Mukta Chakraborty <chakraborty.mukta <at> gmail.com> writes:
>
> Hello,
> I am trying to run a mixed effects nested ANOVA but none of my codes
> are giving me any meaningful results and I am not sure what I am doing
> wrong. I am a new user on R and would appreciate some help.
> The experimental design is that I have some frogs that have been
> exposed to three acoustic Treatments and I am measuring neural
> activity (egr), in 12 brain regions. Some frogs also called different
> calls than others so I am testing for effect of Call as a fixed
> effect.
> I have Treatment (Trt), Brain Region (Region), and Call (Call) as
> fixed effects and I am modeling Subject (Subj) as a random effect with
> brain region nested within subject. I am using lme4 package and I am
> not sure if that is the correct one to use.
> I also have some missing values as NA as part of the dataset. I have
> also set Subj, Region, and Call as factors using as.factor.
> I have run the model which I am sure is wrong:
> model1<-anova(lme(egr ~ Trt* Region, random=~1|Subj/Region,na.action=na.omit))
>
> The output I am getting is:
> numDF denDF F-value p-value
> Min. : 1.00 Min. : 32 Min. : 2.891 Min. :0.000e+00
> 1st Qu.: 1.75 1st Qu.:197 1st Qu.: 12.120 1st Qu.:0.000e+00
> Median : 6.50 Median :252 Median : 20.275 Median :1.146e-05
> Mean : 9.00 Mean :197 Mean : 87.353 Mean :1.383e-05
> 3rd Qu.:13.75 3rd Qu.:252 3rd Qu.: 95.508 3rd Qu.:2.530e-05
> Max. :22.00 Max. :252 Max. :305.972 Max. :3.240e-05
>
> Any help on what I am doing wrong on the coding would be very helpful.
> Thanks a lot.
> Mukta
1. it would probably be a good idea to ask further questions on this
topic on r-sig-mixed-models instead.
2. you probably want to look just at the lme() result, and not immediately
wrap it an anova() frame. I'm a little surprised by your results -- but
since you haven't given a reproducible example I don't know exactly
what's wrong. When I run the lme example in the nlme package and
then do
> anova(fm1)
I get
numDF denDF F-value p-value
(Intercept) 1 80 3096.4889 <.0001
age 1 80 85.8464 <.0001
which doesn't look like your answer.
3. I don't think you want to use Region as both a random factor and
a fixed factor. I would have guessed either
lme(egr ~ Trt*Call, random=~1|Subj/Region,na.action=na.omit))
OR
lme(egr ~ Trt*Call*Region, random=~1|Subj,na.action=na.omit))
I can also imagine that you might be interested in a crossed
design in this case, in which case you should probably use lme4:
library(lme4)
lmer(egr~Trt*Call+(1|Subj)+(1|Region) ...)
[I'm not sure how na.action works for lmer]
good luck
Ben Bolker
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