Package: aedseo 0.1.2.9000

Lasse Engbo Christiansen

aedseo: Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

A powerful tool for automating the early detection of seasonal epidemic onsets in time series data. It offers the ability to estimate growth rates across consecutive time intervals, calculate the sum of cases (SoC) within those intervals, and estimate seasonal onsets within user defined seasons. With use of a disease-specific threshold it also offers the possibility to estimate seasonal onset of epidemics. Additionally it offers the ability to estimate burden levels for seasons based on historical data. It is aimed towards epidemiologists, public health professionals, and researchers seeking to identify and respond to seasonal epidemics in a timely fashion. For reference on growth rate estimation, see Walling and Lipstich (2007) <doi:10.1098/rspb.2006.3754> and Obadia et al. (2012) <doi:10.1186/1472-6947-12-147>. Seasonal burden level calculations have been inspired by The Moving Epidemic Method (MEM), see Vega and Lozano (2012) <doi:10.1111/j.1750-2659.2012.00422.x>.

Authors:Sofia Myrup Otero [aut], Kasper Schou Telkamp [aut], Lasse Engbo Christiansen [aut, cre], Rasmus Skytte Randløv [rev], Statens Serum Institut, SSI [cph, fnd]

aedseo_0.1.2.9000.tar.gz
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aedseo.pdf |aedseo.html
aedseo/json (API)
NEWS

# Install 'aedseo' in R:
install.packages('aedseo', repos = c('https://ssi-dk.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ssi-dk/aedseo/issues

Pkgdown site:https://ssi-dk.github.io

On CRAN:

Conda:

5.78 score 1 stars 8 scripts 281 downloads 11 exports 42 dependencies

Last updated 16 hours agofrom:c0b762c907. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 28 2025
R-4.5-winNOTEMar 28 2025
R-4.5-macNOTEMar 28 2025
R-4.5-linuxNOTEMar 28 2025
R-4.4-winOKMar 28 2025
R-4.4-macOKMar 28 2025
R-4.4-linuxOKMar 28 2025
R-4.3-winOKMar 28 2025
R-4.3-macOKMar 28 2025

Exports:aedseoautoplotcombined_seasonal_outputepi_calendarfit_growth_ratefit_percentilesgenerate_seasonal_dataseasonal_burden_levelsseasonal_onsetto_time_seriestsd

Dependencies:backportscheckmateclicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpracmapurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyselecttimechangeutf8vctrsviridisLitewithr

Automated Detection of Seasonal Epidemic Onset and Burden Levels in R

Rendered fromaedseo.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-11
Started: 2025-01-21

Seasonal Burden Levels

Rendered fromburden_levels.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-11
Started: 2025-01-28

Seasonal Epidemic Onset

Rendered fromseasonal_onset.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-11
Started: 2025-01-28

Simulate Seasonal Epidemic Waves

Rendered fromgenerate_seasonal_wave.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-28
Started: 2025-01-21