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as.Date()summary.projectionnow using the new default random number generator in tests
updated tests to pass check with R 4.0.2; this includes re-generation of most reference objects, which were manually inspected and validated against old references
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() will can now take single dates or single
projections as inputs. (@acori, @zkamvar, #18).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.project() where R was being resampled
recursively was fixed (#11, @jarvisc1; #12, @zkamvar)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
project can now use a Negative Binomial model as an
alternative to the original Poisson model to account for over-dispersion
in new cases / super-spreading.Fixed the calls to sample, which has a rather irrational
behaviour when passing a first argument of length 1 (i.e. not
bootstrapping from the vector).
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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