sampling of donor
observations' binary covariate values.
. . ..
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
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over time for
baseline covariates.
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DrakeGis wrote:
Thanks for the help.
-I'm really sorry, but I'm affraid I can't publish any data in order to
allow a reproduction of the results (enterprise policies :( ).
That is silly. You can surely simulate data that provides an example of
the problem you are having.
Frank Harrell
.
validate will also do data splitting and cross-validation though.
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of
Graphing Data. A MUCH better plot can be produced. And let time be one
of the first variables to vary.
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code generator that gives
beginners a starting script to edit to use their variable names, etc.
Also I think we need a discussion board that has a better memory for
new users, like some of the user forums currently on the web, or using a
wiki.
Frank
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be broken down
by major areas (data import examples, data manipulation examples, many
analysis topics, many graphics topics, etc.). Ultimately the more
elaborate case studies could be peer-reviewied (a la the Journal of
Statistical Software) and updated.
Frank
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programmers to program
an archaic macro language using old statistical methods to produce ugly
tables and the worst graphics in the statistical software world.
Frank Harrell
SAS User, 1969-1991
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('xxx')
Error in strwidth(xxx) : invalid graphics state
Any help appreciated. I have version 2.0.1 of grid and version 0.10-14
of lattice.
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being well-documented. And for clear and
compact tables, R is the winner hands down.
Frank Harrell
If you want to do statistical analyses and graphics (in finite time)
go for R.
Bendix Carstensen
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intervals for a mean.
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On Sun, 21 Nov 2004 07:48:58 -0500, Frank E Harrell Jr
[EMAIL PROTECTED] said:
Jean-Louis Abitbol wrote:
Dear All
I am trying to graph a proportion and CI95% by a factor with ooplot (any
other better solution ?)
It works well until I try to add the confidence interval.
this is the error message
Uwe Ligges wrote:
Prof Brian Ripley wrote:
On Sat, 20 Nov 2004, Frank E Harrell Jr wrote:
In
platform i386-pc-linux-gnu
arch i386
os linux-gnu
system i386, linux-gnu
status
major2
minor0.1
year 2004
month11
day 15
language R
I'm getting an error when using strwidth
errors
introduced in SAS in the days of pen-plotters
(+ signs for points, cross-hatching for area fill).
-Michael
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someday ...
-Frank Harrell
Regards,
Eric Lim
Papworth Hospital
Cambridge, UK
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missingness in a dendogram
naplot(n) # show more details in multiple plots
Frank
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, SPSS tends to lead users to make to many assumptions
(linearity in regression being one of the key ones).
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change its mean.
Jon
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datasets are being imported. Other changes include bug and
documentation fixes.
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are more often nonlinear than linear, given
sufficient sample size. I.e., good analysts are needed. I usually
leave non-significant nonlinearities in the model.
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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.
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- asNumericMatrix(d)
a - subsAttr(d)
m - mApply(x, llist(sex=d$sex,country=d$country), g)
})
system.time({
x - asNumericMatrix(d)
summarize(x, llist(sex=d$sex, country=d$country), g)
})
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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.
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). validate.lrm computes the overfitting-corrected C index.
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of Louisville
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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 XML.
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or at the
least is not enforced in any meaningful way.
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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 fact
://www.nwpho.org.uk/sadb/Poisson%20CI%20in%20spreadsheets.pdf
. . .
Also see http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/ExcelProblems
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www.plymouth.ac.uk
I had hoped that journals engaged in reproducible research by now.
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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
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'overfitting'.
Overfitting can cause the model fit to appear to be excellent, but there
is still a huge problem.
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R
Thanks,
Frank
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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
/affirmative
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of measurement' then xYplot,
describe, and other Hmisc functions will include the units (in a
different font on graphs or when using latex()).
Frank
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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
of the summarize examples!
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to include their names in an
Ack. section, usually. Referencing as a personal communication is
perhaps better.
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in
Wilcoxon. As Somers' Dxy rank correlation coefficient is 2*(1-C) where
C is the concordance or ROC area, the Hmisc package function rcorr.cens
uses U statistic methods to get the standard error of Dxy. You can
easily translate this to a standard error of C.
Frank
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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.
