Does anyone know of an R function for computing the Greenland-Robins
variance for Mantel-Haenszel relative risks?
Thanks
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
ratification factor other than occupational group.
Thanks again
Frank
>
>
>
>
> Frank E Harrell
Paul Johnson wrote:
> This is a follow up to the message I posted 3 days ago about how to
> estimate mixed ordinal logit models. I hope you don't mind that I am
> just pasting in the code and comments from an R file for your
> feedback. Actual estimates are at the end of the post.
. . .
Paul,
ml
>> and provide commented, minimal, self-contained,
>> reproducible code.
>>
>
> ______________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE d
at an upcoming release of the Hmisc package has a new Access
import function for users who have access to the mdbtools package on
their operating system (e.g., linux).
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biost
Paul Johnson wrote:
> On 5/10/07, Frank E Harrell Jr <[EMAIL PROTECTED]> wrote:
>> Paul Johnson wrote:
>>> This is a follow up to the message I posted 3 days ago about how to
>>> estimate mixed ordinal logit models. I hope you don't mind that I am
>>>
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.
>
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of
mymodel, list of covariates you care to specify))
Frank Harrell
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> a
acebo |
> | |(N=263) |(N=237) |
> +---+------+------+
> |age|46.5/49.9/53.2|46.7/50.0/53.4|
> +---+--+--+
> |sex : m| 47% (123) | 44% (104) |
> +---+--+--+
> >
> >
sion deleted]]
>
>
>
> ------------
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
s on t4 it is easy to specify a contrast (after
fitting is completed) that tests t4. If time is continuous this
contrast would involve predicted values at the 4th time, otherwise
testing single parameters.
Frank Harrell
>
> Perhaps somebody can recommend a book or weblink where
> R-help@stat.math.ethz.ch mailing list
> https://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.
>
--
Frank E
proach that it's hard to know
where to begin. But first of all, why care about normality? Why not
use distribution-free methods?
You should examine the power of the tests for n=20. You'll probably
find it's not good enough to reach a reliable concl
gt; [mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
> Sent: Friday, May 25, 2007 12:04 PM
> To: [EMAIL PROTECTED]; Frank E Harrell Jr
> Cc: r-help
> Subject: Re: [R] normality tests [Broadcast]
>
> From: [EMAIL PROTECTED]
>> On 25/05/07, Frank E Harrell Jr <[EMAIL
>> [mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
>> Sent: Friday, May 25, 2007 12:04 PM
>> To: [EMAIL PROTECTED]; Frank E Harrell Jr
>> Cc: r-help
>> Subject: Re: [R] normality tests [Broadcast]
>>
>> From: [EMAIL PROTECTED]
>> >
>> > On 25/05
in testing for stochastic ordering and not just
for a mean.
Frank
>
>
>
>
> Frank E Harrell
> Jr
ange AIC to have it on the chi-square scale. For that you
can do
aic <- function(fit)
round(unname(fit$stats['Model L.R.'] - 2*fit$stats['d.f.']),2)
f <- lrm( )
aic(f)
If unname doesn't exist in S-Plus as it does in R, you can remove that part.
--
Frank E
Martin Henry H. Stevens wrote:
> Hi Folks,
> Mac OS 10.4.4
> R 2.2.1(2005-12-20 r36812)
> Hmisc 3.0-10
> acepack 1.3-2.2
>
> I keep getting a "segmentation fault" when trying to run areg.boot in
> the Hmisc package. I include below output from two different attempts.
> Thank you in advance for a
(513) 529-4243
> http://www.cas.muohio.edu/~stevenmh/
> http://www.muohio.edu/ecology/
> http://www.muohio.edu/botany/
> "E Pluribus Unum"
>
> __
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> https://stat.ethz.ch/mailman/listinfo
t;
>
>
> Kind regards,
> Robin Smit
This was answered just a few days ago in r-help. One way is
library(Hmisc)
rcorr(data matrix)
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
_
ology Department
> Sherbooke University
> Sherbrooke, Québec
> CANADA
>
> [EMAIL PROTECTED]
> [[alternative HTML version deleted]]
>
>
>
>
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do
for your help,
>
> Emilie
See the example I posted 2 hours ago, especially how you need to specify
FUN.
FH
>
> - Original Message - From: "Frank E Harrell Jr"
> <[EMAIL PROTECTED]>
> To: "Emilie Berthiaume" <[EMAIL PROTECTED]>
&
gt;R-help@stat.math.ethz.ch mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>
>
>
Look at wtd.quantile in the Hmisc package.
