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Merged
merged 24 commits into from
Feb 20, 2024
Merged

Simulate infections #557

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3a8a3c7
simulate infections function
sbfnk Feb 13, 2024
db62ef3
add test
sbfnk Feb 18, 2024
fd43468
we always need initial infections
sbfnk Feb 13, 2024
a32036f
add missing truncation
sbfnk Feb 13, 2024
4eef015
swap check for seeding time
sbfnk Feb 14, 2024
dfc611e
update extract function to work with simulations
sbfnk Feb 18, 2024
6bdca31
add news item
sbfnk Feb 18, 2024
1b34849
fix typo
sbfnk Feb 20, 2024
81d0423
add more tests
sbfnk Feb 19, 2024
b3533eb
correctly index infections when no delay
sbfnk Feb 19, 2024
c85dbe6
generation times are now zero-indexed
sbfnk Feb 19, 2024
dbeb911
ensure overdispersion is fixed
sbfnk Feb 19, 2024
b0b1e42
improve checks in simulate_infections
sbfnk Feb 19, 2024
7ae6e1a
expand simulate_infections documentation
sbfnk Feb 19, 2024
1da5b24
add simulate_infections snapshot test
sbfnk Feb 19, 2024
af90765
add backend argument
sbfnk Feb 19, 2024
506b7bb
use simpler Poisson for example
sbfnk Feb 19, 2024
f30f13a
single comment hash for package style
sbfnk Feb 19, 2024
bdd5042
re-render documentation
sbfnk Feb 20, 2024
f0bb605
add reviewer
sbfnk Feb 20, 2024
f159f40
only extract `frac_obs` if `obs_scale_sd` exists
sbfnk Feb 20, 2024
c158a94
Apply suggestions from code review
sbfnk Feb 20, 2024
8e2e2d8
add deprecation context and re-render doc
sbfnk Feb 20, 2024
9bf0212
improve documentation
sbfnk Feb 20, 2024
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add reviewer 
Co-authored-by: James Azam <james.azam@lshtm.ac.uk>
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@sbfnk @jamesmbaazam
sbfnk and jamesmbaazam committed Feb 20, 2024
commit f0bb605dc4f041c0a7d37fdd200c9432991caacd
2 changes: 1 addition & 1 deletion NEWS.md
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* 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 #528 and reviewed by @sbfnk.
* `simulate_infections` has been renamed to `forecast_infections` in line with `simulate_secondary` and `forecast_secondary`. The terminology is: a forecast is done from a fit to existing data, a simulation from first principles. By @sbfnk in #544 and reviewed by @seabbs.
* A new `simulate_infections` function has been added that can be used to simulate from the model from given initial conditions and parameters. By @sbfnk in .
* A new `simulate_infections` function has been added that can be used to simulate from the model from given initial conditions and parameters. By @sbfnk in #557 and reviewed by @jamesmbaazam.

## Documentation

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