- No user facing changes.
- No user facing changes.
- Documentation tweaks and general upkeep for CRAN.
- change of maintainer only.
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.
- 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.
- Any interval
seq.Date()can handle (e.g. "5 weeks") can be handled byincidence()(see #67) - Weekly intervals can start on any day of the week by allowing things like "epiweek", "isoweek", "wednesday week", "2 Saturday weeks", etc. (see #55 (comment))
- the item
$weeksis 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
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.
plot.incidence()argumentlabels_isois deprecated in favor oflabels_week- Incidence objects will still have
$isoweeksif the weeks are ISO 8601 standard, but users should rely intead on$weeksinstead. The$isoweekselement will be removed in a future version of incidence. as.incidence()argumentisoweekshas been deprecated in favour ofstandard
- ISOweek import changed to aweek
- Vignettes have been updated with examples.
incidence()will no longer allow a non-standardfirst_dateto overridestandard = TRUE. The first call toincidence()specifyingfirst_datewithoutstandardwill issue a warning. To use non-standard first dates, specifystandard = FALSE. To remove the warning, useoptions(incidence.warn.first_date = FALSE)`. See #87 for details.
citation("incidence")will now give the proper citation for our article in F1000 research and the global DOI for archived code. See https://github.com/reconhub/incidence/pulls/106- Tests have been updated to avoid randomisation errors on R 3.6.0 See #107
incidence()now returns an error when supplied a character vector that is not formatted as (yyyy-mm-dd). (See #88)fit()now returns correct coefficients when dates is POSIXt by converting to Date. (See #91)plot.incidence()now plots in UTC by default for POSIXt incidence objects. this prevents a bug where different time zones would cause a shift in the bars (See #99).
- A test that randomly failed on CRAN has been fixed. (See #95).
- Plotting tests have been updated for new version of vdiffr (See #96).
- POSIXct incidence are first passed through POSIXlt when initialized.
- A more informative error message is generated for non ISO 8601 formatted
first_dateandlast_dateparameters.
plot.incidence()will now respect single groups. (See #84)as.data.frame.incidence()will now respect single groups. (See #84)
demo("incidence-demo" package = "incidence")has been updated to show use of custom colors.
print.incidence()will now print isoweeks even if the$intervalelement 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 withshow_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.daysoption
- Two bugs regarding the ordering of groups when the user specifies a factor/
column order have been fixed. This affects
plot.incidence(),incidence(), andas.data.frame.incidence()For details, see #79
group_names()allows the user to retrieve and set the group names.get_timespan()returns the$timespanelement.get_n()returns the$nelement.dim(),nrow(), andncol()are now available for incidence objects, returning the dimensions of the number of bins and the number of groups.
- A new argument to
plot()calledshow_caseshas been added to draw borders around individual cases for EPIET-style curves. See #72 for details.
- An example of EPIET-style bars for small data sets has been added to the plot customisation vignette by @jakobschumacher. See #68 for details.
- The incidence class vignette has been updated to use the available accessors.
estimate_peak()no longer fails with integer datesincidence()no longer fails when providing both group information and afirst_dateorlast_dateparameter that is inside the bounds of the observed dates. Thanks to @mfaber for reporting this bug. See #70 for details.
- code has been spread out into a more logical file structure where the
internal_checks.Rfile has been split into the relative components. - A message is now printed if missing observations are present when creating the incidence object.
- The
$lmfield of theincidence_fitclass is now named$modelto 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 aseparate_splitargument that will determine the optimal split separately for groups. -
A new class,
incidence_fit_list, has been implemented to store and summariseincidence_fitobjects within a nested list. This is the class returned by in the$fitelement offit_optim_split().
-
bootstrap()will bootstrap epicurves stored asincidenceobjects. -
find_peak()identifies the peak date of anincidenceobjects. -
estimate_peak()uses bootstrap to estimate the peak time of a partially observed outbreak. -
get_interval()will return the numeric interval or several intervals in the case of intervals that can't be represented in a fixed number of days (e.g. months). -
get_dates()returns the dates or counts of days on the right, center, or left of the interval. -
get_counts()returns the matrix of case counts for each date. -
get_fit()returns a list ofincidence_fitobjects from anincidence_fit_listobject. -
get_info()returns information stored in the$infoelement of anincidence_fit/incidence_fit_listobject.
- The new vignette
incidence_fit_classinstructs the user on howincidence_fitandincidence_fit_listobjects are created and accessed.
- In the
incidence()function, theiso_weekparameter is deprecated in favor ofstandardfor a more general way of indicating that the interval should start at the beginning of a valid date timeframe.
-
The
$timespanitem 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.
- tweak of the plotting of
incidenceobject to avoid conflicts with additional geoms such asgeom_ribbon, now used inprojections::add_projections.
- fixed issue caused by new
version of
ggplot2
-
the argument
n_breakshas been added toplot.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_breaksto 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 anincidenceobject
- fixed issues in testing incidence plots by employing vdiffr package.
-
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
Datedates 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.
- adapting to new names of datasets in
outbreaks:
ebola.sim->ebola_simandebola.sim.clean->ebola_sim_clean
-
add an argument
iso_weekto incidence.Date() and incidence.POSIXt() to support ISO week-based incidence when computing weekly incidence. -
add an argument
labels_iso_weekto 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
- Vignettes titles are now correctly displayed on CRAN (they read 'Vignette title').
First release of the incidence package on CRAN!