NEWS.md

In incidence: Compute, Handle, Plot and Model Incidence of Dated Events

incidence 1.7.3

• change of maintainer only.

incidence 1.7.2

BUG FIXES

• plot.incidence() now reverts to the previous behaviour of plotting ticks on either side of the interval as opposed to centering within the interval.
• The default version for {ggplot2} has been set to 3.3.2.

incidence 1.7.1

BUG FIXES

• Fix for a bug in plot.incidence() introduced with new release of ggplot2 (bug report) As a temporary fix, dates are now centered within the interval instead of to the left of the interval.

incidence 1.7.0

NEW FEATURES

• Any interval seq.Date() can handle (e.g. "5 weeks") can be handled by incidence() (see https://github.com/reconhub/incidence/issues/67)
• Weekly intervals can start on any day of the week by allowing things like "epiweek", "isoweek", "wednesday week", "2 Saturday weeks", etc. (see https://github.com/reconhub/incidence/issues/55#issuecomment-405297526)
• the item $weeks is now added to the incidence object, which contains an "aweek" class
• plotting will now force the first tick to be the starting point of the incidence curve

NEW FUNCTIONS

• make_breaks() will automatically calculate breaks from an incidence object for plotting.
• scale_x_incidence() will produce a ggplot2 "ScaleContinuous" object to add to a ggplot.

DEPRECATED

• plot.incidence() argument labels_iso is deprecated in favor of labels_week
• Incidence objects will still have $isoweeks if the weeks are ISO 8601 standard, but users should rely intead on $weeks instead. The $isoweeks element will be removed in a future version of incidence.
• as.incidence() argument isoweeks has been deprecated in favour of standard

DEPENDENCIES

• ISOweek import changed to aweek

Documentation

• Vignettes have been updated with examples.

incidence 1.6.0 (2019-03-05)

BEHAVIORAL CHANGE

• incidence() will no longer allow a non-standard first_date to override standard = TRUE. The first call toincidence()specifyingfirst_datewithoutstandardwill issue a warning. To use non-standard first dates, specifystandard = FALSE. To remove the warning, useoptions(incidence.warn.first_date = FALSE)`. See https://github.com/reconhub/incidence/issues/87 for details.

MISC

• citation("incidence") will now give the proper citation for our article in F1000 research and the global DOI for archived code. See https://github.com/reconhub/incidence/pulls/106
• Tests have been updated to avoid randomisation errors on R 3.6.0 See https://github.com/reconhub/incidence/issues/107

incidence 1.5.4 (2019-01-15)

BUG FIX

• incidence() now returns an error when supplied a character vector that is not formatted as (yyyy-mm-dd). (See https://github.com/reconhub/incidence/issues/88)
• fit() now returns correct coefficients when dates is POSIXt by converting to Date. (See https://github.com/reconhub/incidence/issues/91)
• plot.incidence() now plots in UTC by default for POSIXt incidence objects. this prevents a bug where different time zones would cause a shift in the bars (See https://github.com/reconhub/incidence/issues/99).

MISC

• A test that randomly failed on CRAN has been fixed. (See https://github.com/reconhub/incidence/issues/95).
• Plotting tests have been updated for new version of vdiffr (See https://github.com/reconhub/incidence/issues/96).
• POSIXct incidence are first passed through POSIXlt when initialized.
• A more informative error message is generated for non ISO 8601 formatted first_date and last_date parameters.

incidence 1.5.3 (2018-12-07)

BUG FIX

• plot.incidence() will now respect single groups. (See https://github.com/reconhub/incidence/issues/84)
• as.data.frame.incidence() will now respect single groups. (See https://github.com/reconhub/incidence/issues/84)

MISC

• demo("incidence-demo" package = "incidence") has been updated to show use of custom colors.

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 https://github.com/reconhub/incidence/issues/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 https://github.com/reconhub/incidence/pull/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 https://github.com/reconhub/incidence/pull/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 https://github.com/reconhub/incidence/issues/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 https://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!

incidence documentation built on Nov. 8, 2020, 4:30 p.m.