NEWS.md
new function merge_projections
permits to join different sets of simulations, adapting the respective time windows accordingly
new function merge_add_projections
permits to add simulated case incidence from different sets of simulations, adapting the respective time windows accordingly; if objects contain different numbers of simulations, the shortest ones are recycled as needed; also implemented as the operator +
new function summary
will summarise projections
objects by day, using a range of pre-defined statistics (mean, sd, min, max, and user-defined quantiles)
bug fix for the use of time-varying R in project
bug fix for as.data.frame(..., long = TRUE)
more consistent handling of inputs for the serial interval; if provided as a vector, si
now starts at a delay of 1 day, rather than 0 and assuming the first entry is 0; for distcrete
inputs, the mass for si$d(0)
is now ignored, and the rest of the distribution is rescaled accorindly to ensure the PMF sums to 1
(documentation) more realistic serial interval distribution used for the Ebola examples
(internal) the force of infection is now calculated by the new internal function compute_force_infection
(testing) revised sets of tests relying less on comparison to references, but testing for meaningful output properties instead
(testing) 100% coverage
project
can now use time-varying R by specifying time_change
, a vector of dates at which R changes, and providing a vector
or a list
of values for R
instead of a vector, in which case it needs to have length(time_change) + 1
components, each of which is a vector of R values.get_dates()
now inherits the generic get_dates()
from incidenceThis is a big release! Plenty of new features have been added, including:
projections
can now be subsetted like matrices using x[i,j]
, or using the function subset
new function cumulate
to compute cumulative incidence for projections
objects, akin to the similar function in the incidence
package
much improved graphics; plot
now call upons add_projections
, which implements many options for plotting projections, including quantiles lines, ribbon, and boxplots; add_projections
can also be used to add such plots to an existing incidence
plot
build_projections
can be used to build a projections
object from an input matrix and optional dates
First release of the package!
project
: a function generating projections from an existing incidence object, a serial interval distribution, and a set of plausible reproduction numbers (R); returns a projections
object.
plot
/print
: plotting and printing methods for projections
objects.
get_dates
: accessors for projections
objects.
as.data.frame
: conversion from projections
objects to data.frame
.