Fix the replication note and turn it into a full replication #442
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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="fix-mishra-note", subdir="EpiAware")
using EpiAware |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #442 +/- ##
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Coverage 89.72% 89.72%
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Files 56 56
Lines 720 720
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Hits 646 646
Misses 74 74 ☔ View full report in Codecov by Sentry. |
Benchmark resultJudge resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
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ResultsBelow is a table of this job's results, obtained by running the benchmarks.
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Julia versioninfoBaseline resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
ResultsBelow is a table of this job's results, obtained by running the benchmarks.
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We had strong priors on the AR parameters in the wrong order (which strongly effects the prior variance of the process etc). Obviously, I could have just swapped them (as well as the other changes) but that felt silly because we'd have just had to swap back after #441. |
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I'm still a bit uncomfortable about #441. I know its annoying but any chance we can decouple? |
Yeah, sure. Probably easiest to wait until we've decided what we want with |
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I was thinking we would rebase this on main but maybe not if its too painful |
SamuelBrand1
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Ok, I |
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ty - sorry for being a pain |
seabbs
approved these changes
Aug 29, 2024
seabbs
previously approved these changes
Aug 29, 2024
Benchmark resultJudge resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
ResultsA ratio greater than
Benchmark Group ListHere's a list of all the benchmark groups executed by this job:
Julia versioninfoTargetBaselineTarget resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
ResultsBelow is a table of this job's results, obtained by running the benchmarks.
Benchmark Group ListHere's a list of all the benchmark groups executed by this job:
Julia versioninfoBaseline resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
ResultsBelow is a table of this job's results, obtained by running the benchmarks.
Benchmark Group ListHere's a list of all the benchmark groups executed by this job:
Julia versioninfoRuntime information
|
seabbs
approved these changes
Aug 29, 2024
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This PR builds on #441 as well as rewriting the Mishra et al replication note to fully replicate that pre-print.
In doing this I think it became clear that the structure of the model makes it hard to identify the AR process std parameter (the other parameters have strong priors) from the neg bin observation cluster factor. In the preprint no prior for neg bin was found (apols if I missed it!). Therefore, I demonstrated conditioning the value and running the inference on the model with conditioned cluster factor.
Closes #435 and #420.