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1) How closely do tests match predicted results for your class/spec?
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Well, for the most part. With warriors I've only really looked at the TPS numbers and general tank theory (avoidance stacking, combat table, taunt, etc) and not so much our dps, but they match my observations.
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2) How do you go about conducting your tests?
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Not with as great an amount of rigour as I should.

I can't really be arsed to be precise for wow and so I tend to opt out of doing any detailed analysis and just do basic "is this value/hypothesis/proposed mechanic reasonable?" tests. Which basically lets me determine if a certain hypothesis is flat-out wrong, but not if its a correct mechanic or just a decent approximation in some/most situations.
For a specific example: I did some testing on Taunt back before anyone was sure how threat worked, which basically consisted about of me around with a Warlock friend in Burning Steppes and taunting mobs off the Warlock after he'd done certain amounts of damage measured by DM. I was able to conclusively determine that Taunt had a specific 4 second focusing effect and that it did something with your threat in addition, which debunked a good number of xor hypothesises for either effect floating around the eu forums at the time, but didn't really say exactly exactly what it did either. My working theory at the time - that Taunt added 2k-3k damage worth of threat - was completely false and that I at all thought it reasonable was a direct result of me being too lazy to test on mobs with a large enough amount of health to allow for extended testing.
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3) Are tests done by multiple people to insure independently good results?
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Mine are, yes. I've got good friends who play the same classes as me and share an interest in knowing the innards of the game, so it's usually painless enough to have my tests independently verified.
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4) Do you have any general purpose tricks for testing that make runs go smoothly (I realize this is very open ended, but I know I've picked up a couple, and am wondering if others have some as well).
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I'd generally advise everyone to do enough rough theorycrafting to have an idea of what to expect before trying to test any mechanic or hypothesis. Take a grab-bag of boundary conditions and assumptions, work out roughly what region your results should end up with according to current theorycraft and do some quick & dirty tests. If they're in the right ballpark, feel free to do a rigorous analysis and thorough test so you can nail down the specific questions and variables left within the theory that your initial tests said fit. If those initial tests don't match at all, however, then you just managed to catch a fundamental error in theory or in your testing methodology that would've made a mess of things if you'd tried doing detailed testing.
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5) How confident are you, if you were to start a new class, that the people doing theory crafting in the Elitist Jerks forum have "figured it all out", at least for the most part, and you could rely on that calculator?
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Very confident, really. Most of the serious theorycrafters I've seen for the warrior & druid bits are keen on exposing their data and reasoning to peer review, which tends to keep the larger threads, spreadsheets and simulators well free of major inaccuracies. I don't expect any of it to be 100% accurate and I'm sure there are plenty of smaller errors, but the results are generally sufficient to determine when a change in strategy, talents or gear is significant enough to overcome the benefits of personal preference and when it is not. Which is about all I need.