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Extend the top end of the adaptive time grid to include large values #7

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hyanwong opened this issue Sep 5, 2019 · 1 comment · May be fixed by #233
Open

Extend the top end of the adaptive time grid to include large values #7

hyanwong opened this issue Sep 5, 2019 · 1 comment · May be fixed by #233
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@hyanwong
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hyanwong commented Sep 5, 2019 •
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At the moment we do not include the quantile=1 upper value, as (for the beta distribution) this is infinite. I think this might explain why we often truncate the oldest MRCAs to be too recent. There should be a relatively easy way to extend the time grid to incorporate a higher upper bound (probably something to ask Gil about)
@hyanwong hyanwong changed the title Extend the top end of the adaptive grid to include large values Extend the top end of the adaptive time grid to include large values Sep 5, 2019
@awohns awohns added this to the Prerelease tsdate milestone Nov 1, 2019
@awohns awohns added the invalid This doesn't seem right label Nov 21, 2020
@swamidass swamidass mentioned this issue Feb 28, 2021
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hyanwong added a commit to hyanwong/tsdate that referenced this issue Jan 9, 2023
@hyanwong
Better timeslices
bb7b048 
Finally fixes tskit-dev#7 and produces a much nicer looking fit for large tree sequences, but leads to slightly worse performance for tiny tree sequences such as those tested in test_accuracy.py, because of tskit-dev#230. When we fix that, this PR should provide uniformly better performance, I hope
@hyanwong hyanwong linked a pull request Jan 9, 2023 that will close this issue
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hyanwong added a commit to hyanwong/tsdate that referenced this issue Mar 21, 2023
@hyanwong
Better timeslices
f9ed454 
Finally fixes tskit-dev#7 and produces a much nicer looking fit for large tree sequences, but leads to slightly worse performance for tiny tree sequences such as those tested in test_accuracy.py, because of tskit-dev#230. When we fix that, this PR should provide uniformly better performance, I hope
hyanwong added a commit to hyanwong/tsdate that referenced this issue Jun 14, 2023
@hyanwong
Better timeslices
748755a 
Finally fixes tskit-dev#7 and produces a much nicer looking fit for large tree sequences, but leads to slightly worse performance for tiny tree sequences such as those tested in test_accuracy.py, because of tskit-dev#230. When we fix that, this PR should provide uniformly better performance, I hope
@hyanwong
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Simple fix is in #233

hyanwong added a commit to hyanwong/tsdate that referenced this issue Jul 13, 2023
@hyanwong
Better timeslices
67756f7 
Finally fixes tskit-dev#7 and produces a much nicer looking fit for large tree sequences, but leads to slightly worse performance for tiny tree sequences such as those tested in test_accuracy.py, because of tskit-dev#230. When we fix that, this PR should provide uniformly better performance, I hope
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Better timeslices hyanwong/tsdate
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