Replace scan usage with accumulate scan #444
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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="384-replace-scan-usage-with-accumulate_scan", subdir="EpiAware")
using EpiAware |
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Aug 29, 2024
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Aug 29, 2024
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This is a really nice step forward. I think we can iterate on this to make the renewal steps use more of the latent model steps and to also be more composable but I think this is a great first step. The only outstanding comment here is that the name in the struct might be a bit duplicative everything else is really a musing.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #444 +/- ##
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+ Coverage 89.72% 89.91% +0.19%
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Files 56 57 +1
Lines 720 734 +14
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+ Hits 646 660 +14
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
|
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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There was an outstanding issue with renewal models that meant we couldn't benchmarks so no useful benchmarks to compare against. We should add some benchmarks in in another PR. |
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This PR primarily changes usage of
scanin Renewal model to usingaccumulate_scan.To do this meant defining callable
Stepstructs. The relevant design decisions I made here were:AbstractConstantRenewalStep <: AbstractAccumulationSteptype to group recurrence/step functions that are intended to be static.Renewal, indicating that for this kind of modelling inference of the GI is not in scope, and avoiding redeclaring the Step at runtime (henceConstantStep).RenewalWithPopulationstruct type, this behaviour is now defined by theConstantRenewalWithPopulationStepstruct.Closes #384 .