[R] odds ratio: how to create reference

Frank E Harrell Jr f.harrell at vanderbilt.edu
Tue Sep 23 14:03:17 CEST 2008

Philip Twumasi-Ankrah wrote:
> To select another reference level from the default that R chooses you can use the "relevel" function
> example;
> Reorder Levels of Factorwarpbreaks$tension <- relevel(warpbreaks$tension, ref="M")
> summary(lm(breaks ~ wool + tension, data=warpbreaks))
> function findlink(pkg, fn) {
> var Y, link;
> Y = location.href.lastIndexOf("\\") + 1;
> link = location.href.substring(0, Y);
> link = link + "../../" + pkg + "/chtml/" + pkg + ".chm::/" + fn;
> location.href = link;
> }
> This sets "M" as the reference level for the analysis. At the prompt on the R workspace, type
> ?relevel 
> A Smile costs Nothing  
>      But Rewards Everything
> Happiness is not perfected until it is shared
>                                                               -Jane Porter    

These calculations are automatic using the Design package, e.g.

dd <- datadist(d); options(datadist='d')
f <- lrm(y ~ pol(age,2)*sex+rcs(weight,4), data=d)
summary(f, sex='m')   # makes 'm' the reference cell if you don't like 
the default; gives odds ratios

For the sex OR age is set to the median (default; easily changed; 
doesn't matter if interaction term omitted).

Bunny in your original post it would be less confusing if you did not 
call levels of an independent variable the outcomes.  Many people refer 
to the dependent variable as the outcome variable.


> --- On Tue, 9/23/08, Bunny, lautloscrew.com <bunny at lautloscrew.com> wrote:
> From: Bunny, lautloscrew.com <bunny at lautloscrew.com>
> Subject: [R] odds ratio: how to create reference
> To: r-help at r-project.org
> Date: Tuesday, September 23, 2008, 4:06 AM
> HI there,
> i know this is a basic question, though i need some help because this  
> is somewhat away from my current issue, but nevertheless interesting  
> to me... Lets assume i have some estimated probabilities, say  
> estimated by a logit model. i know i can also state them as an odds  
> ratio.
> Now i´d like to state these odds ratios as a reference to a specific  
> outcome of my investigated variable.
> for example, if my covariate of interest is race and possible outcomes  
> are white, black and hispanic, whereas the latter are minorities in my  
> case - how can i state the odds ratio in such a way that white is the  
> reference (always 1) and other races' odds ratio are relative to the  
> reference. e.g. hispanics are 1.5 times more likely to ...
> Is creating 3 binary dummies for race the right way  ? And if so how  
> can i go on.
> As i said, i know this is rather basic, i am thankful for any links /  
> references...
> thanks in advance !

Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University

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