Hello all,
I am trying to optimize my logistic regression model by using bootstrap.
I was previously using SAS for this kind of tasks, but I am now
switching to R.
My data frame consists of 5 columns and has 109 rows. Each row is a
single record composed of the following values: Subject_name
the coeffcients
for the model that gives the "nearly unbiased estimates". I greatly
appreciate your help.
--
Michal J. Figurski
HUP, Pathology & Laboratory Medicine
Xenobiotics Toxicokinetics Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
hal J. Figurski
HUP, Pathology & Laboratory Medicine
Xenobiotics Toxicokinetics Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
Frank E Harrell Jr wrote:
Michal Figurski wrote:
Frank,
"How does bootstrap improve on that?"
I don't know, but I
to
ignore that advice and use bootstrap for point estimates rather than the
properties of those estimates (which is what bootstrap is for) then you
are on your own.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Michal Figurski
Sent: Tuesday, July 22, 20
k's book, Regression Modeling Strategies:
http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/RmS
Marc Schwartz
on 07/22/2008 09:43 AM Michal Figurski wrote:
Hmm...
It sounds like ideology to me. I was asking for technical help. I know
what I want to do, just don't know how to do it i
I think the argument supporting the use of bootstrap to determine
coefficients, as opposed to just running linear regression on the whole
dataset, is the comparison of Rsq and prediction errors between these
two approaches - page 1502. There's a substantial difference in favor of
the bootstrap app
Thank you Gustaf,
I apologize for not including an example data in my first email.
Nevertheless, your code worked for me excellently - I only added "55" as
the size of sample.
I must admit this code looks so much simpler, compared to SAS. I am
beginning to love R, despite some disrespectful
u see someone trying to do something silly - eg
pull the trigger while the gun is pointed at their foot - would you
really give them the instruction they asked for on how to get the safety
catch off? Or tell them that what they are doing is silly?
(Me, well, it's their foot bu
greatly appreciate your time and advices in this matter.
--
Michal J. Figurski
Frank E Harrell Jr wrote:
Gustaf Rydevik wrote:
On Wed, Jul 23, 2008 at 4:08 PM, Michal Figurski
<[EMAIL PROTECTED]> wrote:
Hi,
I believe that you misunderstand the passage. Do you know what
multiple stepwi
riginal Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Michal Figurski
Sent: Wednesday, July 23, 2008 10:22 AM
To: r-help@r-project.org
Subject: Re: [R] Coefficients of Logistic Regression from
bootstrap - how to get them?
Thank you all for your words of wisdom.
I sta
e and reject the cosmology because it is
beyond me. That's the "flat earth" philosophy of science, and it is a
terrible obstacle to scientific progress and human enlightenment, in
general.
Cheers,
Bert Gunter
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTEC
Tim,
If I understand correctly, you are saying that one can't improve on
estimating a mean by doing bootstrap and summarizing means of many such
steps. As far as I understand (again), you're saying that this way one
can only add bias without any improvement...
Well, this is in contradiction
vertheless I thank you (all) for relevant criticism on the procedure
(in the points where it was relevant). I plan to use this methodology
further, and it was good to find out that it withstood your criticism. I
will look into the penalized methods, though.
--
Michal J. Figurski
Frank E Harrel
Gustaf,
Summarizing things I don't understand:
- Honestly, I was thinking I can use bootstrap to obtain better
estimate of a mean - provided that I want it. So, I can't?
- If I can't obtain reliable estimates of CI and variance from a small
dataset, but I can do it with bootstrap - isn't it a "
edicine
Xenobiotics Toxicokinetics Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
Gustaf Rydevik wrote:
On Thu, Jul 31, 2008 at 4:30 PM, Michal Figurski
<[EMAIL PROTECTED]> wrote:
Frank and all,
The point you were looking for was in a page that was linked
Hello,
I have made an R script that prepares a NONMEM dataset and I would like
to start the NONMEM run right after the dataset is ready.
I am using windows XP, R 2.9.1 and NONMEM 6.
I have prepared a run.bat file that looks like this:
call K:\nmvi\NMdi
\nmfe6 "K:\nmvi\path\control.txt" "K:\nmvi\path\output.txt"
Alternatively, you could make sure R is working in the right directory. e.g.
setwd('K:\nmvi')
Scott
Scott Sherrill-Mix
Department of Microbiology
University of Pennsylvania
402B Johnson Pavilion
3610 Hamilton
Dear R-Helpers,
I am a novice in survival analysis. I have the following code:
for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a))
I used it to fit the Cox Proportional Hazard models separately for every
available parameter (columns 3:12) in my data set - with intention to
compare t
Thank you, gentlemen.
I greatly appreciate your help.
--
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
__
R-help@r-project.org mailing li
Dear R-helpers,
I am developing a Mixed-Effects model for a study of immunoassays using
'lme4' library. The study design is as follows: 10 samples were run
using 7 different immunoassays, 3 times each, in duplicates. Data
attached. I have developed the following model:
c.lme <- lmer(Result~S
Dear R-Helpers,
I have a problem with displaying the greek "beta" symbol in PDF files
using Cairo library - it displays as an empty box. The same also happens
for a dash symbol in subscript. Both symbols are displayed correctly if
the plot is produced on screen (outside of CairoPDF).
The syn
Dear R-helpers
I am running a simple mixed effects model using lme(). The call looks
like this:
fit <- lme(Analyte~Sample, data=Data, random=~1 | Run)
I am particularly interested in the estimated random effects. When I
print the 'fit' object, it looks something like example below:
(...)
