[R] residual plots for lmer in lme4 package

[Martin Henry H. Stevens]

Hi Margaret,
Have a look at qqmath in the lattice package.
?qqmath
Hank
On Aug 16, 2007, at 2:45 AM, Margaret Gardiner-Garden wrote:

> Hi,
>
>
>
> I was wondering if I might be able to ask some advice about doing  
> residual
> plots for the lmer function in the lme4 package.
>
>
>
> Our group's aim is to find if the expression staining of a  
> particular gene
> in a sample (or "core")  is related to the pathology of the core.
>
> To do this, we used the lmer function to perform a logistic mixed  
> model
> below.  I apologise in advance for the lack of subscripts.
>
>
>
>  logit P(yij=1) = â0 + Ui + â1Patholij where Ui~N(0, óu2),
>
> i indexes patient, j indexes measurement, Pathol is an indicator  
> variable
> (0,1) for benign
>
> epithelium versus cancer and yij is the staining indicator (0,1)  
> for each
> core where yij equals 1 if the core stains positive and 0 otherwise.
>
>
>
> (I have inserted some example R code at the end of this message)
>
>
>
> I was wondering if you knew how I could test that the errors Ui are  
> normally
> distributed in my fit.  I am not familiar with how to do residual  
> plots for
> a mixed logistic regression (or even for any logistic regression!).
>
>
>
> Any advice would be greatly appreciated!
>
>
>
> Thanks and Regards
>
> Marg
>
>
>
> Example code:
>
>
>
> lmer(Intensity.over2.hyp.canc~Pathology + (1|Patient.ID), data=
> HSD17beta4.hyp.canc, family="binomial", na.action="na.omit")
>
>
>
>
>
>
>
>     #Family: binomial(logit link)
>
>      #    AIC      BIC    logLik deviance
>
>    # 414.1101 431.4147 -203.0550 406.1101
>
>    #Random effects:
>
>    #     Groups        Name    Variance    Std.Dev.
>
>    # Patient.ID (Intercept)      4.9558      2.2262
>
>    # of obs: 559, groups: Patient.ID, 177
>
>
>
>    #Estimated scale (compare to 1)  0.6782544
>
>
>
>    #Fixed effects:
>
>     #                    Estimate Std. Error z value  Pr(>|z|)
>
>    #(Intercept)          -2.05734    0.24881 -8.2686 < 2.2e-16 ***
>
>    #PathologyHyperplasia -1.76627    0.44909 -3.9330 8.389e-05 ***
>
>
>
> NB. Intensity.over2.hyp.canc is the staining of the core (ie 0 or 1)
>
> Pathology is Hyperplasia or Cancer
>
>
>
>
>
> Dr Margaret Gardiner-Garden
>
> Garvan Institute of Medical Research
>
> 384 Victoria Street
>
> Darlinghurst Sydney
>
> NSW 2010 Australia
>
>
>
> Phone: 61 2 9295 8348
>
> Fax: 61 2 9295 8321
>
>
>
>
>
>
>         [[alternative HTML version deleted]]
>
> <ATT00001>

Dr. Hank Stevens, Associate Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056

Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
http://www.cas.muohio.edu/~stevenmh/
http://www.muohio.edu/ecology/
http://www.muohio.edu/botany/
"E Pluribus Unum"

If you send an attachment, please try to send it in a format anyone  
can read, such as PDF, text, Open Document Format, HTML, or RTF.  
Please try not to send me MS Word or PowerPoint attachments-
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html