[OFF] Nested or not nested, this is the question.

Hi,

sorry by this off.

I'm still try to understand nested design.

I have the follow example (fiction):

I have 12 plots in 4 sizes in 3 replicates (4*3 = 12)
In each plot I put 2 species (A and B) to reproduce.
After a period I make samples in each board and count the number of 
individuals total (tot) and individuals A and B (nsp). Others individuals 
excepts A and B are in total of individuals.

This make a dataset with the 24 lines and not 12. Its smell pseudoreplication 
in a nested design, OK?

I need to know:

the species are different in proportion?

the size affect the species's proportion?

existe interaction between size and species?

I make the analysis.

m.lme <- lme(nsp/tot~size*specie,random=~1|size/specie)
anova(m.lme)

numDF denDF  F-value p-value
(Intercept)     1    16 374.7121  <.0001
size            1     2  37.8683  0.0254
specie          1     2  18.2036  0.0508
size:specie     1     2   9.3203  0.0926

This is the correct mean to make this analysis?

or

m.lme <- lme(nsp/tot~size*specie,random=~1|plot/specie)
anova(m.lme)

numDF denDF  F-value p-value
(Intercept)     1    10 579.8853  <.0001
size            1    10  58.6030  <.0001
specie          1    10  59.5235  <.0001
size:specie     1    10  30.4760   3e-04

or neither?

I know about the distribution (binomial in this case), but I try to understand 
the nested design.

Thanks for any help.

The dataset is:

   plot size specie nsp tot
1     1   10      A   2  20
2     1   10      B   6  20
3     5   10      A   3  20
4     5   10      B   5  20
5     9   10      A   1  20
6     9   10      B   4  20
7     2   20      A   5  20
8     2   20      B   8  20
9     6   20      A   6  20
10    6   20      B   9  20
11   10   20      A   4  20
12   10   20      B   6  20
13    3   30      A   8  20
14    3   30      B   9  20
15    7   30      A   9  20
16    7   30      B  10  20
17   11   30      A   7  20
18   11   30      B   8  20
19    4   40      A  10  20
20    4   40      B   9  20
21    8   40      A   9  20
22    8   40      B  10  20
23   12   40      A   9  20
24   12   40      B   9  20

Great minds run in great circles.
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