Project Future Case Incidence

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) .


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.

Reference manual

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install.packages("projections")

0.3.1 by Thibaut Jombart, 8 months ago


http://www.repidemicsconsortium.org/projections


Report a bug at http://github.com/reconhub/projections/issues


Browse source code at https://github.com/cran/projections


Authors: Thibaut Jombart [aut, cre] , Pierre Nouvellet [aut] , Sangeeta Bhatia [ctb] , Zhian N. Kamvar [ctb]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports stats, utils, incidence, distcrete, ggplot2

Suggests testthat, vdiffr, roxygen2, knitr, rmarkdown, outbreaks, magrittr


See at CRAN