plot.incidence() now reverts to the previous behaviour
of plotting ticks on either side of the interval as opposed to centering
within the interval.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.seq.Date() can handle (e.g. “5 weeks”) can
be handled by incidence() (see
https://github.com/reconhub/incidence/issues/67)$weeks is now added to the incidence object,
which contains an “aweek” classmake_breaks() will automatically calculate breaks from
an incidence object for plotting.scale_x_incidence() will produce a ggplot2
“ScaleContinuous” object to add to a ggplot.plot.incidence() argument labels_iso is
deprecated in favor of labels_week$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 standardincidence() 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.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/106incidence() 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).first_date and last_date
parameters.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)demo("incidence-demo" package = "incidence") has been
updated to show use of custom colors.print.incidence() will now print isoweeks even if the
$interval element is “week”.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.incidence.max.days optionplot.incidence(), incidence(), and
as.data.frame.incidence() For details, see
https://github.com/reconhub/incidence/issues/79group_names() allows the user to retrieve and set the
group names.get_timespan() returns the $timespan
element.get_n() returns the $n element.dim(), nrow(), and ncol() are
now available for incidence objects, returning the dimensions of the
number of bins and the number of groups.plot() called show_cases
has been added to draw borders around individual cases for EPIET-style
curves. See https://github.com/reconhub/incidence/pull/72 for
details.estimate_peak() no longer fails with integer datesincidence() no longer fails when providing both group
information and a first_date or last_date
parameter that is inside the bounds of the observed dates. Thanks to
@mfaber for reporting
this bug. See https://github.com/reconhub/incidence/issues/70 for
details.internal_checks.R file has been split into the relative
components.$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 https://www.repidemicsconsortium.org/incidence/ generated with pkgdown
First release of the incidence package on CRAN!
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