Re: [R] Problem with 'nls' fitting logistic model (5PL)

/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). -- Bert On Wed, May 2, 2012 at 12:32 PM, Michal Figurski figur

[R] Problem with 'nls' fitting logistic model (5PL)

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

Re: [R] Estimating correlation in multiple measures data

, then proceed as if you had 10 independent measurements. Peter On Thu, Mar 24, 2011 at 10:38 AM, Michal Figurski figur...@mail.med.upenn.edu wrote: Peter, This is actually too simple - it doesn't take into account the fact that the data were measured several times on the same subject. This is one

[R] Estimating correlation in multiple measures data

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

[R] Big data (over 2GB) and lmer

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

Re: [R] Plotting confidence bands around regression line

, 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 1.257584 1.052696 1.679290

[R] Plotting confidence bands around regression line

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 intervals. I

Re: [R] Plotting confidence bands around regression line

. -- 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 graphics gurus

Re: [R] Plotting confidence bands around regression line

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, David Winsemius wrote: On Aug 10, 2010, at 11:23 AM, Michal Figurski wrote: David, I may have

Re: [R] Plotting confidence bands around regression line

. 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 Vanderbilt University On Tue, 10 Aug 2010, Michal Figurski wrote: David, I would

Re: [R] Plotting confidence bands around regression line

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 1.257584 1.052696

Re: [R] Problem with plotting survival predictions from cph model

On 2010-05-27 13:39, Joshua Wiley wrote: On Thu, May 27, 2010 at 10:32 AM, Michal Figurski figur...@mail.med.upenn.edu 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

Re: [R] Problem with plotting survival predictions from cph model

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)

Re: [R] Problem with plotting survival predictions from cph model

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,

[R] Problem with plotting survival predictions from cph model

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,

[R] How to estimate the residual SD for each sample separately in mixed-effects model?

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 -

Re: [R] Problem comparing hazard ratios

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

[R] Problem comparing hazard ratios

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

[R] 'nlme' library - lme function results

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: (...)

[R] Starting NONMEM (nmfe6) from R

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

Re: [R] Starting NONMEM (nmfe6) from R

Dear Scott (and all), Thanks for sharing your idea - it helped me solve the problem. The issue was actually the nmfe6.bat itself - there was plenty of references such as %dir%, %nmdir%, etc. I replaced them all with full paths. Additionally, I put all the PATH settings from NMdirectories.bat

[R] Problem with greek beta symbol in plot using CairoPDF (Windows)

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

[R] Beginner's question: number formatting

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 ifs, but I was wondering

[R] How to store the results of multiple iterations of 'aov' in a data.frame?

. Please help. -- Michal Figurski Michal Figurski wrote: Dear R-helpers, I have a dataset named qu, organized as follows: SampleRunReplicateValue 11125 11240 11333 11429 12137 12244 1

[R] Need to calculate within- and between- run CV

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 2

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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 from the referenced page - I

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

(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 Harrell Jr wrote: Michal Figurski wrote: Tim, If I understand correctly

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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

[R] [Fwd: Re: Coefficients of Logistic Regression from bootstrap - how to get them?]

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 stepwise regression is? Since they used SPSS, I copied from http://www.visualstatistics.net/SPSS

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

- 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 start getting

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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 PROTECTED] On Behalf Of Michal Figurski Sent: Thursday, July 24, 2008 8:03 AM Cc: r

[R] [Fwd: Re: Coefficients of Logistic Regression from bootstrap - how to get them?]

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

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

, it's their foot but if I help them, they may sue me later) If any of the above helps without sounding horribly patronising, I win. If not, well, you have another email to burn! happy booting Steve Ellison Michal Figurski [EMAIL PROTECTED] 22/07/2008 20:42

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

. 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 have an idea. Since

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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, 2008 9:52 AM

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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 in R. I'll go back to SAS

[R] Coefficients of Logistic Regression from bootstrap - how to get them?

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:

Re: [R] Coefficients of Logistic Regression from bootstrap - how to get them?

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 Frank E Harrell Jr wrote: Michal Figurski wrote: Hello

[R] Problem with by(... , median)

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:

Re: [R] Problem with by(... , median)

=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 ready right away