change exp to xexpy #470
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change exp to xexpy #470
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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="469-change-calculation-method-in-epiawarebasegenerate_latent_infsepi_modelexpgrowthrate-rt", subdir="EpiAware")
using EpiAware |
seabbs
previously approved these changes
Oct 3, 2024
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #470 +/- ##
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Coverage 90.02% 90.02%
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Files 57 57
Lines 742 742
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Hits 668 668
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
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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…egenerate_latent_infsepi_modelexpgrowthrate-rt
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updated a hotfix for the doc fix |
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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Seems the relevant bit of the benchmarking? I think thats overall bad? But very big performance gain with not compiled tape AD? |
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Yes agree. I think ideally we would look at:
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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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Good thinking and I've noted #472 |
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So the So quite a mixed bag. I don't have a strong mental model to explain that result |
Me neither. |
seabbs
deleted the
469-change-calculation-method-in-epiawarebasegenerate_latent_infsepi_modelexpgrowthrate-rt
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This is a small PR to replace the calculation of
ExpGrowthRateinfection generating process withLogExpFunctions.xexpyto get their overflow properties.The reason I targeted this specific bit of the code base it that everywhere else we can define
transformationwhereas here theexptransform is baked into the meaning of the igp.Closes #469 .
NB: I also changed from
cumsumtoaccumulate(+, rt; init = init_incidence)to avoid a broadcast add before applying the "safe"xexpy. I wonder if anything shows in benchmarks.