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set GP prior for non-mechanistic infection model #97

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merged 5 commits into from
Feb 26, 2025
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@avallecam avallecam commented Feb 25, 2025

  • Please check if the PR fulfills these requirements
  • I have read the CONTRIBUTING guidelines
  • Checks have been run locally and pass
  • What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

Aims to Fix #96

  • What is the current behavior? (You can also link to an open issue here)

In {EpiNow2} version 1.7.1 the default GP prior is now sd = 0.01. The non-mechanistic infection model used in the estimate infections howto entry was built assuming a GP prior of sd = 0.05 (version 1.6.1). Given that the new default GP prior is more appropriate for the renewal equation model (rt!=NULL) than the non-mechanistic infection model (rt = NULL), the non-mechanistic callings in the corresponding howto entry now specify explicitly sd = 0.05 for the GP prior. For further discussions on this regard, refer to previous and latest issues linked to: epiforecasts/EpiNow2#829

  • What is the new behavior (if this is a feature change)?

The website will keep rendering appropriate infection estimates when upgrading EpiNow2 CRAN version 1.7.1.

  • Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)

No

  • Other information:

@avallecam avallecam marked this pull request as ready for review February 25, 2025 10:45
@avallecam
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issue in GH actions to solve in #100

added also to file to avoid removal in future snapshots
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now runnable checks are passing, so will merge 🚀 thanks!

@avallecam avallecam merged commit 75743e7 into main Feb 26, 2025
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@avallecam avallecam deleted the avallecam-patch-1 branch February 26, 2025 09:58
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add gp argument to epinow2 entry
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