Add support for missing NAs in estimate_infection() model #528
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This is how benchmark results would change (along with a 95% confidence interval in relative change) if cb5705c is merged into main:
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sbfnk
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sbfnk
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Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
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sbfnk
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This is how benchmark results would change (along with a 95% confidence interval in relative change) if 876a533 is merged into main:
|
sbfnk
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* add a lookup to estimate_infections * add R side support * don't internally impute missing as zero * update news * fix data preprocessing order * correction data ingestion * clean up filtering of leading zeros * error check create_clean_reported_cases and add unit tests to cover function * correct handling of missing data in data preprocessing: * refine data preprocessing * update news and tests * update global variables * Update NEWS.md Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * Update R/create.R Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * Update R/create.R Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * Update R/create.R Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * fix line length linting * Document --------- Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> Co-authored-by: GitHub Actions <actions@github.com>
sbfnk
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* add a lookup to estimate_infections * add R side support * don't internally impute missing as zero * update news * fix data preprocessing order * correction data ingestion * clean up filtering of leading zeros * error check create_clean_reported_cases and add unit tests to cover function * correct handling of missing data in data preprocessing: * refine data preprocessing * update news and tests * update global variables * Update NEWS.md Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * Update R/create.R Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * Update R/create.R Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * Update R/create.R Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> * fix line length linting * Document --------- Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk> Co-authored-by: GitHub Actions <actions@github.com>
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This PR adds support for missing data in the form of NAs but dropping them from the likelihood rather than imputing that they are zero and then optionally
Note that this is a breaking change and may be undesirable for some users where missing dates do indicate zeros vs being truly missing.
I have tested by knocking out data from the example and running the model.