One way to deal with this is to employ a phase design:
AB
ABA
ABAB
where 'A' is baseline and 'B' is your treatment (x).
These types of design are very useful as the allow you to return to baseline to ensure that any effects of treatment are not due to uncontrolled factors. Also, you can randomize the order of 'A' and 'B' between the different enclosures:
Week 1 | Week
2 |
Week
3 |
Week
4 |
|
Farm
1 |
A |
B |
A |
B |
Farm
2 |
B |
A |
B |
A |
Farm
3 |
A |
B |
A |
B |
If you sample animals from a small number of farms (2 or 3, for example), you could treat farm as a variable and use it in the analysis to see if there are any systematic differences evident. If you are sampling from many farms, it may be possible to treat farm as a random effect - we will deal with this in the data analysis sections.