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I have only two of the smaller pens covered, one just so the bantams can't fly out, the other because it used to be their coop and now belongs to the old hens. My other pens are mostly too large to cover. And my birds do free range on a rotating basis as well. If birds are penned, they are more likely to be killed by predators if the pen is unstable as far as the wire used because they simply cannot get away nor can they really hide as they could free ranging. So, penned flocks do need predator proof but well-ventilated coops. As long as the fencing is tall and strong and they are all put inside before dusk, all should be well, generally. No one said there was anything intrinsically wrong with Toby's coop, just suggested how to make it more predator proof and that it might need some ventilation-tweaking.
I've seen coops made from the neatest things! They are on our coop pages. Same rules apply for ventilation for healthy birds, no matter what they are made from.