[R-lang] question about model interpretation using lmer

[Austin Frank]

On Wed, Apr 23 2008, Schack Tang, Katie wrote:

> Hi,
>
> I have a question about interpreting a mixed effects model.  I am
> modeling median F0 on a vowel based on a variety of factors.  The one
> I am concerned with here, PrecedingSegment, has 6 levels.  I give the
> R output from a lmer function below.
>
> PrecSegment(none)	-1.716815	4.3652	0.393
> PrecSegment(son)	  3.488424	0.919801	3.793
> PrecSegment(vce)  	0.745261	0.948666	0.786
> PrecSegment(vceless)	7.233391	0.928507	7.79
> PrecSegment(vowel)	8.319552	4.782556	1.74
>
> The withheld value is implosive.
>
> I have two questions:
>
> 1) Does the fact that voiced (vce) fails to reach significance on its
>    own indicate that its effect on F0 is not significantly different
>    from the effect of an implosive on F0?

Assuming you're using the default contrasts (contr.treatment), then yes,
this is the correct interpretation.  If you change to sum-to-zero
contrasts (contr.sum), then you'd be comparing each level to the mean.
You can change which contrast coding scheme is used by

--8<---------------cut here---------------start------------->8---
options(contrasts=c("contr.sum", "contr.poly"))
--8<---------------cut here---------------end--------------->8---

The first element of the vector defines which contrasts to use for
unordered factors, the second is for ordered factors.

> 2) What can I conclude about the sonorant (son) and voiceless
>    (vceless)?  Can I just conclude that they both raise F0 compared to
>    implosives?

You can conclude this.

> Or can I also conclude that voiceless raises F0 more than sonorant
> does?

You cannot conclude this.

> If the former, how can I test the latter?

I have recently seen a recommendation for the method glht from the
package Multcomp.  I haven't used it myself.  If you use it, please
report back and let us know if it's useful!

> is it possible to specify which level of a factor is withheld in lmer?

Sure.  This

--8<---------------cut here---------------start------------->8---
data$factor1 <- relevel(data$factor1, ref="none")
--8<---------------cut here---------------end--------------->8---

will change the factor so that the level coded as "none" is the
reference level.  If you care about the ordering of the levels (this can
be important for graphing the results, for example), you can try

--8<---------------cut here---------------start------------->8---
data$factor1 <- factor(data$factor1,
                       levels=c("none", "vowel", "vce", "vceless", "son"))
--8<---------------cut here---------------end--------------->8---

This will place the levels of the factor in that specific order.  If you
don't do this, R defaults to ordering the levels of the factor
alphabetically.  Even if you use relevel(), R will still order the
remaining levels alphabetically.

HTH,
/au

-- 
Austin Frank
http://aufrank.net
GPG Public Key (D7398C2F): http://aufrank.net/personal.asc
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