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I just purchased pio today and it struck me that I don't put in stack depth in the format of big blinds, only effective stacks and starting pot. Does not pio care about how many blinds deep I am?
Yes, it doesn't matter how many blinds that is. Starting pot and effective stacks are enough.
Please notice though that for example if BTN raises to 3bb in a 6max 100b game, SB folds and BB calls the starting pot/stacks combo is 65/970 at 5/10 blinds but 13/194 at 1/2 game. It's only stacks/pot ratio that matters for the solution.
If you are accustomed to thinking in blinds instead of chips you can just always use 5/10 or 50/100 blinds and read it as 10 = 1bb or 100 = bb.
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If you solve a spot over lets say 72 preset flops and then later you solve a few more flops same scenario, the new flops won't have any weights towards them. Will that skew the results of the Runouts aggregated frequencies analysis?
The aggregation report reads the weights from the script file. It also displays the list of all flops with weights before it's run so you can verify what kind of weight new flops have or if they are included as well. I am not 100% sure if they are included or not in current implementation. If that's important information for you and you can't get it from looking at the list of flops before running the report let me know and I will ask juggler97531 on 2p2 (PioViewer developer) how it works exactly.
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If we add 5 more flops will it not matter much, but if we add another say 36 flops will it make a big difference?
If they are included in the report they will almost surely make results worse.