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Issue 46: refactor model definition #69

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Merged
merged 11 commits into from
Apr 7, 2025
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kaitejohnson
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@kaitejohnson kaitejohnson commented Mar 28, 2025

Description

This PR closes #46.

It restructures the methods to be more consistent with the code (linking to the explicitly linking to the functions that pertain to the model components).

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codecov bot commented Apr 1, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (3957643) to head (581a4d1).
Report is 11 commits behind head on main.

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  Files           11        11           
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+ Hits           305       325   +20     

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@kaitejohnson kaitejohnson marked this pull request as ready for review April 1, 2025 09:54
@kaitejohnson kaitejohnson requested a review from seabbs April 1, 2025 09:55
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seabbs commented Apr 2, 2025

I had a go at shortening the overview as I felt like it was a bit wordy. This might be a bit drastic.

The baselinenowcast model, initially developed as a reference for the COVID-19 hospital admissions nowcasting challenge in Germany (2021-2022), utilises reporting triangles of preliminary case counts and their delays. It applies a multiplicative approach, using empirically observed historical delay distributions to estimate yet-to-be-observed cases.
Users can specify whether delay distributions are estimated from the current reporting triangle, fully observed past data, or data from different strata. The model produces point nowcasts by "filling in" the reporting triangle.
Probabilistic nowcasts are generated using a negative binomial model with means from the point nowcast and dispersion parameters estimated from past nowcast errors. These parameters can also be flexibly sourced from current data, historical data, or alternative settings.

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This looks good to me but the language here depends on our answers to #74 (because here you are using point nowcast to mean fill in the reporting triangle, which is also how I have used it, but in other places it means the estimate of the sum across delays for each reference time).

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Aside from the nomenclature discussion this looks good.

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I think I would prefer to merge this now and then open a new PR to update all the docs and function names after we decide on the naming convention

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seabbs commented Apr 7, 2025

sounds good

@kaitejohnson kaitejohnson added this pull request to the merge queue Apr 7, 2025
Merged via the queue into main with commit 64e107c Apr 7, 2025
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@kaitejohnson kaitejohnson deleted the 46-refactor-methods branch April 7, 2025 14:33
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Refactor the connections between model components in the methodology overview
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