bootf2bca v1.2 [Software]

posted by Helmut Homepage – Vienna, Austria, 2019-10-04 22:59  – Posting: # 20665
Views: 631

Dear all,

we discussed the code at BioBridges…

The problem with reproducibility can easily be solved.
In F2_boot.R after line 270 #main algorithm add e.g., set.seed(123456).

» Be warned: The source code is hard to read, nearly no comments at all.

The current version 1.2 is a little bit better. Still heavy stuff.

The cut-off preferred by the EMA is implemented:

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Don’t get confused by Q>=85%. Actually it is the correct >85%. Still missing: one value >85% for the test (FDA) and one value >85% for the reference (WHO).

» Be further warned: If you rise the number of bootstrap samples (default is 1000, too low IMHO) the result file will contain a huge number of entries, each bootstrap sample is recorded! The same mess as in the 'Object Pascal' implementation. But could of course also changed with a little knowledge of R.

Hint: In F2_boot.R comment out the loop in lines 317-329. Then the report-file shrinks from a couple of megabytes to some kilobytes. I would keep the rest for documentation. Useful to read the bootstrapped ƒ2 values from the file and generate your own histogram (density instead of counts). I don’t like the one of plotly. Way too many bins for my taste (here an example with 5,000 bootstraps).

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I prefer [image] Freed­man–Dia­conis* and show additionally the median and 90% CI.

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Cheers,
Helmut Schütz
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