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NEWS.md

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aedseo (development version)

Deprecations

  • aedseo() is now deprecated. Please use seasonal_onset() instead. A warning is shown when using aedseo() (#41).

  • tsd() is now deprecated. Please use to_time_series() instead. A warning is shown when using tsd() (#41).

Features

  • Added a new argument only_current_season to seasonal_onset(), seasonal_burden_levels() and combined_seasonal_output() which gives the possibility to either get output from only the current season or for all available seasons (#45).

  • Added combined_seasonal_output() as the main function to run both seasonal_onset() and seasonal_burden_levels() to get a combined result for the newest season (#44).

  • Added seasonal_onset() as a replacement for the deprecated aedseo() function (#41).

  • Added to_time_series() as a replacement for the deprecated tsd() function (#41).

  • Added the seasonal_burden_levels() function, which calculates burden levels based on data from previous seasons with two different methods; "peak_levels" or "intensity_levels" (#37).

  • Added the fit_quantiles() function, which optimises a user selected distribution and calculates the quantiles based on observations and weights. It is meant to be used within the seasonal_burden_levels() function (#35, #37).

Improvements

  • Improved the epi_calendar() function to work for a season spanning new year (#34).

  • The aedseo() function now allows for the choice of adding season as an input argument (#34).

  • {checkmate} assertions have been added to enhance user feedback with clearer error messages and to ensure functions operate correctly by validating inputs (#33).

  • Improved the aedseo() function to work with NA values. The user now defines how many NA values the function should allow in each window (#32).

Minor changes

  • The disease_threshold argument now reflects the disease threshold in one time step. If the total number of cases in a window of size k exceeds disease_threshold * k, a seasonal onset alarm can be triggered (#32).

aedseo 0.1.2

Minor changes

  • Transferring maintainership of the R package to Lasse Engbo Christiansen.

aedseo 0.1.1

Improvements

  • Enhanced clarity and user guidance in the introductory vignette, providing a more comprehensive walkthrough of the application of the 'aeddo' algorithm on time series data with detailed explanations and illustrative examples.

Minor changes

  • Updated LICENSE.md to have Statens Serum Institut as a copyright holder.

  • Fixed installation guide for the development version in the README.Rmd and README.md

  • Added Lasse Engbo Christiansen as an author of the R package.

  • Added a new function epi_calendar() that determines the epidemiological season based on a given date, allowing users to easily categorize dates within or outside specified seasons.

  • Introduced additional visualizations in the autoplot() method, enhancing the capabilities of the plot() method with new displays of observed cases and growth rates.

aedseo 0.1.0

Features

  • Added the aedseo function, which automates the early detection of seasonal epidemic onsets by estimating growth rates for consecutive time intervals and calculating the Sum of Cases (sum_of_cases).

  • Introduced autoplot and plot methods for visualizing aedseo and aedseo_tsd objects. These functions allow you to create insightful ggplot2 plots for your data.

  • Included the fit_growth_rate function, enabling users to fit growth rate models to time series observations.

  • Introduced the predict method for aedseo objects, which allows you to predict observations for future time steps given the growth rates.

  • Added the summary method for aedseo objects, providing a comprehensive summary of the results.

  • Introduced the tsd function, allowing users to create S3 aedseo_tsd (time-series data) objects from observed data and corresponding dates.