$lm field of the incidence_fit class is now named $model to clearly indicate that this can contain any model.incidence() will now accept text-based intervals that are valid date intervals: day, week, month, quarter, and year.
incidence() now verifies that all user-supplied arguments are accurate and spelled correctly.
fit_optim_split() now gains a separate_split argument that will determine the optimal split separately for groups.
A new class, incidence_fit_list, has been implemented to store and summarise incidence_fit objects within a nested list. This is the class returned by in the $fit element of fit_optim_split().
bootstrap() will bootstrap epicurves stored as incidence objects.
find_peak() identifies the peak date of an incidence objects.
estimate_peak() uses bootstrap to estimate the peak time of a partially observed outbreak.
get_interval() will return the numeric interval or several intervals in the case of intervals that can’t be represented in a fixed number of days (e.g. months).
get_dates() returns the dates or counts of days on the right, center, or left of the interval.
get_counts() returns the matrix of case counts for each date.
get_fit() returns a list of incidence_fit objects from an incidence_fit_list object.
get_info() returns information stored in the $info element of an incidence_fit/incidence_fit_list object.
incidence_fit_class instructs the user on how incidence_fit and incidence_fit_list objects are created and accessed.incidence() function, the iso_week parameter is deprecated in favor of standard for a more general way of indicating that the interval should start at the beginning of a valid date timeframe.The $timespan item in the incidence object from Dates was not type-stable and would change if subsetted. A re-working of the incidence constructor fixed this issue.
Misspelled or unrecgonized parameters passed to incidence() will now cause an error instead of being silently ignored.
Plotting for POSIXct data has been fixed.
incidence object to avoid conflicts with additional geoms such as geom_ribbon, now used in projections::add_projections.ggplot2the argument n_breaks has been added to plot.incidence, to specify the ideal number of breaks for the date legends; will work with ggplot2 > 2.2.1
added the internal function make_iso_weeks_breaks to generate dates and labels for date x-axis legends using ISO weeks
added a function add_incidence_fit, which can be used for adding fits to epicurves in a piping-friendly way
added a function cumulate, which computes cumulative incidence and returns an incidence object
new generic as.incidence, to create incidence objects from already computed incidences. Methods for: matrix, data.frame, numeric vectors
better processing of input dates, including: automatic conversion from characters, issuing errors for factors, and silently converting numeric vectors which are essentially integers (issuing a warning otherwise)
new vignette on conversions to and from incidence objects
new tests
fixed issues caused by variables which changed names in some datasets of the outbreaks package, used in the documentation
disabled by default the isoweeks in incidence; this part of the code will break with changes made in the devel version of ggplot2, which is now required by plotly
it is now possible to subset an incidence object based on Date dates using numeric values, which are interpreted as number of intervals since the first date (origin = 1)
NAs are no longer removed from the input dates, as it would cause mismatches with grouping factors.
ebola.sim -> ebola_sim and ebola.sim.clean -> ebola_sim_cleanadd an argument iso_week to incidence.Date() and incidence.POSIXt() to support ISO week-based incidence when computing weekly incidence.
add an argument labels_iso_week to plot.incidence() to label x axis tick marks with ISO weeks when plotting ISO week-based weekly incidence.
The README.Rmd / README.md now contains information about various websites for incidence as well as guidelines for posting questions on the RECON forum.
incidence now has a dedicated website http://www.repidemicsconsortium.org/incidence/ generated with pkgdown
First release of the incidence package on CRAN!