Final changes for 1.3.3 #322
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* Correct implementation of zero_threshold in create_clean_reported_cases * Add option to filter zeros at start of reported case time series * revert change to rolling sum and update docs * change arg name and add llyod as a contributor * update documentation * refresh docs Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
* Update incubation-period.R * Fixed a few typos * update from main Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
* add estimate_secondarry and estimate_truncation simple tests * update link in news
* upgrade pkgdown version * add snapshot tests
* optimisations and updates * port in changes from #311 * update news * update depreciated testthat features * use gamma for generation time * tests for renewal passing (i.e as previous behaviour * update to new snaps format * rebuild README
* add doc skeleton * add rough documentation
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I am seeing these performance issues in Docker but with a local install this PR runs faster than main. Investigating now if its an issue with my development environment vs a package issue. |
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I've tested this on Mac and Linux and seeing comparable results for all models compared to |
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WIP - tracking down a 10 times performance reversion.
This PR adds final changes for 1.3.3. In particular, it includes some extensions to documentation, improved test coverage, and performance tweaks.
Currently, I am tracking down a significant reversion in performance meaning this is not ready for merging. I assume this was a result of the optimisations to the discrete distributions but I had very poor performance both before and after meaning it may be something else.