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Dear all,

I want to fit a multiple logistic regression together with cross validation of it including ROC curves, bootstraps and ... .
And then, my main work is to draw a nomogram for the fitted logistic regression.
But, I'm a little confused about the right packages for doing these in R, especially for drawing nomogram.
I would be very pleased if you assist me with your good knowledge and introducing good references possibly with examples concerning the issue of Nomogram and Cross Validation.


Thank you very much,
Amir
-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------

Take a look at Hmisc and rms by Frank Harrell

-------------------------------------------
Carlos Alzola
President
Data Insights Inc.
-------------------------------------------

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-09-2012 18:07
From: Carlos Alzola
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Take a look at Hmisc and rms by Frank Harrell

-------------------------------------------
Carlos Alzola
President
Data Insights Inc.
-------------------------------------------

 If you don't already have it, see Harrell's textbook "REGRESSION MODELING STRATEGIES with Applications to Linear Models, Logistic Regression, and Survival Analysis" for more examples

-------------------------------------------
Chris Barker, Ph.D.
President - San Francisco Bay Area Chapter of the American Statistical Association
www,barkerstats.com

----------------------------------------------
"In composition you have all the time you want to decide what to say in 15 seconds, in improvisation you have 15 seconds."
-Steve Lacy
-------------------------------------------







Original Message:
Sent: 03-14-2012 12:28
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Dear all,

My many thanks for your nice replies.

I think my main problem is with R coz I'm an amateur R user.

I found the package "rms" in R which is written by Harrell. I can draw my nomogram and one of my ROC curves. But, I should be able to validate my model by several methods including cross-validation, bootstrap and any other available methods and I should do all of them with R.

Just need to orient how can I do my affairs with R. For example, I still have a problem with Validation and Calibration in 'rms' package. Unfortunately the examples in the rms package can not help me well.
What can help me more I think is some better examples with explanations.
Thank you very much for all your attention.

Any other comment from you will be appreciated.

Regards,
Amir

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------

Dear Prof. Barker,

Many thanks for reply.
Unfortunately I couldn't find this book in our university library, even in any library in Iran.
I heard from many that it's a great book, but it is not available for me.

Is there any other references or sources concerning the issue?

Thank's for attention.

Amir



-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 12:51
From: Christopher Barker
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


 If you don't already have it, see Harrell's textbook "REGRESSION MODELING STRATEGIES with Applications to Linear Models, Logistic Regression, and Survival Analysis" for more examples

-------------------------------------------
Chris Barker, Ph.D.
President - San Francisco Bay Area Chapter of the American Statistical Association
www,barkerstats.com

----------------------------------------------
"In composition you have all the time you want to decide what to say in 15 seconds, in improvisation you have 15 seconds."
-Steve Lacy
-------------------------------------------







Original Message:
Sent: 03-14-2012 12:28
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Dear all,

My many thanks for your nice replies.

I think my main problem is with R coz I'm an amateur R user.

I found the package "rms" in R which is written by Harrell. I can draw my nomogram and one of my ROC curves. But, I should be able to validate my model by several methods including cross-validation, bootstrap and any other available methods and I should do all of them with R.

Just need to orient how can I do my affairs with R. For example, I still have a problem with Validation and Calibration in 'rms' package. Unfortunately the examples in the rms package can not help me well.
What can help me more I think is some better examples with explanations.
Thank you very much for all your attention.

Any other comment from you will be appreciated.

Regards,
Amir

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------

If you have a valid credit card you could order the book through amazon.com.  Sometimes they have used copies available at much lower prices.  Just look up Frank Harrell.
-------------------------------------------
Michael Chernick
Director of Biostatistical Services
Lankenau Institute for Medical Research
-------------------------------------------







Original Message:
Sent: 03-14-2012 13:35
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Dear Prof. Barker,

Many thanks for reply.
Unfortunately I couldn't find this book in our university library, even in any library in Iran.
I heard from many that it's a great book, but it is not available for me.

Is there any other references or sources concerning the issue?

Thank's for attention.

