Hi All,

I am frustrated by mixed-effects model! I have searched the web for 
hours, and found lots on the nested anova, but nothing useful on my 
specific case, which is: a random factor (C) is nested within one of the 
fixed-factors (A), and a second fixed factor (B) is crossed with the 
first fixed factor:

C/A

A

B

A x B

My question: I have a functioning model using the aov command (see 
below), and I would now would like to recode it, using a more flexible 
command such as lme or lmer. Once I have the equivalent syntax down, I 
would ideally like to re-run my analysis using "family = poisson", as CO 
is actually count data.

I have a dataset including a response variable CO, measured once per 
Week (for 11 weeks) at 13 Locations. The 13 Locations are divided into 2 
habitat types (Control and Treatment).

Thus:

CO is a continuous response variable,

Week is a fixed categorical factor,

Habitat is a fixed categorical factor, and

Location is a random categorical factor nested within Habitat.

Here is my model in R:

mCO = aov(CO ~ Week * Habitat + Error(Location/Week))

summary(mCO)

And the output:

Error: Location

           Df Sum Sq Mean Sq F value   Pr(>F)   

Habitat     1 182566   182566   8.6519 0.01341 *

Residuals 11 232115    21101                   

  

Error: Location:Week

              Df Sum Sq Mean Sq F value     Pr(>F)     

Week          10 596431    59643 11.0534    7.5e-13 ***

Week:Habitat 10 196349    19635   3.6389 0.0003251 ***

Residuals    110 593551     5396                       

Given that this is a mixed model, I believe the appropriate error terms 
are as follows:

For the F test of Habitat, the denominator MS is that for location/habitat;

For the F test of Week, the denominator MS is the residual; and

For the F test of Habitat x Week, the denominator MS is the residual.

My tinkering with lmer and lme have not produced results similar to the 
above

For example,

m. = lmer(CO ~ Week * Habitat + (1|Habitat/Location))

anova(m.)

produces:

Analysis of Variance Table

               Df Sum Sq Mean Sq F value

Week           10 596431    59643 11.0534

Habitat        1   28652    28652   5.3100

Week:Habitat 10 196349    19635   3.6389

Any coding advice would be greatly appreciated!

Thanks for your consideration,

Dave Robichaud


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