[R] Interpretation of lme results with intercorrelation between fixed factors

[Vasillis Papathanasiou]

I’m running a mixed model analysis with 2 fixed factors that are intercorrelated using the lme function and I’m having difficulties in interpreting the results.
As I’m quite novice I’ll try to use a very simple example.

My model is lme(Y~A*B). A has 3 levels (1, 2 and 3) and B has 2 levels (I and II).
My results are something like this:



P statistic

B:II

P=0.01

A:2

P=0.01

A:3

P=0.09

II*2

P=0.61

II*3

P=0.031


My question is as follows. I understand that R keeps a level of each factor and reports any statistical differences to it. So in this example it reports that II is different than I and 2 against 3. However when it comes to the intercorrelation, what does it report? Does it compare II*2 and II*3 to II*1 and if so what happens with I*2 and I*3? Or does it compare II*2 to I*2 and II*3 to I*3 and if so what happens to I*1 and II*1?

Thank you


Vasillis


	[[alternative HTML version deleted]]