☣:chart_with_upwards_trend::chart_with_downwards_trend:☣ Compute and visualise incidence
This version introduces a re-written incidence constructor, support for text-based intervals, and a formalization of lists of incidence_fit
classes.
$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.
CRAN release candidate. Incorporates isoweek support.
Version submitted to CRAN on 31st October 2016. Fully documented, 3 vignettes, 100% code coverage.