary with the type of patient being diagnosed.
Frank
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Department
ordinary logistic models
to allow for nonlinear effects on the log odds scale using regression
splines.
Frank
Pierre-Jean
-Original Message-
From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 13, 2008 5:00 PM
To: Breton, Pierre-Jean-EXT RD/FR
Cc: r-help@r
is the most effective and which threshold
value I should apply to discriminate positives and negatives.
So, any idea for my problem ?
Pierre-Jean
-Original Message-
From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 13, 2008 5:00 PM
To: Breton, Pierre-Jean-EXT RD/FR
Cc
,...){
panel.xyplot(x,y,...)
ltext(x=list(1,2,3,4),
y=list(13,14,15,16),
labels=list(A,B,C,D), pos=2)})
One of the purposes of xYplot is to use panel.xYplot
Frank
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/expect)
P - 1 - pchisq(chisq, g - 2)
c(X^2 = chisq, Df = g - 2, P(Chi) = P)
}
I want to know how can i use the another method which is not use the
probability of success. i want to know how can i revise above program to
achieve an objective.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Department of Biostatistics
the curve is labeled. How do you think?
Should be options for that too.
Frank
I really appreciate any help you give.
Best regards,
Jiang Lu
Statistician
Department of Epidemiology
University of Pittsburgh
On Thu, Nov 6, 2008 at 1:21 PM, Frank E Harrell Jr
[EMAIL PROTECTED] mailto:[EMAIL
this easy.
Frank
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PLEASE do
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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Department of Biostatistics Vanderbilt University
Tom Backer Johnsen wrote:
Frank E Harrell Jr wrote:
Tom Backer Johnsen wrote:
Frank E Harrell Jr wrote:
Tom Backer Johnsen wrote:
Frank E Harrell Jr wrote:
Tom Backer Johnsen wrote:
I hadn't thought of the 'different random sample' approach.
That's neat.
Frank
Yes, I am quite proud
?
I really would appreciate some suggestions.
Tom
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variation or predictive discrimination. R^2 can be
high and there be a major misspecification in the model (e.g., omitting
an interaction or nonlinearity term or omitting an important variable).
Frank
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Longwood Ave
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617-355-6058(tel)/617-730-0495(fax)
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is aa very heterogeneous group; those ages
should not
have been combined.
Frank
___
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Department of Biostatistics Vanderbilt University
[EMAIL PROTECTED] wrote:
I'm presumably missing something very obvious, but how does one use the
key.opts argument in labcurve (via Ecdf)?
In this example, I want the key to be big and have a blue background, but
it isn't and doesn't.
ch - rnorm(1000, 200, 40)
sex -
Gad Abraham wrote:
Frank E Harrell Jr wrote:
Gad Abraham wrote:
This approach leaves much to be desired. I hope that its
practitioners start gauging it by the mean squared error of
predicted probabilities.
Is the logic here is that low MSE of predicted probabilities equals a
better
. It's a
two-dimensional issue and we don't always know how to weigh the two.
For many purposes calibration is a must. In those we don't look at
discrimination until calibration-in-the-small is verified at high
resolution.
Frank
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Gabor Grothendieck wrote:
On Mon, Oct 13, 2008 at 11:47 PM, Frank E Harrell Jr
[EMAIL PROTECTED] wrote:
Gabor Grothendieck wrote:
On Mon, Oct 13, 2008 at 11:21 PM, Frank E Harrell Jr
[EMAIL PROTECTED] wrote:
[EMAIL PROTECTED] wrote:
I recall a concept of Snout: sensitivity that is high
/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt
/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
R-help@r
Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Frank E Harrell Jr [EMAIL PROTECTED] 10/13/2008 12:27 PM
Maithili Shiva wrote:
Dear Mr Peter Dalgaard and Mr Dieter Menne,
I sincerely thank you for helping
(Please call phone number above prior to faxing)
Frank E Harrell Jr [EMAIL PROTECTED] 10/13/2008 2:35 PM
John Sorkin wrote:
Jumping into a thread can be like jumping into a den of lions but here goes . .
.