Amir



-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 12:51
From: Christopher Barker
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


 If you don't already have it, see Harrell's textbook "REGRESSION MODELING STRATEGIES with Applications to Linear Models, Logistic Regression, and Survival Analysis" for more examples

-------------------------------------------
Chris Barker, Ph.D.
President - San Francisco Bay Area Chapter of the American Statistical Association
www,barkerstats.com

----------------------------------------------
"In composition you have all the time you want to decide what to say in 15 seconds, in improvisation you have 15 seconds."
-Steve Lacy
-------------------------------------------

Dear Prof. Chernick,

Unfortunately, Amazon company does not do any trade directly with my country and ordering the book with other methods takes at least one month.

I think it's the result of the boycott!

kind regards,
Amir

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 14:02
From: Michael Chernick
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


If you have a valid credit card you could order the book through amazon.com.  Sometimes they have used copies available at much lower prices.  Just look up Frank Harrell.
-------------------------------------------
Michael Chernick
Director of Biostatistical Services
Lankenau Institute for Medical Research
-------------------------------------------







Original Message:
Sent: 03-14-2012 13:35
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Dear Prof. Barker,

Many thanks for reply.
Unfortunately I couldn't find this book in our university library, even in any library in Iran.
I heard from many that it's a great book, but it is not available for me.

Is there any other references or sources concerning the issue?

Thank's for attention.

Amir



-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 12:51
From: Christopher Barker
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


 If you don't already have it, see Harrell's textbook "REGRESSION MODELING STRATEGIES with Applications to Linear Models, Logistic Regression, and Survival Analysis" for more examples

-------------------------------------------
Chris Barker, Ph.D.
President - San Francisco Bay Area Chapter of the American Statistical Association
www,barkerstats.com

----------------------------------------------
"In composition you have all the time you want to decide what to say in 15 seconds, in improvisation you have 15 seconds."
-Steve Lacy
-------------------------------------------

Amir,
Did you try looking into R package called caret?

http://caret.r-forge.r-project.org/Classification_and_Regression_Training.html

It has several convenience functions to facilitate cross-validation, bootstrapping, etc. for many different models (including glm). It has also decent introduction papers.

Moni

-------------------------------------------
Moni Neradilek
Statistical Consultant
The Mountain-Whisper Light Statistics
-------------------------------------------







Original Message:
Sent: 03-14-2012 14:55
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


Dear Prof. Chernick,

Unfortunately, Amazon company does not do any trade directly with my country and ordering the book with other methods takes at least one month.

I think it's the result of the boycott!

kind regards,
Amir

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 14:02
From: Michael Chernick
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


If you have a valid credit card you could order the book through amazon.com.  Sometimes they have used copies available at much lower prices.  Just look up Frank Harrell.
-------------------------------------------
Michael Chernick
Director of Biostatistical Services
Lankenau Institute for Medical Research
-------------------------------------------







Original Message:
Sent: 03-14-2012 13:35
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Dear Prof. Barker,

Many thanks for reply.
Unfortunately I couldn't find this book in our university library, even in any library in Iran.
I heard from many that it's a great book, but it is not available for me.

Is there any other references or sources concerning the issue?

Thank's for attention.

Amir



-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------

A google search - Some links here, which reference either Dr. Harrell's book or software or both

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356406/

http://www.google.com/url?sa=t&rct=j&q=hmisc%20nomograms&source=web&cd=6&ved=0CE0QFjAF&url=http%3A%2F%2Ficcle.googlecode.com%2Fsvn%2Ftrunk%2Fshare%2Fpdf%2Fmozina04.pdf&ei=wfRgT8-oD-a3sQK_lLCWCA&usg=AFQjCNH36PEXAX4FlFIQi6sziVJQB6vskA&cad=rja

http://tinyurl.com/6uonmqf

http://jco.ascopubs.org/content/18/19/3352.full.pdf

http://humrep.oxfordjournals.org/content/27/2/451.abstract


http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatGraphCourse/graphscourse.pdf

http://archotol.ama-assn.org/cgi/content/abstract/137/11/1154


-------------------------------------------
Chris Barker, Ph.D.
President - San Francisco Bay Area Chapter of the American Statistical Association
www,barkerstats.com

---
"In composition you have all the time you want to decide what to say in 15 seconds, in improvisation you have 15 seconds."
-Steve Lacy
-------------------------------------------







Original Message:
Sent: 03-14-2012 14:55
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


Dear Prof. Chernick,

Unfortunately, Amazon company does not do any trade directly with my country and ordering the book with other methods takes at least one month.

