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Add support for missing NAs in estimate_infection() model #528

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Merged
merged 18 commits into from
Jan 9, 2024
Merged

Add support for missing NAs in estimate_infection() model #528

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0ddc548
add a lookup to estimate_infections
seabbs Dec 18, 2023
9ed7b4e
add R side support
seabbs Dec 18, 2023
2041e56
don't internally impute missing as zero
seabbs Dec 18, 2023
c4967b0
update news
seabbs Dec 18, 2023
254d5b8
fix data preprocessing order
seabbs Dec 18, 2023
549c509
correction data ingestion
seabbs Dec 18, 2023
b48feff
clean up filtering of leading zeros
seabbs Dec 18, 2023
3ee24d3
error check create_clean_reported_cases and add unit tests to cover f…
seabbs Dec 19, 2023
9ad395a
correct handling of missing data in data preprocessing:
seabbs Dec 19, 2023
966ceb3
refine data preprocessing
seabbs Dec 20, 2023
8ae6fa0
update news and tests
seabbs Dec 20, 2023
e064672
update global variables
seabbs Dec 20, 2023
982dacd
Update NEWS.md
seabbs Jan 8, 2024
647f0aa
Update R/create.R
seabbs Jan 8, 2024
f693577
Update R/create.R
seabbs Jan 8, 2024
7533201
Update R/create.R
seabbs Jan 8, 2024
a7aab1c
fix line length linting
seabbs Jan 8, 2024
e678d23
Document
actions-user Jan 8, 2024
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Update NEWS.md 
Co-authored-by: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
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@seabbs @sbfnk
seabbs and sbfnk committed Jan 8, 2024
commit 982dacddf9bf6be320e6f4f57872708fa5988699
2 changes: 1 addition & 1 deletion NEWS.md
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* The functions `get_dist`, `get_generation_time`, `get_incubation_period` have been deprecated and replaced with examples. By @sbfnk in #481 and reviewed by @seabbs.
* The utility function `update_list()` has been deprecated in favour of `utils::modifyList()` because it comes with an installation of R. By @jamesmbaazam in #491 and reviewed by @seabbs.
* The `fixed` argument to `dist_spec` has been deprecated and replaced by a `fix_dist()` function. By @sbfnk in #503 and reviewed by @seabbs.
* Updated `estimate_infections()` so that rather than imputing missing data, it now skips these data points in the likelihood. This is a breaking change as it alters the behaviour of the model when dates are missing from a time series but are known to be zero. We recommend that users check their results when updating to this version but expect this to in most cases improve performance. By @seabbs in # and reviewed by @sbfnk.
* Updated `estimate_infections()` so that rather than imputing missing data, it now skips these data points in the likelihood. This is a breaking change as it alters the behaviour of the model when dates are missing from a time series but are known to be zero. We recommend that users check their results when updating to this version but expect this to in most cases improve performance. By @seabbs in #528 and reviewed by @sbfnk.

## Documentation

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