Sensitivity and specificity are not designed to determine the quality of a fit (i.e
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PLEASE do read the posting
/diagnostictests.html
--Chris Ryan
Original message
Date: Mon, 13 Oct 2008 18:14:39 -0400
From: John Sorkin [EMAIL PROTECTED]
Subject: Re: [R] Fw: Logistic regresion - Interpreting (SENS) and (SPEC)
To: Ph.D. Robert W. Baer [EMAIL PROTECTED], Frank E Harrell Jr [EMAIL PROTECTED]
Cc: r-help@r
PM
- Original Message -
From: Frank E Harrell Jr [EMAIL PROTECTED]
To: John Sorkin [EMAIL PROTECTED]
Cc: r-help@r-project.org; [EMAIL PROTECTED];
[EMAIL PROTECTED]
Sent: Monday, October 13, 2008 2:09 PM
Subject: Re: [R] Fw: Logistic regresion - Interpreting (SENS) and (SPEC)
John
: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of John Sorkin [EMAIL
PROTECTED]
Sent: Monday, October 13, 2008 4:14 PM
To: Ph.D. Robert W. Baer; Frank E Harrell Jr
Cc: r-help@r-project.org; [EMAIL PROTECTED]; [EMAIL PROTECTED]
Subject: Re: [R] Fw: Logistic regresion - Interpreting (SENS
Gabor Grothendieck wrote:
On Mon, Oct 13, 2008 at 11:21 PM, Frank E Harrell Jr
[EMAIL PROTECTED] wrote:
[EMAIL PROTECTED] wrote:
I recall a concept of Snout: sensitivity that is high enough to
essentially rule out the presence of disease. And Spin: specificity that
is high enough
to
condition on what was already known). Your test sample is too small.
You are not addressing absolute calibration through precise
high-resolution methods. My book Regression Modeling Strategies goes
into this.
Frank
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://biostat.mc.vanderbilt.edu/RS
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in LaTeX; it's not that simple.
Frank
-Ursprüngliche Nachricht-
Von: Frank E Harrell Jr [mailto:[EMAIL PROTECTED]
Gesendet: Donnerstag, 9. Oktober 2008 04:17
An: Erich Studerus, Psychiatrische Uni-Klinik
Cc: r-help@r-project.org
Betreff: Re: [R] NA's in multiple choice summary table
, the NA's
should be 1 instead of 2 cases.
I tried to specify na.include=FALSE but it does not work.
Any help is highly appreciated.
Erich
Instead of NA put '' or and it should work.
Frank
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-guide.html
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sj wrote:
I have a set of values and their corresponding weights. I can use the
function weighted.mean to calculate the weighted mean, I would like to be
able to similarly calculate the weighted median and quantiles? Is there a
function in R that can do this?
thanks,
Spencer
library(Hmisc)
))
attach(X)
/pre
Thank you
Sören
library(Hmisc)
?spss.get
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calibration). (What is PD?)
Frank, you are referring the #1 and I am referring to #2.
Nonetheless, I would never create a rating system if my model doesn't
discriminate better than a coin toss.
For sure
Frank
Regards,
Pedro
-Original Message-
From: Frank E Harrell Jr
www.decisionstats.com http://www.decisionstats.com
On Wed, Oct 8, 2008 at 1:33 AM, Frank E Harrell Jr
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote:
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote:
Hi Frank,
Thanks for your feedback! But I think we are talking about two
on the subject.
Also , Deciles specific performance is easy to explain and monitor for
faster execution/re modeling.
That's too low resolution. loess is superior for estimating the
calibration curve.
Frank
Regards,
Ajay
On Wed, Oct 8, 2008 at 4:01 AM, Frank E Harrell Jr
[EMAIL PROTECTED
Bernardo Rangel Tura wrote:
Em Ter, 2008-09-30 às 18:56 -0500, Frank E Harrell Jr escreveu:
Bernardo Rangel Tura wrote:
Em Sáb, 2008-09-27 às 10:51 -0700, milicic.marko escreveu:
I have a huge data set with thousands of variable and one binary
variable. I know that most of the variables
-guide.html
and provide commented, minimal, self-contained, reproducible code.
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or mean difference is a complex
function of all the covariate values in the sample).