I think it's the result of the boycott!

kind regards,
Amir

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 14:02
From: Michael Chernick
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


If you have a valid credit card you could order the book through amazon.com.  Sometimes they have used copies available at much lower prices.  Just look up Frank Harrell.
-------------------------------------------
Michael Chernick
Director of Biostatistical Services
Lankenau Institute for Medical Research
-------------------------------------------







Original Message:
Sent: 03-14-2012 13:35
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Dear Prof. Barker,

Many thanks for reply.
Unfortunately I couldn't find this book in our university library, even in any library in Iran.
I heard from many that it's a great book, but it is not available for me.

Is there any other references or sources concerning the issue?

Thank's for attention.

Amir



-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------

Dear Dr. Barker,

My many thanks for your warm attention.

but none of the second and third links opened.

Again, Thank you so much.

Rgds,
Amir

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 15:52
From: Christopher Barker
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model



A google search - Some links here, which reference either Dr. Harrell's book or software or both

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356406/

http://www.google.com/url?sa=t&rct=j&q=hmisc%20nomograms&source=web&cd=6&ved=0CE0QFjAF&url=http%3A%2F%2Ficcle.googlecode.com%2Fsvn%2Ftrunk%2Fshare%2Fpdf%2Fmozina04.pdf&ei=wfRgT8-oD-a3sQK_lLCWCA&usg=AFQjCNH36PEXAX4FlFIQi6sziVJQB6vskA&cad=rja

http://tinyurl.com/6uonmqf

http://jco.ascopubs.org/content/18/19/3352.full.pdf

http://humrep.oxfordjournals.org/content/27/2/451.abstract


http://biostat.mc.vanderbilt.edu/twiki/pub/Main/StatGraphCourse/graphscourse.pdf

http://archotol.ama-assn.org/cgi/content/abstract/137/11/1154


-------------------------------------------
Chris Barker, Ph.D.
President - San Francisco Bay Area Chapter of the American Statistical Association
www,barkerstats.com

---
"In composition you have all the time you want to decide what to say in 15 seconds, in improvisation you have 15 seconds."
-Steve Lacy
-------------------------------------------







Original Message:
Sent: 03-14-2012 14:55
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


Dear Prof. Chernick,

Unfortunately, Amazon company does not do any trade directly with my country and ordering the book with other methods takes at least one month.

I think it's the result of the boycott!

kind regards,
Amir

-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------







Original Message:
Sent: 03-14-2012 14:02
From: Michael Chernick
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model


If you have a valid credit card you could order the book through amazon.com.  Sometimes they have used copies available at much lower prices.  Just look up Frank Harrell.
-------------------------------------------
Michael Chernick
Director of Biostatistical Services
Lankenau Institute for Medical Research
-------------------------------------------







Original Message:
Sent: 03-14-2012 13:35
From: Amir Kasaeian
Subject: Drawing Nomogram - Cross Validation of Logistic Regression Model

Dear Prof. Barker,

Many thanks for reply.
Unfortunately I couldn't find this book in our university library, even in any library in Iran.
I heard from many that it's a great book, but it is not available for me.

Is there any other references or sources concerning the issue?

Thank's for attention.

Amir



-------------------------------------------
Amir Kasaeian
PhD Student in Biostatistics
Tehran University of Medical Sciences (TUMS)
amir_kasaeian@yahoo.com
akasaeian@razi.tums.ac.ir
-------------------------------------------

Check Dr. Harrell's website and the An Introduction to S and The Hmisc and Design Libraries (http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RS/sintro.pdf). Although this set of notes is S-Plus based and somewhat old (it uses the Design library which has been superseded by rms) it should still be helpful. It has examples of bootstrap and validate.

-------------------------------------------
Carlos Alzola
President
Data Insights Inc.
-------------------------------------------