Using censor utils in double censored observation inference #453
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Try this Pull Request!Open Julia and type: import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", rev="primary-cens-example", subdir="EpiAware")
using EpiAware |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #453 +/- ##
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+ Coverage 89.91% 90.02% +0.10%
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Files 57 57
Lines 734 742 +8
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+ Hits 660 668 +8
Misses 74 74 ☔ View full report in Codecov by Sentry. |
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seabbs
reviewed
Sep 9, 2024
seabbs
reviewed
Sep 9, 2024
seabbs
reviewed
Sep 9, 2024
seabbs
reviewed
Sep 9, 2024
seabbs
reviewed
Sep 9, 2024
seabbs
reviewed
Sep 9, 2024
seabbs
reviewed
Sep 9, 2024
seabbs
requested changes
Sep 9, 2024
I'd like to try a few quick tries at stability improvements (e.g. split up integral, look at |
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Julia versioninfoBaseline resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
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Is this ready for review? |
Not yet :-( |
3 tasks
…ithout-renewal into primary-cens-example
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@seabbs I've merged in a refactor of The Turing model using Steps
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SamuelBrand1
changed the title
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OK, this is ready for review. Its aimed at recreating the current state of https://primarycensoreddist.epinowcast.org/articles/fitting-dists-with-stan.html and it does that. It now works as well with numerical quadrature. The problem with the underlying quadrature was fixed by:
I then went carefully through the Minor changes/not-dones
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This was referenced Sep 26, 2024
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Nice. I think this should move over to |
github-merge-queue
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removed this pull request from the merge queue due to a conflict with the base branch
Benchmark resultJudge resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
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Julia versioninfoBaseline resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
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Agreed there. I had to write some custom functions to make this work which would make alot more sense in |
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This draft PR represents a first pass at using
censored_pmfinside an inference problem. The addition here is an extra notebook which follows the vignette here.Following on from numerical stability issues described epinowcast/primarycensoreddist#34 I've put together a short replication of a vignette and currently find similar/possibly worse numerical instabilities using
censored_pmf.