[R-sig-ME] extracting residuals in lmer glmm
Douglas Bates
bates at stat.wisc.edu
Sat Aug 16 11:04:26 CEST 2008
On Thu, Aug 14, 2008 at 9:47 AM, Hank Stevens <HStevens at muohio.edu> wrote:
> In answer (sort of) to my own question, resid() now works on both mer and
> summary.mer objects.
> All of these results (resid() working and not working) have occurred while
> using yesterday's CRAN version of lme4 {R package version 0.999375-24}.
> I have no idea what would have caused the problem yesterday and this
> morning, but not now. Oh well.
I was just going to write that you must be using a very old version of
the lme4 package. The wrkres slot was removed in the transition from
the 0.99875 to 0.999375 series.
What is returned by the resid generic applied to a generalized linear
mixed model is
(m1 at y - m1 at mu)/sqrt(m1 at var)
That is one of the many possible definitions of "residuals" for a
generalized linear model. There is a name for those residuals but I
can't remember right now what they are callled - perhaps after I have
recovered from the trans-Atlantic flight returning from the useR!2008
conference, which was wonderful. Thanks again to the organizers and
to the more than 400 attendees who made it such a success. We hope to
see many of you again in Rennes, France for useR!2009 next July.
>
> Hank
>
>
> y <- rpois(100, lambda=10)
> xz <- expand.grid(x=gl(2,5), z=gl(10,1))
> m1 <- lmer(y ~ x + (1|z), xz, family="poisson")
> m1s <- summary(m1)
> resid(m1)
> [1] -0.04336 -0.98556 0.89885 0.27071 -0.67149 -0.14260
> ...
> resid(m1s)
> [1] -0.04336 -0.98556 0.89885 0.27071 -0.67149 -0.14260
> ...
>
> On Aug 14, 2008, at 9:32 AM, Martin Henry H. Stevens wrote:
>
>> Hi folks,
>> I seem unable to figure out how to extract residuals from a Poisson
>> lmer model.
>>
>> And, I am not sure what to do with the working residuals.
>>
>> Any references or ideas would be appreciated.
>>
>> # Example:
>> y <- rpois(100, lambda=10)
>> xz <- expand.grid(x=gl(2,5), z=gl(10,1))
>> m1 <- lmer(y ~ x + (1|z), xz, family="poisson")
>>
>> resid(m1)
>> Error: 'resid' is not implemented yet
>>
>> residuals(m1)
>> Error: 'residuals' is not implemented yet
>>
>> summary(m1 @ wrkres)
>> Min. 1st Qu. Median Mean 3rd Qu. Max.
>> 1.38 1.98 2.20 2.22 2.50 3.13
>>
>>
>> Hank Stevens
>>
>>
>>
>>
>
>
>
> Dr. Hank Stevens, Associate Professor
> 338 Pearson Hall
> Botany Department
> Miami University
> Oxford, OH 45056
>
> Office: (513) 529-4206
> Lab: (513) 529-4262
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> http://www.cas.muohio.edu/~stevenmh/
> http://www.cas.muohio.edu/ecology
> http://www.muohio.edu/botany/
>
> "If the stars should appear one night in a thousand years, how would men
> believe and adore." -Ralph Waldo Emerson, writer and philosopher (1803-1882)
>
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