Ra
Dear R-helpers
I have a data set of roughly 10 million records, 7 columns. It has only
about 500MB as a csv, so it fits in the memory. It's painfully slow to
do anything with it, but it's possible. I also have another dataset of
covariates that I would like to explore - with about 4GB of data.
Dear R-helpers and graphics gurus,
I have two problems with plotting confidence bands:
1. First is relatively simple. I am using the Passing-Bablok procedure
to obtain "unbiased" regression coefficients. This procedure yields the
"a" & "b" coefficient values along with their confidence interva
27; models.
--
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
W dniu 2010-08-10 11:09, David Winsemius pisze:
On Aug 10, 2010, at 10:56 AM, Michal Figurski wrote:
Dear R-helpers and
;nls' class currently *ignores* the
interval parameter - as it is stated in documentation.
Regards
--
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
On 2010-08-10 11:38, Dav
13
On 2010-08-10 12:29, Frank Harrell wrote:
Please give the prescription. The article is not available on our
extensive online library. I wonder if the method can compete with the
bootstrap.
Frank
Frank E Harrell Jr Professor and Chairman School of Medicine
Department of Biostatistics Va
Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
On 2010-08-10 13:12, Peter Dalgaard wrote:
Michal Figurski wrote:
# And the result of the Passing-Bablok regression on this data frame:
Estimate 5%CI 95%CI
Intercept -4.306197 -9.948438 -1.374663
Slope
y
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
On 2010-08-10 13:12, Peter Dalgaard wrote:
Michal Figurski wrote:
# And the result of the Passing-Bablok regression on this data frame:
Estimate 5%CI 95%CI
Intercept -4.306197 -9.948438 -1.374663
Slope 1.2575
Dear R-helpers,
I am working with 'cph' models from 'rms' library. When I build simple
survival models, based on 'Surv(time, event)', everything is fine and I
can make nice plots using plot(Predict(f, time=3)).
However, recently I tried to be more specific and used 'Surv(start,
stop, event)'
Well, I am very proud of myself. Here is something to help you.
The dataset is attached, with "anonymized" column names. The code to
reproduce the error is below:
library(rms)
d <- datadist(x)
options(datadist="d")
f <- cph(Surv(start,stop,status)~P1*P2 + P3, data=x, x=T, y=T, surv=T)
plot(Pre
Actually, I have another problem with the same data - this time with
plotting simple KM lines. The dataset is attached.
In this excercise I was testing two ways of representing time from the
previously attached interval dataset. Here t1 is the "stop" time at the
last interval for each patient,
On 2010-05-27 13:39, Joshua Wiley wrote:
On Thu, May 27, 2010 at 10:32 AM, Michal Figurski
wrote:
Actually, I have another problem with the same data - this time with plotting
simple KM lines. The dataset is attached.
Michal,
Just as a heads up, only certain types of files can be atta
Dear R-helpers,
This may sound simple to you, but I'm a beginner in this, so please be
forgiving.
I have a following problem: two analytes were measured in patient's
blood on 4 occasions: ProteinA and ProteinB. How to correctly evaluate
correlation between ProteinA and ProteinB?
I tried:
x <
ient are very similar, you could
simply average them, then proceed as if you had 10 independent
measurements.
Peter
On Thu, Mar 24, 2011 at 10:38 AM, Michal Figurski
wrote:
Peter,
This is actually too simple - it doesn't take into account the fact that the
data were measured several tim
Dear R-Helpers,
I'm working with immunoassay data and 5PL logistic model. I wanted to
experiment with different forms of weighting and parameter selection,
which is not possible in instrument software, so I turned to R.
I am using R 2.14.2 under Win7 64bit, and the 'nls' library to fit the
m
7 Maloney S
Philadelphia, PA 19104
tel. (215) 662-3413
On 5/2/2012 3:47 PM, Bert Gunter wrote:
Plot the data. You're clearly overfitting.
(If you don't know what this means or why it causes the problems you
see, try a statistical help list or consult your local statistician).
Hello everyone,
I am new to R, I have been using SAS for a while. Not surprisingly, I
find R much better in graphics, which is publication ready right away.
Recently, I have been trying to calculate some basic statistics using R.
I have a dataset of multiple rows per subject. For example:
S
FUN=median, na.rm = T)
On Tue, Jun 10, 2008 at 10:18 AM, Michal Figurski
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
Hello everyone,
I am new to R, I have been using SAS for a while. Not surprisingly,
I find R much better in graphics, which is publication
Dear R-helpers,
I have a dataset named "qu", organized as follows:
Sample Run Replicate Value
1 1 1 25
1 1 2 40
1 1 3 33
1 1 4 29
1 2 1 37
1 2
the structure of aov object, but the sums of squares are not
listed there, though 'summary(a)' prints them. Please help.
--
Michal Figurski
Michal Figurski wrote:
Dear R-helpers,
I have a dataset named "qu", organized as follows:
SampleRunReplicateValue
11
Hello R-helpers,
I have a problem with formatting a single number to show leading zeros.
For example, I want "2" displayed as "002".
My numbers have 1 to 3 digits and I would like them all to display 3
digits for printing. I know I could use "paste" in a loop with several
"if"s, but I was wo
Thank you all for quick responses,
This was very helpful. I knew there was a simple way!
--
Michal J. Figurski
Prof Brian Ripley wrote:
sprintf("%03d", 2)
formatC(2, width=3, flag="0")
both give
[1] "002"
On Fri, 17 Oct 2008, Michal Figurski wrote:
Hell
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