Frank
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Frank E Harrell Jr Professor and Chair
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
Frank E Harrell Jr Professor and Chair School of Med
Jing Yang wrote:
> Dear R-users,
>
> Does anyone have an idea of how to calculate the quantile of the weighted
> data?
> Any suggestion will be appreciated!
>
> Best,Jing
library(Hmisc)
?wtd.quantile
--
Frank E Harrell Jr Professor and Chair
> graduate student
> Biology Department
> Sherbrooke University
> Sherbrooke, Quebec
> CANADA
>
> [EMAIL PROTECTED]
> [[alternative HTML version deleted]]
>
> __
> R-help@stat.math.ethz.ch mailing list
>
or helping me, maybe others out there will find it usefull too.
>
> Best
> Ronny
library(Hmisc)
?xYplot
Frank Harrell
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
_
rgument and the use of the skey function that is generated
by xYplot.
Frank
>
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info/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>
> __
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> PLEASE do read the posting guide! http://w
sured up to 30 days from randomization.
>
> Thanks for the help.
> Peter
library(Hmisc)
?spower
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
(signal)}
> \]
>
> I believe that your attempt to minimize false positives while
> maximizing true positives amounts to maximizing the proportion of
> correct answers. For that you just set $\beta = 0$. Otherwise it
> might be best to explicitly state your costs and benefits b
mometer plots
which give some of the most accurate human perception of a continuous
variable. For the first 2 ideas you may have to round probabilities to
give just 10 intervals (or use deciles).
If you choose cutpoints from the data, there is uncertainty from the
cutpoint that may have to be
I have never taken a statistics class nor read a statistics text, but
I am in dire need of help with a trivial data analysis problem for
which I need to write a report in two hours. I have spent 10,000
hours of study in my field of expertise (high frequency noise-making
plant biology) but I've alw
y example :
> boxplot(serie,range=91) for french boxplot ?
>
> jean-pierre gerbal
>
> http://mathazay.free.fr/spip/
library(Hmisc)
?panel.bpplot
With library(lattice), bwplot, and panel.bpplot you can show all deciles
or any vector of quantiles.
--
Frank E Har
> Benn
Once you adjust for clustering using robcov or bootcov, only Wald
chi-square tests are available.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
___
on the file produced by latex()
>
>
> The last bit is easy. It's the print method that does that, so just
> don't print. E.g.
>
> invisible(latex(....))
Or do w <- latex(.., file='...')
Frank
>
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Frank E Harrell Jr Professor and Chair
h mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt Unive
ates to the mean of all 4 groups (see for example the ols function
in the Design package).
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
R-
Brian Quinif wrote:
> Does anyone out there use dcolumn=TRUE in the latex() function in the
> Hmisc library?
>
> I would like to line up the data in a latex table I'm making using
> latex(), but I'm having some issues with this feature. Since there is
> no description of it in the help, I thought
e odds ratio depends only
> on beta1.
>
> Cheers,
>
This makes me think you are trying to go against maximum likelihood to
optimize an improper criterion. Forcing a single cutpoint to be chosen
seems to be at the heart of your problem. There's nothing wrong
Ramón Casero Cañas wrote:
> Frank E Harrell Jr wrote:
>
>>This makes me think you are trying to go against maximum likelihood to
>>optimize an improper criterion. Forcing a single cutpoint to be chosen
>>seems to be at the heart of your problem. There's nothing wro
X may have any number
of categories as long as they are ordered.
Frank Harrell
>
> Thanks and regards,
>
> -Antti Arppe
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
___
s.
FH
>
> __
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> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
Frank E Harrell Jr Profe
second that. Helping people do things known to have major problems
with the approaches can actually hurt others in the long run. 2-D pie
charts are terrible. That makes 3-D pie charts terrible to the 3/2
power. Excel has serious errors and is not a good model for
reproducible research.
--
F
se e.g.
library(Hmisc)
?ecdf (look at groups argument)
Someday I may rename ecdf in Hmisc to avoid confusion with the builtin
ecdf function.
Frank
>
>
> [[alternative HTML version deleted]]
>
> ______________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz
ind many cases where one model increases C by only 0.02 but it has
many more useful (more extreme) predictions.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
___
27;fun').
Frank
>
>>> Please read the documentation and see the examples. The first
>>> argument to summarize is a matrix or vector and if a matrix, FUN must
>>> use matrix operations if you want column-by-column results.
>>>
>
== 20, 6, 10 ))
>
> Duncan Murdoch
>
>>
>> So the O/P looks like this
>>
>>V1 V2
>>10 4
>>20 6
>>30 10
>>10 4
>>10 4
>>20 6
>>
>> Thanks in advance.
