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) . The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.

News

projections 0.3.1

get_dates() now inherits the generic get_dates() from incidence

projections 0.3.0

New features

This 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

projections 0.1.1

New features

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.

Bug fixes

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).

projections 0.0.1

First release of the package!

New features

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.