I am working on similar stuff.  I use aov(), I didn't use any package.
And here's what I've been looking at
http://www.gardenersown.co.uk/Education/Lectures/R/anova.htm
http://www.personality-project.org/r/r.anova.html
HTH
On Sun, Dec 18, 2011 at 11:20 AM, David Winsemius <dwinsemius@comcast.net>wrote:

>
> On Dec 17, 2011, at 9:42 PM, Junli wrote:
>
>  Hi All,
>>
>> I am doing linear mixed model analysis for my multi-location
>> experiment using R package "lme4". I just wonder whether I should
>> check my data first to see whether they meet the three assumptions of
>> ANOVA, that is, independence,
>>
>
> Independence is not part of the data, but rather is a property that arises
> from the design and conduct of the study.
>
>
>  normality and homogeneity. I saw a lot
>> of examples and the manual of lme4, but no one did data check first.
>>
>
> Perhaps because they know more about regression than you do?
>
>
>  In my experiment, the assumption of homogeneity usually cannot be met.
>> I do not know whether it will affect the result a lot or not.
>>
>
> I'm guessing that you are talking about homogeneity of variances or
> homoschedasticity. I'm wondering how you propose to test that assumption
> _before_ you construct a model? You should refer back to your text book to
> see how this assumption was actually presented. If it tells you that one
> can check for that assumption before the model is created, then toss that
> book in the garbage.
>
> --
>
> David Winsemius, MD
> West Hartford, CT
>
>
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