5. The model will not validate in new data.
Frank
--
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Department of Biostatistics Vanderbilt University
Gavin Simpson wrote:
On Sun, 2008-09-28 at 21:23 -0500, Frank E Harrell Jr wrote:
Darin Brooks wrote:
I certainly appreciate your comments, Bert. It is abundantly clear that I
snip /
Darin Brooks
Darin,
I think the point is that the confidence you can assign to the best
available
Greg Snow wrote:
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Frank E Harrell Jr
Sent: Saturday, September 27, 2008 7:15 PM
To: Darin Brooks
Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED];
[EMAIL PROTECTED]
Subject: Re: [R] FW: logistic
PROTECTED]
[mailto:[EMAIL PROTECTED]
] On
Behalf Of Ted Harding
Sent: Saturday, September 27, 2008 4:30 PM
To: [EMAIL PROTECTED]
Subject: Re: [R] FW: logistic regression
On 27-Sep-08 21:45:23, Dieter Menne wrote:
Frank E Harrell Jr f.harrell at vanderbilt.edu writes:
Estimates from this model
.
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PLEASE do read
regression
On 27-Sep-08 21:45:23, Dieter Menne wrote:
Frank E Harrell Jr f.harrell at vanderbilt.edu writes:
Estimates from this model (and especially standard errors and
P-values)
will be invalid because they do not take into account the stepwise
procedure above that was used to torture
-of-link function;simulation
setup}
}
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(Design)
?validate.lrm
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? And if so how
can i go on.
As i said, i know this is rather basic, i am thankful for any links /
references...
thanks in advance !
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-contained, reproducible code.
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option in the xYplot function in the Hmisc
package.
Frank
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\lstloadlanguages{R}
\lstset{language=R,basicstyle=\smaller[2],commentstyle=\rmfamily\smaller,
showstringspaces=false,%
xleftmargin=4ex,literate={-}{{$\leftarrow$}}1 {~}{{$\sim$}}1}
\lstset{escapeinside={(*}{*)}} % for (*\ref{ }*) inside lstlistings (S
code)
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hadley wickham wrote:
On Fri, Sep 19, 2008 at 4:05 PM, Frank E Harrell Jr
[EMAIL PROTECTED] wrote:
Mike Prager wrote:
David Carslaw [EMAIL PROTECTED] wrote:
I find Tinn-R to be an excellent editor for R, but I have one question I
have not been able to answer.
I wish to include some R code
all the other measures) and rank indexes
other than C.
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ran2 wrote:
Frank E Harrell Jr wrote:
That is a high variance procedure as compared with covariate adjustment
using the propensity score, or stratification.
Frank Harrell
Ah, wait what if I got very high dimensional X ? Even with 20 binary
covariates i would end up with more than 1
, Frank E Harrell Jr /[EMAIL PROTECTED]/*
wrote:
From: Frank E Harrell Jr [EMAIL PROTECTED]
Subject: Re: [R] Hosmer- Lemeshow test
To: [EMAIL PROTECTED]
Cc: R list [EMAIL PROTECTED]
Date: Tuesday, 16 September, 2008, 4:38 PM
saggak wrote:
Dear R - help,
I
, and other measures.
I haven't seen an example where drawing the ROC curve provides useful
information that leads to correct actions.
Frank
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PLEASE do read the posting guide
not
to use dynamite plots.
Frank
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plot does not contain enough information
when the sample size is moderate or large IMHO. But for small samples,
raw data points supplemented by the 3 quartiles and the mean work well.
Frank
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Harrell's book on _Regression modeling strategies_.
cheers
Ben Bolker
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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.
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PLEASE do read
with the Hmisc package's panel.bpplot function
will provie the 0.05 and 0.95 quantiles and several more, plus the mean.
Type ?panel.bpplot and example(panel.bpplot) for more information.
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to switch to lme (better documented, currently), and use
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/20725.html
as a starter when trying to do multiple comparisons.
Dieter Menne (Tübingen)
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For all those useRs who didn't make it to Dortmund Germany for useR!
2008 you missed a great conference. Hats off to Uwe Ligges and the
other organizers and assistants who planned and executed the meeting
superbly.
Frank
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: [EMAIL PROTECTED]
http://med.kuleuven.be/biostat/staff/LD.htm
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) 380-8895
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PLEASE do read
,
Fernando
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PLEASE do read
with
y='a' at time='time 1').
I am running R 2.7.1 under windows.
Regards,
-Cody
The xYplot function in the Hmisc package can do that. It may be more
elegant using ggplot2.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department
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