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 R0 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.