aedseo 0.3.0
CRAN release: 2025-04-09
Deprecations
aedseo()
is now deprecated. Please useseasonal_onset()
instead. A warning is shown when usingaedseo()
(#41).tsd()
is now deprecated. Please useto_time_series()
instead. A warning is shown when usingtsd()
(#41).
Features
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_percentiles()
function, which optimises a user selected distribution and calculates the percentiles based on observations and weights. It is meant to be used within theseasonal_burden_levels()
function (#35, #37) - Renamedfit_quantiles()
tofit_percentiles()
(#60).Added
combined_seasonal_output()
as the main function to run bothseasonal_onset()
andseasonal_burden_levels()
to get a combined result for the newest season (#44).Added
consecutive_growth_warnings()
function to help the user with a method to define the disease-specific threshold (#80).Added a new argument
only_current_season
toseasonal_onset()
,seasonal_burden_levels()
andcombined_seasonal_output()
which gives the possibility to either get output from only the current season or for all available seasons (#45).Added
historical_summary()
which uses atsd_onset
object to summarise historical estimations (#75).plot()
andautoplot()
can now plottsd_combined_seasonal_output
andtsd_consecutive_growth_warning
objects (#57, #80).Added
generate_seasonal_data()
to generate synthetic data for testing and documentation purposes (#56).Added
seasonal_onset()
as a replacement for the deprecatedaedseo()
function (#41).Added
to_time_series()
as a replacement for the deprecatedtsd()
function (#41).
Improvements
-
Enhanced clarity and user guidance in the vignettes:
-
vignette("generate_seasonal_wave")
, -
vignette("aedseo")
, vignette("seasonal_onset")
-
vignette("burden_levels")
providing a comprehensive walkthrough of the application of the functions provided by theaedseo
package with detailed explanations and illustrative examples (#56, #57, #58, #59, #60, #61).
-
Improved the
autoplot()
function which can now visualise dates as days, weeks and months on the x-axis with thetime_interval
argument (#56).Improved the
epi_calendar()
function to work for a season spanning new year (#34).Using
predict()
ontsd_onset
objects now uses the same time-scale as the given object (#61). That is, thetime_interval
attribute controls if predictions are by “days”, “weeks” or “months”.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 withNA
values. The user now defines how manyNA
values the function should allow in each window (#32).
Minor changes
Added Sofia Myrup Otero as an author of the R package (#55).
Added Rasmus Skytte Randløv as a reviewer of the R package (#55).
The
disease_threshold
argument now reflects the disease threshold in one time step. If the total number of cases in a window of sizek
exceedsdisease_threshold * k
, a seasonal onset alarm can be triggered (#32).
aedseo 0.1.1
CRAN release: 2023-11-16
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 theplot()
method with new displays of observed cases and growth rates.
aedseo 0.1.0
CRAN release: 2023-11-07
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
andplot
methods for visualizingaedseo
andaedseo_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 foraedseo
objects, which allows you to predict observations for future time steps given the growth rates.Added the
summary
method foraedseo
objects, providing a comprehensive summary of the results.Introduced the
tsd
function, allowing users to create S3aedseo_tsd
(time-series data) objects from observed data and corresponding dates.