Change transformation for Renewal model in test suite #491
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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-ci-fail", subdir="EpiAware")
using EpiAware |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #491 +/- ##
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- Coverage 90.02% 89.56% -0.47%
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Files 57 51 -6
Lines 742 738 -4
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- Hits 668 661 -7
- Misses 74 77 +3 ☔ View full report in Codecov by Sentry. |
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
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From f2f I think the conclusion was not to do this and instead solve issue elsewhere in the package? |
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but to pin the link function as a future research question |
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actually maybe we do need this as well for now? |
seabbs
approved these changes
Oct 10, 2024
I think both of these. I think it is reasonable to have this as a CI unit test but unreasonable to quietly drop using |
This was referenced Oct 10, 2024
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This PR closes #490
This PR makes the CI parameter recovery more robust by changing the
transformationdefined byEpiDatafromexptosoftplus.NB: Since the$R_t$ for example in EpiNow2 we might want to consider the problem in more detail despite this fix.
exptransform is very commonly used forMathematical details
Softplus transformation and its inverse:
In the parameter recovery test I have modified to do:
Where$Z_t$ is the latent process being tested (e.g. random walk, AR(1) and Diff AR(1)).