incidence version 1.4.1

This version introduces a re-written incidence constructor, support for text-based intervals, and a formalization of lists of incidence_fit classes.

incidence 1.4.1

BEHAVIORAL CHANGES

• The $lm field of the incidence_fit class is now named $model to clearly
  indicate that this can contain any model.

NEW FEATURES

• 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().

NEW FUNCTIONS

• 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.

DOCUMENTATION

• The new vignette incidence_fit_class instructs the user on how
  incidence_fit and incidence_fit_list objects are created and accessed.

DEPRECATED

• In the 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.

BUG FIXES

• 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.

1.3.1

incidence 1.3.1 (2018-06-11)

BUG FIXES

• tweak of the plotting of incidence object to avoid conflicts with additional
  geoms such as geom_ribbon, now used in projections::add_projections.

1.2.0

removing plotly from suggest

1.1.2

updated news

1.1.0

CRAN release candidate. Incorporates isoweek support.

First CRAN release

Version submitted to CRAN on 31st October 2016. Fully documented, 3 vignettes, 100% code coverage.