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Validation of PhEq_bootstrap [Software]

posted by ElMaestro - Denmark, 2018-07-12 22:21  - Posting: # 19040
Views: 1,195

Hi Hötzi,

» Bootstrapping converges to the true value with increasing repetitions. If you want to get reproducible results you have to use a workaround and go for 25,000+ bootstraps. Then the results are stable but you have to accept ~80MB result-files…
» Of course this is only valid for these data sets (12 tablets, 4 sampling time points). Good luck with more time points.

The magnitude of the variability of the estimate is dependent on the number of bootstraps and the within- and between-variability. This is just the nature of it.

What I don't quite get is how the need for 80 Mb files (files, really???) arises. For 25000 bootstraps you should only need to allocate e.g. 25000x a double datatype (8 bytes) for the storage of f2*, which isn't even a megabyte from the heap. But note I did not care to read any of the Pascal source code. However, speed or memory consumption is a mundane issue. If the calculation is proper then no need to whine at all.

When I do this in C, I allocate 8 Mbs from the heap, and it takes a blink of an eye or two with a million bootstraps and sorting, and no intermediary files anywhere, and it provides derivation of the bootstrap CI in various flavours: Raw, bias corrected, and bias corrected and accelerated.

if (3) 4

Best regards,
ElMaestro

"(...) targeted cancer therapies will benefit fewer than 2 percent of the cancer patients they’re aimed at. That reality is often lost on consumers, who are being fed a steady diet of winning anecdotes about miracle cures." New York Times (ed.), June 9, 2018.

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