>>
&
true that the larger the sample size the greater the
complexity of the model we can afford to fit, and the better the fit of
the model. This is the "AIC" school. The "BIC" school assumes there is
an actual model out there waiting for us, of finite dimension, and the
co
2 X13 X23/SELECTION=STEPWISE;
> RUN;
>
> Any help will be really appreciated.
>
> Wishes,
>
> Jinsong Zhao
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
___
>
> -thomas
>
> Thomas Lumley Assoc. Professor, Biostatistics
> [EMAIL PROTECTED] University of Washington, Seattle
>
> __
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> https://stat.ethz.ch/mailman/
for some
> more promising projects...
>
> Just my first thoughts, just go on with your project if you are convinced.
>
> Best,
> Uwe Ligges
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mai
ulation section on the Alzola Harrell
document available on CRAN under contributed docs, or a slightly more up
to date version at biostat.mc.vanderbilt.edu
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt
d like SAS, SPSS tends to lead users to make to many assumptions
(linearity in regression being one of the key ones).
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt
quot;)
print(rsq)
attr(xt, "rsq") <- rsq
attr(xt, "omitted") <- omitted
invisible(xt)
}
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PLEASE do read the posting guide! http://www.R-project.
t that missing data at
the high or low end of each variable (each member's ratings)
would change its mean.
Jon
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
datasets are being imported. Other changes include bug and
documentation fixes.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
___
R-packages mailing list
icant results
cause you to reduce an effect to linear, confidence levels and type I
errors are no longer preserved. I use tests of linearity mainly to
demonstrate that effects are more often nonlinear than linear, given
sufficient sample size. I.e., good analysts are needed. I usually
leave
g that you use P-values but do not care that the
strategy you use (variable selection as opposed to pre-specifying models
or just using shrinkage) does not preserve type I error or confidence
interval coverage probabilities in subsequent analyses with mgcv.
--
Frank E Harrell Jr Professor
dian(x[,'y1']-x[,'y2']),
med.sum =median(x[,'y1']+x[,'y2']))
names(y) <- c('med.diff','med.sum')
y
}
system.time(by(d, llist(sex=d$sex,country=d$country), g))
system.time({
x <- asNumericMatrix(d)
a &
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messages in a
day, Thunderbird inefficiently handles all the mime 'attachments', and
navigating them all is incredibly slow. I didn't have the decoding
problem you mentioned though.
--
Frank E Harrell Jr Professor and Chair School of Medicine
ndard output in the lrm function in the Design package (the "C
Index"). validate.lrm computes the overfitting-corrected C index.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
c!=9], from, to),")",sep="")
#change wrapping function to h()
h <- function(x,...) deparse(substitute(x))
for(i in (1:pm)) trans[i] <- eval(parse(text=trans[i]))
This may indirectly give you an idea, or you might see if the Design
package does what you need in ge
mation Sciences
University of Louisville
--
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Department of Biostatistics Vanderbilt University
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rding CDISC, the SAS transport format that is now accepted by FDA is
deficient because there is no place for certain metadata (e.g., units of
measurement, value labels are remote from the datasets, variable names
are truncated to 8 characters). The preferred format for CDISC will
become
fairly certain that it is not applicable or at the
least is not enforced in any meaningful way.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
___
Henric Nilsson wrote:
Frank E Harrell Jr said the following on 2004-12-18 15:03:
That is not clear.
Perhaps. And I think this is the issue. From the clients' perspective,
not a single FDA document states that you can use other software than
SAS. They haven't really thought about the
mple
http://www.nwpho.org.uk/sadb/Poisson%20CI%20in%20spreadsheets.pdf
. . .
Also see http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/ExcelProblems
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt
ake Circus
Plymouth PL4 8AA
tel (01752) 232778
fax (01752) 232780
email [EMAIL PROTECTED]
www.plymouth.ac.uk
I had hoped that journals engaged in reproducible research by now.
--
Frank E Harrell Jr Professor and Chair School of Medicine
D
the dotchart2 function used by
plot.summary.formula.reverse, and the addition of a new argument to it
from plot I have found symbols (esp. circle vs. triangle) to be
more effective for this purpose so I am not motivated to work on this
very soon but would consider it. -Frank
--
Frank E Har
ck of fit) from 'overfitting'.
Overfitting can cause the model fit to appear to be excellent, but there
is still a huge problem.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistic
xplanation using S and not
R. Am I right or I´m looking in the wrong place ?
Thanks a lot!
