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Vaniver comments on Open thread, Jan. 18 - Jan. 24, 2016 - Less Wrong
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Temple Grandin has some work that's relevant, and argues for quantitative measures. One of the easy metrics to use now are bodily integrity things, like the percentage of animals who are lame when they make it to the slaughterhouse. A lame animal is unlikely to be a happy or well-treated animal, and it seems easy to measure and compare.
She's also done work on what animals are willing to take some trouble to get-- chickens apparently care more about having a secluded place to lay eggs than they care about getting outside.