From: Joshua Wiley <jwiley.psych_at_gmail.com>

Date: Mon, 11 Apr 2011 10:36:11 -0700

Date: Mon, 11 Apr 2011 10:36:11 -0700

Hi Elizabeth,

On Mon, Apr 11, 2011 at 9:59 AM, Elizabeth Pringle
<epringle_at_stanford.edu> wrote:

*> Hi,
**>
**> I have a dataset that I am trying to analyze and plot as an ordered logistic
**> regression (y = ordinal categories 1-3, x = continuous variable with values
**> 3-9).
**>
**> First is a problem with cdplot:
**> Produces a beautiful plot, with the "right" trend, but my independent factor
**> values are transformed. The factor has values from 3-9, but the plot
**> produces an x-axis with values from 20-140. When I force the xlim to be
**> 3-9, it produces a plot without the trend, which can't be correct.
*

This is difficult to really help with without some data (we do not have LogAntDensity). Certainly, if the graph shows values form 20 - 140, it makes sense that if you then force the range to be from 3 - 9, you do not see anything. The problem is not range, it is data/setup.

*>
**> Second is a problem with polr:
**> The output of the summary command of the model built with polr includes t
**> values for lots (if not all) of my independent factor values, but does not
**> produce a summary of the fit of the model or of the overall fit of the
**> factor. Also, intercepts are different from those produced with a logistic
**> fit in JMP...
*

Does it not output the Residual Deviance and AIC? Those relate to model fit. Two models can be compared using anova(m1, m2), so to compare the overall effect of a factor or multiple factors, just fit and compare two separate models.

*>
**> Code below, any help much appreciated.
**>
**> Thanks
**> Beth
**>
**> LogAntDensityFactor<-as.factor(LogAntDensity)
**>
**>
**> ###order ordinal variable
**>
**> HammerCatOrd<-ordered(HammerCat)
**>
**>
**> ###set ordered ordinal dependent variable as factor
**>
**> HammerCatOrdFactor<-as.factor(HammerCatOrd)
*

This is repetivie. ordered() makes a factor, and you could do the same with:

factor(HammerCat, ordered = TRUE)

Another note/commet, cdplot() and polr() have formula methods and can access data from a data frame elegantly. It would be better to keep all your data bundled together in a data frame, than have different variables in various stages of transformation but with similar names floating around. This may not be true, but wildly unexpected values almost sounds like a typo may have happened at some point either in using the name in cdplot OR in assigning data to the variable initially.

*>
**> ###density plot with three levels
**>
**> cdplot(HammerCatOrdFactor~LogAntDensityFactor,xlab="Log(Ant
**> Density)",ylab="Latency
**> of response to disturbance (1-3)")
*

What does str(HammerCatOrdFactor) or summary(HammerCatOrdFactor) (and ditto for LogAntDensityFactor) give? My guess is you will find they are not quite what you thought they were.

*>
**> require(MASS)
**>
**> logordered<-polr(HammerCatOrdFactor~LogAntDensityFactor,Hess=TRUE)
*

Side note, why is LogAntDensity a factor? or do you mean factor in a vernacular sense not in a technical is.factor(LogAntDensityFactor) sense? If LogAntDensityFactor is your only other term in the model, an example comparison could be:

lognull <- polr(HammerCatOrdFactor ~ 1, Hess=TRUE) logordered <- polr(HammerCatOrdFactor ~ LogAntDensityFactor, Hess=TRUE)

anova(lognull, logordered)

Cheers,

Josh

*>
**> summary(logordered,digits=3)
**>
*

> [[alternative HTML version deleted]]

Plain text emails are preferred.

> ______________________________________________

*> 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.
*

-- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.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.Received on Mon 11 Apr 2011 - 17:42:20 GMT

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