[R] Fitting a polynomial using lrm from the Design library

[David Winsemius]

On Jun 18, 2010, at 5:13 PM, David Winsemius wrote:

>
> On Jun 18, 2010, at 12:02 PM, Josh B wrote:
>
>> Hi all,
>>
>> I am looking to fit a logistic regression using the lrm function  
>> from the Design library. I am interested in this function because I  
>> would like to obtain "pseudo-R2" values (see http://tolstoy.newcastle.edu.au/R/help/02b/1011.html) 
>> .
>>
>> Can anyone help me with the syntax?
>>
>> If I fit the model using the stats library, the code looks like this:
>> model <- glm(x$trait ~ x$PC1 + I((x$PC1)^2) + I((x$PC1)^3), family  
>> = binomial)
>>
>> What would be the equivalent syntax for the lrm function?
>
> Not sure if the code you gave above produces an orthogonal set, but  
> perhaps this will be meaningful to some of r-help's readers (but not  
> necessarily to me):
>
> require(Design)
> mod.poly3 <- lrm( trait ~ poly(PC1, 3), data=x)
>
> This does report results, but I'm not sure how you would interpret.  
> (See below for one attempt)
>
> I think Harrell would probably recommend using restricted cubic  
> splines, however.
>
> mod.rcs3 <- lrm( trait ~ rcs(PC1, 3), data=x)
>
> For plotting with Design/Hmisc functions, you will get better  
> results with the datadist facilities.
> > ddx <- datadist(x)
> > options(datadist="ddx")
> > plot(mod3, PC1=NA)

Forgot to fix this:
  plot(mod.rcs3, PC1=NA)

> # Perfectly sensible plot which includes the OR=0 line that would be  
> the theoretically ideal result.
>
> # Whereas plot.Design does not know how to plot the earlier result
>
> > plot(mod.poly3, PC1=NA)
> Error in plot.Design(mod.poly3, PC1 = NA) :
>  matrix or interaction factor may not be displayed
>
> May still get meaningful results with predict:
>
> plot(seq(-3, 2, by=.1), predict(mod.poly3, data.frame(PC1=seq(-3, 2,  
> by=.1)) ) )
>
> Bit it appears to be less satisfactory that the rcs fit, since it  
> blows up at the extremes.
>
> -- 
> David.
>>
>> Thanks very much in advance,
>> -----------------------------------
>> Josh Banta, Ph.D
>> Center for Genomics and Systems Biology
>> New York University
>> 100 Washington Square East
>> New York, NY 10003
>> Tel: (212) 998-8465
>> http://plantevolutionaryecology.org
>>
>>
>>
>>
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>>
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>
> David Winsemius, MD
> 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.

David Winsemius, MD
West Hartford, CT