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EpiInvert, an R application to restore, analyze, compare and forecast epidemiological time series

Morel, J.-D.; Morel, J.-M.; Alvarez, L. M.

2024-12-14 epidemiology
10.1101/2024.12.13.24319011 medRxiv
Show abstract

The Covid-19 pandemic produced regional time series of incidence, hospital, ICU admission and death. The EpiInvert package estimates the incidence trend and the daily reproduction number Rt of any infectious disease, compares related time series such as incidence and death, and provides incidence forecasts. EpiInvert is an R package with the following features: (1) EpiInvert inputs raw daily incidence time series and the pandemic time serial interval. It outputs a weekly seasonality, an incidence trend and its reproduction number. (2) EpiIndicators inputs two related epidemiological time series such as daily incidence and death count. It outputs a daily ratio and delay between both time series. (3) EpiInvertForecast inputs an incidence trend obtained by EpiInvert and a database of past observed time series. Using the most similar past series, it forecasts the incidence in the next four weeks. EpiInvert is in the CRAN repository https://cran.r-project.org/web/packages/EpiInvert/index.html.

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The top 9 journals account for 50% of the predicted probability mass.

1
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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.