Re: [R] Residuals from GLMMs in the lme4 package

From: Renaud Lancelot <renaud.lancelot_at_gmail.com>
Date: Fri 09 Dec 2005 - 23:29:44 EST

I guess you are using obsolete versions of lme4 / Matrix. Please update and try again. The current versions are:

> help(package = "Matrix")

                Information on package 'Matrix'

Description:

Package:              Matrix
Version:              0.99-2
Date:                 2005-11-14

[snip]

> help(package = "lme4")

                Information on package 'lme4'

Description:

Package:       lme4
Version:       0.98-1
Date:          2005-07-27

[snip]

Best,

Renaud

2005/12/9, Mairead Maclean <M.M.Maclean@exeter.ac.uk>:
> Hello there
>
> This is the first time I have used r-help message board so I hope I have got
> the right address.
>
> I am trying to check the residuals of a GLMM model(run using the package
> lme4). I have been able to check the residiuals of REMLs in lme4 using the
> following:
>
> m1<-lmer(vTotal~Week+fCollar+ (1|fCat), collars)
>
> res<-resid(m1)
> plot(res)
> qqnorm(res)
> library(MASS)
> par(mfrow=c(2,3))
> res<-residuals(m1)
> truehist(res,main="Histogram of Residuals")
> curve(dnorm(x,mean=mean(res),sd=sd(res)),add=TRUE)
> qqnorm(fitted(m1),resid(m1), ylim=range(fitted(m1)), main="QQNorm Plot")
> plot(residuals(m1)~fitted(m1),main="Resid
> vs.Fits",xlab="Fits",ylab="Resids");abline(h=0)
> plot(residuals(m1),type="l",main="Resid vs Order",ylab="Resids")
> acf(residuals(m1), main="Resid Autocorrelation")
> boxplot(vTotal~fCollar, data=collars,main="Box plot of Collars", ylab="No.of
> Prey", xlab="Collar")
>
> but with this model:
>
> m1<-lmer(vTotal~Week+fCollar+ (1|fCat), collars, poisson(), method = "PQL")
>
> I can not get the above code line for residuals to work. The stumbling
> block is the residual command. When I run it I get the following:
> > res<-resid(m1)
> > res
> numeric(0)
>
> Can not find any other way to get the residuals and I even tried getting the
> fitted values from the model but get a similar output:
>
> > catfit<-fitted(m1)
> > catfit
> numeric(0)
>
> Do you think there may be something wrong with the model itself or is it
> just that there is an alternative way to checking residuals in GLMMs? I
> would be very grateful for any help!
>
> Many thanks
>
> Mairead Maclean
> Centre for Ecology and Conservation Biology
> Exeter University
> Tremough Campus
> CORNWALL
> UK
> TR10 9EZ
>
> ______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

--
Renaud LANCELOT
Département Elevage et Médecine Vétérinaire (EMVT) du CIRAD
Directeur adjoint chargé des affaires scientifiques

CIRAD, Animal Production and Veterinary Medicine Department
Deputy director for scientific affairs

Campus international de Baillarguet
TA 30 / B (Bât. B, Bur. 214)
34398 Montpellier Cedex 5 - France
Tél   +33 (0)4 67 59 37 17
Secr. +33 (0)4 67 59 39 04
Fax   +33 (0)4 67 59 37 95

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Received on Fri Dec 09 23:43:20 2005

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