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guage R
Thanks,
Frank
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Department of Biostatistics Vanderbilt University
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P
Deepayan Sarkar wrote:
On Sunday 02 January 2005 19:40, Frank E Harrell Jr wrote:
What is the most elegant way to specify that strip panels are to have
transparent backgrounds and graphs are to be in black and white when
lattice is being used with Sweave? I would prefer a global option
that stays
Douglas Bates wrote:
Christoph Buser wrote:
Hi all
I tried to reproduce an example with lme and used the Orthodont
dataset.
library(nlme)
fm2a.1 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1 |
Subject)
anova(fm2a.1)
...
Regards,
Christoph Buser
No. The calculation of denominator deg
/affirmative
action employer; all qualified persons are encouraged to apply. CVs may
be sent electronically to both [EMAIL PROTECTED] and
[EMAIL PROTECTED] Please state in the subject of the E-mail the
position for which you are applying or inquiring.
--
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o units(x) <- 'whatever units of measurement' then xYplot,
describe, and other Hmisc functions will include the units (in a
different font on graphs or when using latex()).
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of B
iling list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt
Prof Brian Ripley wrote:
On Sun, 9 Jan 2005, Anne wrote:
I'm about to present a report (for internal use of governmental
agency). I used extensively R , contibuted packages, as well as
communications on the R-list
As well as citing R, I would like to know how to cite the contributed
packages (i
#x27;s in one of the summarize examples!
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Department of Biostatistics Vanderbilt University
__
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le to include their names in an
Ack. section, usually. Referencing as a personal communication is
perhaps better.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt Unive
U statistic methods to get the standard error of Dxy. You can
easily translate this to a standard error of C.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
frame with the NA values filled up?
Or is there any other function that i could use?
Thank you
avneet
It's in the help file for transcan. But multiple imputation is much
better, and transcan does not do multiple imputation as well as the
newer Hmisc function aregImpute.
--
Frank E Harre
l confidence
intervals.
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Department of Biostatistics Vanderbilt University
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PLE
Dan Bolser wrote:
On Wed, 12 Jan 2005, Frank E Harrell Jr wrote:
Dan Bolser wrote:
Hello,
I am making some use of ROC curve analysis.
I find much help on the mailing list, and I have used the Area Under the
Curve (AUC) functions from the ROC function in the bioconductor project...
http
//stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
constant? I
can't use lm(), because robcov() needs an object from the Design() series.
Or is there a different way to go about this?
Tobias Muhlhofer
ols does not support this. Sorry.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department
affecting the scale), you will have to modify the
panel.bwplot function in addition to using the above.
--sundar
You may also want to try
library(Hmisc)
library(lattice)
bwplot(..., panel=panel.bpplot)
?panel.bpplot
--
Frank E Harrell Jr Professor and Chair School of
(parametric model) ?
Thanks
Virginie
In the Design package look at the pphsm function that converts a survreg
Weibull fit (fitted by the psm function which is an adaptation of
survreg) to PH form.
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hz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt Unive
ntour' to get other types of graphs
plot(f, sun=NA, trees=NA, fun='plogis') # probability scale
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
library(Design)
d <- datadist(mydata); options(datadist='d')
f <- lrm(incidence ~ sun*trees) # lrm is for binary or ordinal response
plot(f, sun=NA, trees=NA)
# add method='image' or 'contour' to get other types of graphs
plot(f, sun=NA, trees=NA, fun='plogis') # probability scale
Correction: fun
cter" to the specified formal class" but I do not know and have not
figured out how to do that.
Any suggestion(s) would be greatly appreciated.
Thanks,
Charles
The csv.get function in the Hmisc package may do most of what you want.
--
Frank E Harrell Jr Professor and Chair Schoo
can get them?
Thanks
The Design package's survplot function can print n.risk over equally
spaced time points. You might see an easy way to print this by looking
at the code. -Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Depar
te data but don't store
with(test(data, ),{...})# reference variables in temporary
dataset
If we know what your ultimate goal is, there may be a much better
approach than the test function. In many cases, you do not need to
create new variables at all.
Franc
--
Frank E Harrell
ation.
.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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PLEASE do rea
unctions available at the Bioconductor website. There
was also some
code sent around on the list a few months back for calculating trapeziodal AUC,
se's
from ROC, and comparing two ROC curves...search the archives if interested, or
I can
probably dig them out for you offline...
Cheers,
Joe
Quot
redictive
accuracy and that violates every aspect of statistical inference, you
are on the right track. See
http://www.stata.com/support/faqs/stat/stepwise.html for details.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics V
uuld be some extended view of available ressources
(manuals, FAQ, community) as a starter to learn, use and program R by
themselves.
I think this would do for a 40 minutes presentation without taking the
risk to deter people due to overcomplexity.
regards
Thomas
--
Frank E Harrell Jr
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