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First of all I assumed (learned the hard way) that the real positions you posted are for the middle line.
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Analyzing weighted 5 reel drive:
Number of spins: 248832
Total line win as multiples of total bet per spin: 186200.99473494824
Scatter win: 66046.05549368466
Payout ratio: 1.0137243209419724
I guess I have it now. After experiencing problems with the scatter payout I realized that if the reels are weighted, winlines DO matter. You can't simplify the analysis to one winline any more. I try to explain it. Basically it's because the symbols are not equally likely on different positions on a reel. With other words the fact that a symbol has double weighting on reel1 at middle position means that the symbol below it will have double probability of landing on bottom position on reel1. And 5reel drive has only one payline starting from the middle position. So analyzing different individual winlines will lead to different payout, and you have to analyze all paylines.
Take the following imaginary reel segment for the first reel, x means the weighting, so if there's 12 symbols on a reel, 2x means 2/12 chance, 1x means 1/12 chance.
2x 0.2x 1x 0.1x 1x
Pie, Dice, Wheel, Scatter, Yellow truck
If that weighting is for the middle reel, than the wheel will be in middle position with 1/12 chance, at bottom position with 0.2*(1/12) chance, and at top position with 0.1*(1/12) chance. But please note that middle position on reel 1 is crossed by only one payline, but top and bottom positions are crossed by 4 paylines each. So if you only measure the middle straight payline with that weighting, you will get false results, because you calculate the wheel on reel1 on a winline with 1/12 (=0.0833) probability. In fact it is 1/12 probability on the middle straight winline, 4*(0.2)/12 probability on the bottom, and similarly 4*(0.1)/12 on the top. That means that the real probability for the Wheel being on first reel on a winline is:
(1/12 + 0.8/12 + 0.4/12)/9 ~= 0.02 instead of the above 0.0833.
I hope it was clear. After finding that out, I went back to a version of my program with all winlines, set the winlunes up for middle position weighting, and the results are much accurate I guess:
Number of spins: 248832
Total line win: 1541986.3517717584
Scatter win: 66046.05549368466
Total win as multiplies of total bet: 171331.81686352871
Payout ratio: 0.9539684299335028
But it would be still interesting to see a larger sample.
The attached file has two versions of the calculation, one with all winlines included (method analyze1), and another with only a single winline (method analyze). Furthermore I added the weights from kimss (weightreel), and a uniform weighting (weightreel1). You can easily switch between the reel weightings by exchanging their names. It's funny to see that the two methods give the same result in case of uniform reels, but differ in case of weighted reels.