[R-sig-ME] Difficulties in trying to do a mixed effects model using the lmer function
Riedel Judith
judith.riedel at ipw.agrl.ethz.ch
Thu Oct 4 11:41:17 CEST 2012
Dear people of the help list
I am drying to analyze my data using the 'lmer' function and I keep having problems.
This is the model:
> fm1<-lmer(dbh~spec+scheme+(1|Plot),data=d, REML=FALSE).
I analyse tree size (dbh) of 3 different species (spec) and 3 planting schemes (scheme). I have 5 plots, which I hope to model as a random factor. (However, the subsequent output is based on some simplified dummy data, which is based on only two plots and ha only few observations).
No I do:
> anova(fm1)
and I get some output, which I don't understand. Looks like this:
Analysis of Variance Table
Df Sum Sq Mean Sq F value
spec 2 6.098 3.0490 0.6142
scheme 2 13.161 6.5803 1.3255
The problems I have are:
(1) How can I get the P-values?
(2) How can I get the overall model statistic?
Than I do:
> summary(fm1)
and get:
Linear mixed model fit by maximum likelihood
Formula: dbh ~ spec + scheme + (1 | Plot)
Data: d
AIC BIC logLik deviance REMLdev
147.2 157 -66.6 133.2 125.8
Random effects:
Groups Name Variance Std.Dev.
Plot (Intercept) 0.0000 0.0000
Residual 4.9644 2.2281
Number of obs: 30, groups: Plot, 2
Fixed effects:
Estimate Std. Error t value
(Intercept) 6.9074 0.9424 7.329
specCED 0.3859 1.0265 0.376
specTAB 0.8585 0.9828 0.874
schemeMON 0.6572 0.9554 0.688
schemePRO -1.0344 1.1259 -0.919
Correlation of Fixed Effects:
(Intr) spcCED spcTAB schMON
specCED -0.537
specTAB -0.529 0.500
schemeMON -0.588 0.002 -0.072
schemePRO -0.565 0.064 0.063 0.510
What is this? What does it tell me?
The statistics help advised me to do a second model, like this:
> fm2<-lmer(dbh~scheme+(1|Plot),data=d,REML=FALSE)
> anova(fm1,fm2)
But why would I compare the two models?
What I get is:
Data: d
Models:
fm2: dbh ~ scheme + (1 | Plot)
fm1: dbh ~ spec + scheme + (1 | Plot)
Df AIC BIC logLik Chisq Chi Df Pr(>Chisq)
fm2 5 143.96 150.97 -66.982
fm1 7 147.21 157.01 -66.602 0.7584 2 0.6844
What does this mean? Why Chi?
Finally I would like to do some LSD post hoc tests, but I have no idea how to do it.
In the end I would like to be able to report something like: 'DBH differed significantly between, species, planting schemes, and plots (Fx,xx = X; P = X). DBH of species 1 was significantly larger than DBH of species 2 (LSD post hoc test, P = X)'.
I greatly appreciate any suggestions! Thank You a lot for Your help!
Kind regards,
Judith
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Judith Riedel
ETH Zurich
Institute of Agricultural Sciences
Applied Entomology
Schmelzbergstrasse 9/LFO
8092 Zurich
Switzerland
Tel: ++41 44 632 3923
Fax: ++41 44 632 1171
judith.riedel at ipw.agrl.ethz.ch<mailto:judith.riedel at ipw.agrl.ethz.ch>
http://www.em.ipw.agrl.ethz.ch
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