[R] Understanding lm-based analysis of fractional factorial experiments

[Kjetil Kjernsmo]

On Wednesday 6. March 2013 16.33.34 Peter Claussen wrote:
> But you don't have enough data points to estimate all of the possible
> interactions; that's why you have NA in your original results.

Yes, but it seems to me that lm is doing the right thing, or at least the 
expected thing, here, the NA's are simply telling me these are aliased, which 
is correct and expected.

> You could
> add the just the first order interactions manually, i.e.,  + B:C + B:D …

Yeah, I tried that, but then it returns to the "unexpected" result, i.e., I 
get the same result as with the yavg ~ B * C * D * E * Q formula. Therefore, I 
think the problem doesn't lie with the formula, nor does it lie with any of 
the code, it is just a matter of understanding defaults...

I have consulted local help (of course), but what they say is that "R has some 
odd defaults, you need to ask them or use something different". I don't want to 
use something different, I like R, I have contributed to R in the past and will 
do so again if only I can get my head around this... :-)

Kjetil