Hi Lara,
As Gavin said, aov, lm, and glm are all fitting exactly the same model
(when using the defaults for each), you are just getting different
information from the default summary commands.
If you want "type III" SS for your ANOVA table, use the command
Anova(model, type = 3) inside the 'carr' package. (It will also provide
"type II" SS if you want them). The default for aov() or anova() is the
"type I" SS table. Contrary to what often appears in Google searches,
using drop1() will *not* give you the "type III" SS -- those are more
like "type II", in that R follows the marginality principle and keeps
interaction terms last. As Chris said, you're on your own to decide
which of those SS flavors you want.
However, since you mention you're using clutch size as the response, I'm
skeptical that any of the options you are using is appropriate. Clutch
size is probable better modeled with a discrete distribution such as
Poisson or negative binomial, not a normal distribution. You should
probably consider a GLM with Poisson distribution, check for
overdispersion, and then ask for more help if you've got overdispersion
problems.
-Brian Inouye
On 11/11/2011 6:00 AM, [email protected] wrote:
> On 11/11/2011, at 10:25, "Lara R. Appleby 04"
> <[email protected]> wrote:
>
>> I'm trying to basically do a two way ANOVA on the dependent variable
(clutchsize)
>> with the two independent variables (treatment and species). It seems that
there
>> are three ways I can say this in R:
>>
>> 1. glm(clutchsize~treatment*species)
>> 2. aov(clutchsize~treatment*species)
>> 3. anova(lm(clutchsize~treatment*species)
>>
>> Methods 2 and 3 yield equivalent results, but Method 1 is completely
different!
>>
>> Any idea why?
>>
>> Lara Appleby
>>
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