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The while loop in simplify.R takes a long time with large data sets. It seems to iterate from one end of the list to close to the minimum threshold.
Line 162 in 08d1103
| while(min(pct) < pct_thr && length(pct) > k_thr) { |
I don't entirely follow the code at the moment but if min(pct) always decreases monotonically then one can use a binary search to reduce the number of calculations. This will work in O(log n) time instead of O(n), on average.
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