Issue 529: Create null Latent model #530
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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="529-create-nulllatentmodel", subdir="EpiAware")
using EpiAware |
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I think this is fine to go in for now. Noting that we only need this whilst we take |
seabbs
previously approved these changes
Nov 20, 2024
…v/Rt-without-renewal into 529-create-nulllatentmodel
Yes, hard to imagine we'll need this with a suitably flexible interface. |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #530 +/- ##
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+ Coverage 90.51% 90.54% +0.03%
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Files 56 57 +1
Lines 822 825 +3
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+ Hits 744 747 +3
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Benchmark resultJudge resultBenchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewalJob Properties
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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:
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seabbs
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Nov 20, 2024
seabbs
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Dec 5, 2024
* Patch: Switch to fork of benchmarkCI (#520) * patch to fork of benchmarkCI * put fork version of BenchmarkCI in [sources] * swap order * add EpiAware [source] * fix path * rm benchmarkCI from project * Patch fix: add `Manifest.toml` to benchmarking (#524) * trigger * Update benchmark.yaml * Update benchmark.yaml * commit benchmark Manifest * try alternate approach * Update benchmark.yaml * Update EpiMethod.jl * Update benchmark.yaml * change baseline to origin/main * remove trigger * rm other trigger * Issue 465: Add an infection generating model for ODE problems (#510) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) (#516) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) * Update Project.toml * fix Project.toml --------- Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]> Co-authored-by: Samuel Brand <[email protected]> Co-authored-by: Samuel Brand <[email protected]> * CompatHelper: bump compat for DynamicPPL to 0.30 for package EpiAware, (drop existing compat) (#528) Co-authored-by: CompatHelper Julia <[email protected]> * rename IDD -> IID * rename test file * Issue 529: Create null Latent model (#530) * Null Latent model * Null Latent model * fix doctest * fix generate_epiaware unit tests New usage of RW * fix turing method test underlying std of step size changed name * fix broadcast test Underlying std param changed name * fix HN unit test Default std prior had changed * fix AR unit tests --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]>
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* draft MA method * draft MA methd * use IDD for epsilon in all models * add MA benchmark * Add docs and tests for IDD * make episilon_t a arg of the latent model constructors * improve MA correctness * fully import EpiAwareUtils * add a test for IDD * add tests for MA.jl * add doc tests and unit tests + start on helper fn * more updatres to AR appraoc * chase down partial arg changes * clean up AR * clean up and add arma and arima helpers * Contributions towards Arma/Arima models (#531) * Patch: Switch to fork of benchmarkCI (#520) * patch to fork of benchmarkCI * put fork version of BenchmarkCI in [sources] * swap order * add EpiAware [source] * fix path * rm benchmarkCI from project * Patch fix: add `Manifest.toml` to benchmarking (#524) * trigger * Update benchmark.yaml * Update benchmark.yaml * commit benchmark Manifest * try alternate approach * Update benchmark.yaml * Update EpiMethod.jl * Update benchmark.yaml * change baseline to origin/main * remove trigger * rm other trigger * Issue 465: Add an infection generating model for ODE problems (#510) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) (#516) * CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) * Update Project.toml * fix Project.toml --------- Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]> Co-authored-by: Samuel Brand <[email protected]> Co-authored-by: Samuel Brand <[email protected]> * CompatHelper: bump compat for DynamicPPL to 0.30 for package EpiAware, (drop existing compat) (#528) Co-authored-by: CompatHelper Julia <[email protected]> * rename IDD -> IID * rename test file * Issue 529: Create null Latent model (#530) * Null Latent model * Null Latent model * fix doctest * fix generate_epiaware unit tests New usage of RW * fix turing method test underlying std of step size changed name * fix broadcast test Underlying std param changed name * fix HN unit test Default std prior had changed * fix AR unit tests --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Sam Abbott <[email protected]> * revert define_ namming * clean out repeated utils from merge * fix MA tests * fix RW tests - feel made about RandomWalk vs AR naming * fix remaining unit tests that aren't doctests * update latent recovery test * try and fix doctests automatically * update all doctests to output nothing - this is awful * add doctests for arima and arma * fix doctest * clean up deps * update replication studies * add interface tests for combination functions and add benchmarks * add some basic theoretical properties tests * name change IDD -> IID benchmarks * moving all the constructors because this PR is too contained * catch missing using * update iid benchmark: * update extraction * remove old param namme from case study * get the dot * get the dot * fix initial guess point for MAP opt * Update index.jl * add a compile time branch for HN * add a compile time branch for HN * update test * add a new constructor to get old default behaviour * update docs * update docs - using the structs for priors is very brittle * reorder prior plots --------- Co-authored-by: Samuel Brand <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Samuel Brand <[email protected]>
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This small PR closes #529 .
This PR contributes a
Nullstruct which defines the concept of having anothinglatent process. This is useful to reusing patterns that we already have (e.g.EpiProblem) in situations where we don't actually want a latent process.Potentially it might be better to sequence this to after resolving #525 , because like the ODE parameter objects this not a naturally indexable latent model.