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incidence 1.5.3 (2018-12-07)

BUG FIX

  • plot.incidence() will now respect single groups. (See reconhub#84)
  • as.data.frame.incidence() will now respect single groups. (See reconhub#84)
  • incidence() now returns an error when dates argument is character object. (See reconhub#88)
  • fit() now returns correct coefficients when dates is POSIXt by converting to Date. (See reconhub#91)
  • fit() now returns Inf for the upper bound of the doubling / halving time if the
    confidence interval on the growth rate spans 0. (See reconhub#28)

MISC

  • demo("incidence-demo" package = "incidence") has been updated to show use of custom colors.
  • incidence() no longer accepts characters as input for dates, first_date, or last_date arguments
  • fit() now returns an error if growth rate estimates for groups have different signs. (See reconhub#28)

incidence 1.5.2 (2018-11-30)

BUG FIX

  • print.incidence() will now print isoweeks even if the $interval element is "week".

MISC

  • subset.incidence() will now give a more informative error message when the user specifies a group that does not exist.
  • demo('incidence-demo', package = 'incidence') now shows plotting with show_cases = TRUE.
  • In the the case where a date is accidentally mis-typed leading to a gross mis-calculation of the date range (i.e. 2018 is mis-typed as 3018), a warning will be issued. The default threshold is set at 18262 days (50 years), but the user can define their own threshold by setting the incidence.max.days option

incidence 1.5.1 (2018-11-14)

BUG FIX

  • Two bugs regarding the ordering of groups when the user specifies a factor/ column order have been fixed. This affects plot.incidence(), incidence(), and as.data.frame.incidence() For details, see reconhub#79

incidence 1.5.0 (2018-11-01)

NEW FUNCTIONS

  • group_names() allows the user to retrieve and set the group names.
  • get_timespan() returns the $timespan element.
  • get_n() returns the $n element.
  • dim(), nrow(), and ncol() are now available for incidence objects, returning the dimensions of the number of bins and the number of groups.

NEW FEATURES

  • A new argument to plot() called show_cases has been added to draw borders around individual cases for EPIET-style curves. See reconhub#72 for details.

DOCUMENTATION UPDATES

  • An example of EPIET-style bars for small data sets has been added to the plot customisation vignette by @jakobschumacher. See reconhub#68 for details.
  • The incidence class vignette has been updated to use the available accessors.

BUG FIX

  • estimate_peak() no longer fails with integer dates
  • incidence() no longer fails when providing both group information and a first_date or last_date parameter that is inside the bounds of the observed dates. Thanks to @mfaber for reporting this bug. See reconhub#70 for details.

MISC

  • code has been spread out into a more logical file structure where the internal_checks.R file has been split into the relative components.
  • A message is now printed if missing observations are present when creating the incidence object.

incidence 1.4.1 (2018-08-24)

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.

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.

incidence 1.3.0 (2018-06-01)

BUG FIXES

  • fixed issue caused by new version of ggplot2

NEW FEATURES

  • the 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

incidence 1.2.1 (2017-10-19)

BUG FIXES

  • fixed issues in testing incidence plots by employing vdiffr package.

incidence 1.2.0 (2017-04-03)

NEW FEATURES

  • 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

BUG FIXES

  • 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

incidence 1.1.2 (2017-03-24)

BUG FIXES

  • 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.

incidence 1.1.1 (2017-02-15)

BUG FIXES

  • adapting to new names of datasets in outbreaks: ebola.sim -> ebola_sim and ebola.sim.clean -> ebola_sim_clean

incidence 1.1.0 (2016-12-13)

NEW FEATURES

  • add 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.


incidence 1.0.1 (2016-11-23)

NEW FEATURES

  • 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

MINOR IMPROVEMENTS

  • Vignettes titles are now correctly displayed on CRAN (they read 'Vignette title').

incidence 1.0.0 (2016-11-03)

First release of the incidence package on CRAN!