R help - Feb 2010 - Plot of odds ratios obtained from a logistic model

Hi all!

I am trying to develop a plot a figure in which I would like to show
the odds ratios obtained from a logistic model. I  have tried with the
dotplot option but no success. Could you help me? Is there any option
when modelling the logistic model in R?

Thank you in advance

Hi,

On Sat, Feb 6, 2010 at 1:28 PM, gepeto <geppetto5st at gmail.com>
wrote:
> Hi all!
>
> I am trying to develop a plot a figure in which I would like to show
> the odds ratios obtained from a logistic model. I ?have tried with the
> dotplot option but no success. Could you help me?
You can help us help you by showing the code you tried with dotplot
that didn't turn out as you expected ... it's easier to help you get
where you're going if you showed us the direction you started in ..
>  Is there any option when modelling the logistic model in R?
I'm sure there are many.

Take a look at some of the graphics from:

http://addictedtor.free.fr/graphiques/
http://bm2.genes.nig.ac.jp/RGM2/index.php
http://had.co.nz/ggplot2/

And look at the source code/man pages of the graphs that are of the
type you'd like to make, and take it from there.

Including code + a reproducible example (even if it doesn't work) will
get you a long way ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

You might want to look at the plot.Predict function in the rms package - it
allows you to plot the logits or probablities vs the predictor variable at
specified levels of other covariates (if any) in the model.  There are many
examples in http://cran.r-project.org/web/packages/rms/rms.pdf

David Freedman
-- 
View this message in context:
http://n4.nabble.com/Plot-of-odds-ratios-obtained-from-a-logistic-model-tp1471496p1471566.html
Sent from the R help mailing list archive at Nabble.com.

On Feb 6, 2010, at 4:13 PM, David Freedman wrote:
>
> You might want to look at the plot.Predict function in the rms  
> package - it
> allows you to plot the logits or probablities vs the predictor  
> variable at
> specified levels of other covariates (if any) in the model.  There  
> are many
> examples in http://cran.r-project.org/web/packages/rms/rms.pdf
But it will not work on a glm( ..., family=binomial)  object. To work  
with such an object you would need to plot exp(fit$linear.predictors)  
or fit$fitted.values

plot.Predict will only work with the functions in the rms package, ...  
in the case of logistic models that would be lrm().
>
> David Freedman
> -- 
> View this message in context:
http://n4.nabble.com/Plot-of-odds-ratios-obtained-from-a-logistic-model-tp1471496p1471566.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org 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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

Also take a look at summary.rms and its plot method which produces odds 
ratio dot charts directly.

Frank

David Winsemius wrote:
> 
> On Feb 6, 2010, at 4:13 PM, David Freedman wrote:
> 
>>
>> You might want to look at the plot.Predict function in the rms package 
>> - it
>> allows you to plot the logits or probablities vs the predictor 
>> variable at
>> specified levels of other covariates (if any) in the model.  There are 
>> many
>> examples in http://cran.r-project.org/web/packages/rms/rms.pdf
> 
> But it will not work on a glm( ..., family=binomial)  object. To work 
> with such an object you would need to plot exp(fit$linear.predictors) or 
> fit$fitted.values
> 
> plot.Predict will only work with the functions in the rms package, ... 
> in the case of logistic models that would be lrm().
> 
>>
>> David Freedman
>> -- 
>> View this message in context: 
>>
http://n4.nabble.com/Plot-of-odds-ratios-obtained-from-a-logistic-model-tp1471496p1471566.html
>>
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> R-help at r-project.org 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.
> 
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
> 
> ______________________________________________
> R-help at r-project.org 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 Harrell Jr   Professor and Chairman        School of Medicine
                      Department of Biostatistics   Vanderbilt University