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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
-help
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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.
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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
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(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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=NA, fun='plogis') # probability scale
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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:
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.
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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
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not need to
create new variables at all.
Franc
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.
.
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PLEASE do read
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
Quoting Frank E Harrell Jr [EMAIL
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.
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(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
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linear models
(particularly the fitting
of logistic relationships), the complexity is greatly increased.
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PROTECTED] On Behalf Of Frank
E Harrell Jr
Sent: Wednesday, March 02, 2005 5:13 AM
To: Wittner, Ben
Cc: [EMAIL PROTECTED]
Subject: Re: [R] subset selection for logistic regression
Wittner, Ben wrote:
R-packages leaps and subselect implement various methods of
selecting best or
good subsets
Congratulations Dirk on the article in linuxtoday.com today about Quantian.
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on prespecified models. It is not
valid when stepwise variable selection is used (unless perhaps you use
alpha=0.5).
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Trevor Wiens wrote:
On Thu, 10 Mar 2005 16:19:41 -0600
Frank E Harrell Jr [EMAIL PROTECTED] wrote:
The goodness of fit test only works on prespecified models. It is not
valid when stepwise variable selection is used (unless perhaps you use
alpha=0.5).
Perhaps I'm blind, but I can't find any
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www.peterflom.com
New York, NY 10010
(212) 845-4485 (voice)
(917) 438-0894 (fax)
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Baarle
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You didn't say which prostate cancer study that represented. One famous
one has data in R form on our web site http://biostat.mc.vanderbilt.edu.
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I wish to perform brain surgery this afternoon at 4pm and don't know
where to start. My background is the history of great statistician
sports legends but I am willing to learn. I know there are courses and
numerous books on brain surgery but I don't have the time for those.
Please direct me
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Frank Harrell
On Tue, 5 Apr 2005, Frank E Harrell Jr wrote:
[EMAIL PROTECTED] wrote:
Dear R-list,
i have 6 different sets of samples. Each sample has about 5000 observations,
with each observation comprised of 150 baseline covariates (X), 125 of which
are dichotomous. Roughly 20
.
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PLEASE do read
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.
FH
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== 10, 4,
ifelse( V1 == 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.
Sachin
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, of finite dimension, and the
complexity of our models should not grow very fast as N increases. I
find the AIC approach gives me more accurate predictions.
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,
Jinsong Zhao
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of Washington, Seattle
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at biostat.mc.vanderbilt.edu
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to devide it?
For example, the result of cut() as a new variable to the data.frame and
afterwards split() the data.frame by the resulting factor.
Or
library(Hmisc)
xg - cut2(x, g=10)# labels deciles nicely
Frank
Uwe Ligges
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-values is not
straightforward even in that far simpler situation.
Frank
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a recycle of a smaller
vector. (I do often use a recycle of a scalar.)
regards,
/iaw
The current behavior is logical to me. Are you looking for if(test) a
else b?
Frank
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), Room 731
212-854-7075
Mailing address:
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(fax) 212-851-2164
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Andrew Gelman wrote:
Frank,
Just to check: are you saying that this model can be fit in lmer()?
Thanks.
Andrew
Not sure about that. Greenland probably used BUGS but doesn't mean you
can't do it with lmer.
Frank
Frank E Harrell Jr wrote:
A great reference for that kind of model
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( )
variable to hand to Design.
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Prof Brian Ripley wrote:
On Mon, 22 May 2006, Frank E Harrell Jr wrote:
Rick Bilonick wrote:
When I run lrm from the Design package, I get a warning about
contrasts when I include an ordinal variable:
Warning message:
Variable ordfac is an ordered factor.
You should set
options
object and using text( ).
Frank
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! is one of the most fun conferences I've attended.
Thanks again!
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Matthew Bridgman wrote:
Does anyone know a simple way of calculating effect sizes?
Thanks
MB
Yes - the following formula is simple and fairly universal:
2
:-)
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)
plot(f, fun=plogis) # plot partial effects of all predictors,
probability scale
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on a easy to use
R package one can use for generating publication quality reports?
Outputting HTML or PDF.
Doing this without LaTeX is like doing statistical analysis without
linear models and the Wilcoxon test.
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