Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017)
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
.