[R] ask for help about lme function

[Bert Gunter]

The mixed models list is r-sig-mixed-models .

nlme:lme is not really designed for crossed random effects. IIRC, it's
possible, but not easy. As Kevin said, lme4:lmer is really what you should
use.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Jul 20, 2021 at 9:12 AM Kevin Thorpe <kevin.thorpe using utoronto.ca>
wrote:

> You might get better answers on the r-sig-ME list.
>
> The lmer() function from lme4 handles crossed and non-nested random
> effects quite seamlessly. I cannot comment on whether or not lme() can as
> well.
>
> --
> Kevin E. Thorpe
> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: kevin.thorpe using utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>
> > On Jul 20, 2021, at 10:32 AM, Juan Liu <21707095 using zju.edu.cn> wrote:
> >
> > EXTERNAL EMAIL:
> >
> > Dear R project,
> >
> > I am a doctoral student in Zhejiang university in China, I am using lme
> function in nlme package and learning the function by Package 'nlme'
> document. I am writing this email for some help to build a lme model.
> >
> > My goal was to include two non-nested random effects in the lme model.
> the document described how to write the random effects while I found it
> difficult for me to understand. My problem are as below:
> >
> >
> >
> >
> > In these model, site and year were considered as non nested effects. I
> want to set the structure in lme model the same as lmer model(the 1st model
> below), and I used the structure "random=list(site=~1,year=~1)"(the 2nd
> model below) . According to the result, the  lme model was obviously wrong,
> for the R2 and AIC were different from that of lmer model. I want to know
> to get the same result as lmer model, how should I set the random argument?
> >
> > Below is the model and results in R,
> >
> >
> >
> >
> > ################################################################1. lmer
> function
> > lmer<-lmer(data, y~x1+x2+x3+(1|site)+(1|year))
> > r2(lmer)##58.8%；29.7%
> > r.squaredGLMM(lmer)##58.8%; 29.72%;AIC=462.4
> > ###################################################################2.
> lme1
> > lme1<-lme(data, y~x1+x2+x3,random = list(site=~1,year=~1))
> > r2(lme1)## NA(can't get the result)
> > r.squaredGLMM(lme1)##92.4%; 30.89%;AIC=533
> >
> >
> >
> >
> > I will be appreciated for your help.
> >
> >
> >
> >
> > Yours sincerely,
> >
> > Juan Liu
> >
> > Juan Liu
> >
> > PhD candidate
> >
> > College of Life Sciences, Zhejiang University
> >
> > 866 Yuhangtang Road, Hangzhou
> >
> > Zhejiang 310058, P.R.China
> >
> > 21707095 using zju.edu.cn； liujuan_1994 using outlook.com
> >
> >
> >
> >        [[alternative HTML version deleted]]
> >
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>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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